Discovering regulatory binding-site modules using rule-based learning

CSRE(1) AND RAP1(1) => SimExpr(other) OR SimExpr(YJR145C) : 3 8

EXPR: (0.080) CSRE (P < 0.000) RAP1 (P < 0.184)

ORF	SYMBOL	P	F	C	TF
YKL152C	GPM1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphoglycerate mutase activity -> phosphoglycerate mutase activity	cytosol -> cytosol	GCR1, GCR2, HSF1, RAP1
\|YER047C\|	SAP1				MSS11
YDR450W	RPS18A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosol, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, ribosome	FHL1, GAT3, HIR2, RAP1, RGM1, YAP5
\|YOR213C\|	SAS5	chromatin silencing at telomere -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	acetyltransferase activity -> acetyltransferase activity	nuclear chromosome\, telomeric region, nuclear chromatin -> chromosome\, telomeric region, chromatin, nuclear chromosome	GRF10(Pho2), SUM1
\|YGR254W\|	ENO1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphopyruvate hydratase activity -> phosphopyruvate hydratase activity	phosphopyruvate hydratase complex, cytoplasm -> cytosol, cytoplasm	FKH2, MSN4, PDR1, SWI5, YAP5
YJR145C	RPS4A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya), cytoplasm -> cytosol, cytoplasm, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, ribosome	ACE2, CIN5, FHL1, INO4, MTH1, RAP1, YAP6
YGL147C	RPL9A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, MBP1, RAP1, SWI4
YLR344W	RPL26A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, RAP1
YGR214W	RPS0A	protein biosynthesis, ribosomal small subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosol, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, ribosome	FHL1, RAP1
YPL090C	RPS6A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosol, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, ribosome	FHL1, GAT3, INO4, RAP1, YAP5
YNL069C	RPL16B	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, GAT3, PDR1, RAP1, RGM1, YAP5
Main:		biosynthesis (0.90)	structural constituent of ribosome (0.70)	cytosol (0.90)	RAP1 (0.73)
Score:		0.82	0.47	0.80	0.564
P-value:		8.785E-03 (protein biosynthesis)	5.221E-05 (structural constituent of ribosome)	1.964E-05 (cytosol)	1.131E-05 (RAP1)

RAP1(1) AND SFF(1) AND SWI5(1) => SimExpr(YJR145C) OR SimExpr(other) : 10 4

EXPR: (0.090) SFF (P < 0.000) SWI5 (P < 0.000) RAP1 (P < 0.415)

ORF	SYMBOL	P	F	C	TF
\|YBR295W\|	PCA1	copper ion homeostasis -> cell homeostasis	P-type ATPase activity -> ATPase activity\, coupled to transmembrane movement of substances, P-P-bond-hydrolysis-driven transporter activity, cation transporter activity	membrane -> membrane	GAL4, SMP1
\|YLR452C\|	SST2	signal transduction, adaptation to pheromone during conjugation with cellular fusion -> signal transduction, conjugation, perception of external stimulus, sexual reproduction, response to abiotic stimulus	GTPase activator activity -> GTPase activator activity	plasma membrane -> membrane	DIG1, FHL1, RAP1, STE12
YOR369C	RPS12	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ARG80, FHL1, FKH2, LEU3, NDD1, PDR1, RME1, SMP1, YAP6
\|YMR224C\|	MRE11	DNA repair, double-strand break repair via nonhomologous end-joining, meiotic DNA double-strand break formation, meiotic DNA double-strand break processing, double-strand break repair via break-induced replication -> DNA metabolism, cell proliferation, catabolism	endonuclease activity, 3'-5' exonuclease activity, protein binding -> endonuclease activity, 3'-5' exonuclease activity, protein binding	nucleus -> nucleus	RAP1
YJR145C	RPS4A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya), cytoplasm -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ACE2, CIN5, FHL1, INO4, MTH1, RAP1, YAP6
YKR092C	SRP40	nucleocytoplasmic transport -> transport	chaperone activity -> chaperone activity	nucleolus -> nucleus	CUP9, MET4, RAP1
YBL087C	RPL23A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, IXR1, MSS11, PDR1, RAP1, SMP1, SOK2
\|YDR406W\|	PDR15	transport -> transport	ATP-binding cassette (ABC) transporter activity -> ATPase activity\, coupled to transmembrane movement of substances, P-P-bond-hydrolysis-driven transporter activity	integral to membrane -> membrane
YKL006W	RPL14A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, GRF10(Pho2), GTS1, RAP1
YLR441C	RPS1A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1, YAP5
YLR344W	RPL26A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
YER074W	RPS24A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, SMP1, YAP5
YNL069C	RPL16B	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, YAP5
Main:		biosynthesis (0.64)	structural constituent of ribosome (0.57)	cytoplasm (0.64)	RAP1 (0.77)
Score:		0.41	0.32	0.44	0.731
P-value:		3.354E-04 (protein biosynthesis)	9.333E-05 (structural constituent of ribosome)	1.252E-05 (cytosolic ribosome (sensu Eukarya))	3.620E-07 (FHL1)

RAP1(1) AND LYS14(1) => SimExpr(YJR145C) OR SimExpr(other) : 5 2

EXPR: (0.092) LYS14 (P < 0.002) RAP1 (P < 0.484)

ORF	SYMBOL	P	F	C	TF
YKL152C	GPM1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphoglycerate mutase activity -> phosphoglycerate mutase activity	cytosol -> cytoplasm	GCR1, GCR2, HSF1, RAP1
YNL302C	RPS19B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YKL180W	RPL17A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya), cytoplasm -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1
\|YBL093C\|	ROX3	transcription from Pol II promoter -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA polymerase II transcription mediator activity -> RNA polymerase II transcription mediator activity	mediator complex, nucleus -> nucleus	FHL1, RAP1
YJR145C	RPS4A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya), cytoplasm -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ACE2, CIN5, FHL1, INO4, MTH1, RAP1, YAP6
\|YHL038C\|	CBP2	RNA splicing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pre-mRNA splicing factor activity -> pre-mRNA splicing factor activity	mitochondrion -> cytoplasm	RAP1
YBR118W	TEF2	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	FHL1, RAP1
Main:		biosynthesis (0.71)	structural constituent of ribosome (0.43)	cytoplasm (0.86)	RAP1 (1.00)
Score:		0.52	0.14	0.71	1.000
P-value:		1.041E-01 (protein biosynthesis)	9.819E-02 (structural constituent of ribosome)	4.950E-02 (ribosome)	4.839E-07 (RAP1)

CSRE(1) AND mRRPE(1) AND SWI5(1) => SimExpr(YOR310C) OR SimExpr(other) : 5 1

EXPR: (0.088) mRRPE (P < 0.014) SWI5 (P < 0.000) CSRE (P < 0.001)

ORF	SYMBOL	P	F	C	TF
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, SWI6
YDR399W	HPT1	purine nucleotide biosynthesis -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	hypoxanthine phosphoribosyltransferase activity -> hypoxanthine phosphoribosyltransferase activity
YNL111C	CYB5	sterol biosynthesis -> alcohol metabolism, biosynthesis, lipid metabolism	electron transporter activity -> electron transporter activity	microsome -> membrane fraction	ABF1, GCR2, GTS1, NRG1, REB1, ROX1
\|YKL093W\|	MBR1	aerobic respiration -> energy pathways
YOR063W	RPL3	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	GRF10(Pho2)
YKL181W	PRS1	histidine biosynthesis, tryptophan biosynthesis, purine salvage, 'de novo' IMP biosynthesis, 'de novo' pyrimidine base biosynthesis -> amine metabolism, nucleotide biosynthesis, purine ribonucleotide metabolism, aromatic compound metabolism, amino acid derivative biosynthesis, biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, amino acid and derivative metabolism, organic acid metabolism, heterocycle metabolism	ribose-phosphate pyrophosphokinase activity -> ribose-phosphate pyrophosphokinase activity
Main:		biosynthesis (0.67)	ribose-phosphate pyrophosphokinase activity (0.25)	ribonucleoprotein complex (0.67)	ABF1 (0.67)
Score:		0.60	0.00	0.33	0.333
P-value:		7.359E-03 (purine nucleotide biosynthesis)	8.645E-01 (transferase activity)	9.991E-01 (ribonucleoprotein complex)	5.694E-01 (ABF1)

mRRPE(1) AND PAC(1) => SimExpr(YOR310C) OR SimExpr(other) : 27 2

EXPR: (0.089) mRRPE (P < 0.000) PAC (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YGR159C	NSR1	ribosomal small subunit assembly and maintenance, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	single-stranded DNA binding, RNA binding -> DNA binding, RNA binding	nucleolus, nucleus -> nucleus
\|YGL016W\|	KAP122	protein-nucleus import, response to drug -> response to abiotic stimulus, protein metabolism, cell growth and/or maintenance	protein carrier activity -> transporter activity	cytoplasm, nuclear pore -> cytoplasm, nucleus, integral to membrane, endomembrane system	MSN2
YOR272W	YTM1	chromosome organization and biogenesis (sensu Eukarya), ribosomal large subunit biogenesis -> cell growth and/or maintenance		nucleus, nucleolus -> nucleus	LEU3, PUT3, REB1
YER110C	KAP123	protein-nucleus import -> protein metabolism, cell growth and/or maintenance	protein carrier activity -> transporter activity	cytoplasm, nuclear pore, nucleus -> cytoplasm, nucleus, integral to membrane, endomembrane system
YBR104W	YMC2	transport -> cell growth and/or maintenance	transporter activity -> transporter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	FKH1, FKH2
YOR095C	RKI1	pentose-phosphate shunt -> coenzymes and prosthetic group metabolism, alcohol metabolism, water-soluble vitamin metabolism, carbohydrate metabolism, energy derivation by oxidation of organic compounds, catabolism	ribose-5-phosphate isomerase activity -> intramolecular isomerase activity		FHL1, FKH2, RAP1
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, SWI6
YGL171W	ROK1	35S primary transcript processing, mRNA splicing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ATP dependent RNA helicase activity, ATPase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleus	RGT1
YJL148W	RPA34	transcription from Pol I promoter -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	DNA-directed RNA polymerase activity -> transferase activity\, transferring phosphorus-containing groups	DNA-directed RNA polymerase I complex, nucleus, nucleolus -> nucleus	AZF1, CHA4, CUP9, DAL81, DIG1, FZF1, GCR1, GCR2, GLN3, HAL9, HAP2, HAP3, HMS1, LEU3, MAC1, MBP1, MET31, MOT3, NDD1, PDR1, PHD1, REB1, RLM1, RME1, ROX1, RPH1, RTS2, SKN7, SWI5, YAP6, ZAP1
YJL050W	MTR4	35S primary transcript processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ATP dependent RNA helicase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleus
YDR184C	ATC1	response to stress, polar budding -> response to stress, asexual reproduction		nucleus -> nucleus	ARO80, GLN3, SIP4, SKO1
YDR399W	HPT1	purine nucleotide biosynthesis -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	hypoxanthine phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups
YBR247C	ENP1	processing of 20S pre-rRNA, rRNA processing, cell growth and/or maintenance -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	nucleolus, nucleus -> nucleus
YNL112W	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
YJL033W	HCA4	35S primary transcript processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ATP dependent RNA helicase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleus	HIR2, USV1
YHR089C	GAR1	rRNA modification, 35S primary transcript processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	RNA binding -> RNA binding	nucleolus, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	CBF1, FZF1
YAL059W	ECM1	cell wall organization and biogenesis -> cell growth and/or maintenance			MOT3
YGR162W	TIF4631	translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	HSF1
YMR229C	RRP5	rRNA processing, processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding, snoRNA binding -> RNA binding	nucleolus, nucleolus organizer complex -> nucleus	FHL1, RAP1
YJR002W	MPP10	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nucleolar ribonucleoprotein complex, small nuclear ribonucleoprotein complex, nucleolus, nucleus -> nucleus, ribonucleoprotein complex
YNL209W	SSB2	protein biosynthesis -> biosynthesis, protein metabolism	chaperone activity, ATPase activity -> chaperone activity, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	polysome, cytoplasm -> cytoplasm, ribonucleoprotein complex	ABF1, RFX1
YLR197W	SIK1	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex, nucleus, nucleolus -> nucleus, ribonucleoprotein complex	DAL81, HAL9
YPL043W	NOP4	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus
YMR239C	RNT1	35S primary transcript processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ribonuclease III activity -> hydrolase activity\, acting on ester bonds, RNA binding	nucleolus -> nucleus
YJL138C	TIF2	translational initiation, regulation of translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity, RNA helicase activity -> translation factor activity\, nucleic acid binding, RNA binding	ribosome, cytoplasm -> cytoplasm, ribonucleoprotein complex	PHD1
YGL078C	DBP3	ribosomal large subunit assembly and maintenance, 35S primary transcript processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ATP dependent RNA helicase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleus
YNL292W	PUS4	tRNA modification -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pseudouridylate synthase activity -> carbon-oxygen lyase activity	mitochondrion, nucleus -> cytoplasm, nucleus	RCS1
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
\|YHR128W\|	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups		CIN5
Main:		cell growth and/or maintenance (0.64)	RNA binding (0.52)	nucleus (0.76)	ABF1 GLN3 FZF1 FKH2 PHD1 REB1 LEU3 FHL1 DAL81 RAP1 MOT3 HAL9 (0.11)
Score:		0.62	0.30	0.71	0.053
P-value:		9.273E-14 (ribosome biogenesis)	6.040E-06 (RNA binding)	6.059E-16 (nucleolus)	1.000E+00

CSRE(1) AND PAC(1) => SimExpr(other) OR SimExpr(YOR310C) : 3 7

EXPR: (0.090) PAC (P < 0.033) CSRE (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YGR159C	NSR1	ribosomal small subunit assembly and maintenance, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	single-stranded DNA binding, RNA binding -> single-stranded DNA binding, RNA binding	nucleolus, nucleus -> nucleus
YPL143W	RPL33A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, MET4, NDD1, PDR1, RAP1, RME1
\|YBL066C\|	SEF1
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, SWI6
YBR034C	HMT1	peptidyl-arginine modification, mRNA-nucleus export -> protein metabolism, transport, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	protein-arginine N-methyltransferase activity -> protein-arginine N-methyltransferase activity	nucleus -> nucleus
YDR087C	RRP1	rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism
YDR399W	HPT1	purine nucleotide biosynthesis -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	hypoxanthine phosphoribosyltransferase activity -> hypoxanthine phosphoribosyltransferase activity
\|YER088C\|	DOT6	filamentous growth, regulation of transcription from Pol II promoter, chromatin silencing at telomere, chromatin silencing at ribosomal DNA (rDNA), cell elongation -> cell growth, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, DNA packaging, cell organization and biogenesis			RAP1, SKN7
\|YML043C\|	RRN11	transcription from Pol I promoter -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA polymerase I transcription factor activity -> RNA polymerase I transcription factor activity	RNA polymerase I transcription factor complex -> nucleus	MAL13
YHR170W	NMD3	ribosomal large subunit assembly and maintenance -> cell organization and biogenesis	RNA binding, protein binding -> RNA binding, protein binding	cytosol, cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribosome	PHD1, REB1, SIP4
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.78)	RNA binding (0.33)	nucleus (0.67)	RAP1 (0.40)
Score:		0.75	0.07	0.53	0.100
P-value:		3.384E-03 (transcription from Pol I promoter)	1.145E+00 (RNA binding)	3.786E-02 (nucleolus)	1.000E+00

mRRPE(1) AND PAC(1) AND SCB(1) => SimExpr(YOR310C) : 11

EXPR: (0.079) mRRPE (P < 0.000) PAC (P < 0.000) SCB (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YGR159C	NSR1	ribosomal small subunit assembly and maintenance, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	single-stranded DNA binding, RNA binding -> DNA binding, RNA binding	nucleolus, nucleus -> nucleus
YBR104W	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	FKH1, FKH2
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, SWI6
YDR184C	ATC1	response to stress, polar budding -> response to stress, asexual reproduction		nucleus -> nucleus	ARO80, GLN3, SIP4, SKO1
YDR399W	HPT1	purine nucleotide biosynthesis -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	hypoxanthine phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups
YNL112W	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
YLR197W	SIK1	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex, nucleus, nucleolus -> nucleus, ribonucleoprotein complex	DAL81, HAL9
YMR239C	RNT1	35S primary transcript processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ribonuclease III activity -> hydrolase activity\, acting on ester bonds, RNA binding	nucleolus -> nucleus
YJL138C	TIF2	translational initiation, regulation of translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity, RNA helicase activity -> translation factor activity\, nucleic acid binding, RNA binding	ribosome, cytoplasm -> cytoplasm, ribonucleoprotein complex	PHD1
YNL292W	PUS4	tRNA modification -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pseudouridylate synthase activity -> carbon-oxygen lyase activity	mitochondrion, nucleus -> cytoplasm, nucleus	RCS1
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.60)	RNA binding (0.50)	nucleus (0.60)	ABF1 (0.14)
Score:		0.40	0.25	0.56	0.000
P-value:		9.830E-04 (RNA modification)	5.976E-02 (RNA binding)	2.724E-03 (nucleolus)	9.048E-01 (SKO1)

ALPHA1'(1) AND SFF'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YOR310C) : 7

EXPR: (0.089) ALPHA1' (P < 0.000) SFF' (P < 0.000) mRRPE (P < 0.007) PAC (P < 0.033)

ORF	SYMBOL	P	F	C	TF
YBR104W	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	FKH1, FKH2
YJL033W	HCA4	35S primary transcript processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ATP dependent RNA helicase activity -> RNA helicase activity, ATP dependent helicase activity, RNA dependent ATPase activity	nucleolus -> nucleus	HIR2, USV1
YER110C	KAP123	protein-nucleus import -> protein metabolism, transport	protein carrier activity -> transporter activity	cytoplasm, nuclear pore, nucleus -> cytoplasm, nucleus, integral to membrane, endomembrane system
YNL112W	DBP2		RNA helicase activity -> RNA helicase activity	bud neck -> site of polarized growth (sensu Fungi)
YNL292W	PUS4	tRNA modification -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pseudouridylate synthase activity -> pseudouridylate synthase activity	mitochondrion, nucleus -> cytoplasm, nucleus	RCS1
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, SWI6
YOR095C	RKI1	pentose-phosphate shunt -> coenzymes and prosthetic group metabolism, alcohol metabolism, water-soluble vitamin metabolism, carbohydrate metabolism, energy derivation by oxidation of organic compounds, catabolism	ribose-5-phosphate isomerase activity -> ribose-5-phosphate isomerase activity		FHL1, FKH2, RAP1
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.50)	RNA helicase activity (0.33)	nucleus (0.67)	FKH2 (0.40)
Score:		0.27	0.13	0.53	0.100
P-value:		1.821E-02 (RNA modification)	2.382E-02 (RNA helicase activity)	1.639E-01 (nucleolus)	1.689E-01 (FKH2)

CSRE(1) AND LYS14(1) AND ALPHA1'(1) => SimExpr(other) OR SimExpr(YOR063W) : 2 7

EXPR: (0.100) LYS14 (P < 0.001) ALPHA1' (P < 0.001) CSRE (P < 0.001)

ORF	SYMBOL	P	F	C	TF
\|YGL038C\|	OCH1	N-linked glycoprotein maturation -> biosynthesis, protein metabolism	transferase activity\, transferring glycosyl groups, alpha-1\,6-mannosyltransferase activity -> transferase activity\, transferring glycosyl groups	Golgi cis cisterna -> cytoplasm	CRZ1, SKN7, SWI4, SWI6
YLR153C	ACS2	acetyl-CoA biosynthesis -> biosynthesis, coenzymes and prosthetic group metabolism, organic acid metabolism	acetate-CoA ligase activity -> ligase activity\, forming carbon-sulfur bonds	cytosol -> cytoplasm
YBR143C	SUP45	translational termination -> biosynthesis, protein metabolism	translation release factor activity\, codon specific -> translation factor activity\, nucleic acid binding	cytosol -> cytoplasm	FZF1
YOL052C	SPE2	pantothenate biosynthesis -> biosynthesis, coenzymes and prosthetic group metabolism	adenosylmethionine decarboxylase activity -> carbon-carbon lyase activity
YDL048C	STP4				HIR2
YOR063W	RPL3	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	GRF10(Pho2)
YDL131W	LYS21	lysine biosynthesis\, aminoadipic pathway -> amine metabolism, amino acid and derivative metabolism, organic acid metabolism, biosynthesis	homocitrate synthase activity -> carbon-carbon lyase activity	nucleus -> nucleus
\|YNL241C\|	ZWF1	pentose-phosphate shunt -> coenzymes and prosthetic group metabolism, alcohol metabolism, water-soluble vitamin metabolism, carbohydrate metabolism, energy derivation by oxidation of organic compounds, catabolism	glucose-6-phosphate 1-dehydrogenase activity -> oxidoreductase activity\, acting on CH-OH group of donors	cytoplasm -> cytoplasm	ACE2, ADR1, FKH2, HIR1, IME4, MBP1, NDD1, PHO4, RCS1, SFP1, SKN7, SWI5
YIL052C	RPL34B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	RME1
Main:		biosynthesis (0.88)	structural constituent of ribosome (0.25)	cytoplasm (0.86)	SKN7 (0.33)
Score:		0.82	0.07	0.71	0.067
P-value:		1.004E-02 (coenzyme metabolism)	1.446E-01 (carbon-carbon lyase activity)	3.665E-01 (cytosol)	6.794E-01 (SKN7)

SWI5(1) AND PAC(1) => SimExpr(YDR399W) OR SimExpr(other) : 8 3

EXPR: (0.104) SWI5 (P < 0.000) PAC (P < 0.135)

ORF	SYMBOL	P	F	C	TF
\|YGL016W\|	KAP122	protein-nucleus import, response to drug -> response to abiotic stimulus, protein metabolism, transport	protein carrier activity -> protein carrier activity	cytoplasm, nuclear pore -> cytoplasm, nucleus, integral to membrane, endomembrane system	MSN2
YDR399W	HPT1	purine nucleotide biosynthesis -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	hypoxanthine phosphoribosyltransferase activity -> hypoxanthine phosphoribosyltransferase activity
YMR229C	RRP5	rRNA processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding, snoRNA binding -> RNA binding, snoRNA binding	nucleolus, nucleolus organizer complex -> nucleus	FHL1, RAP1
YJR002W	MPP10	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nucleolar ribonucleoprotein complex, small nuclear ribonucleoprotein complex, nucleolus, nucleus -> nucleus, ribonucleoprotein complex
YPL143W	RPL33A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, MET4, NDD1, PDR1, RAP1, RME1
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, SWI6
YKR092C	SRP40	nucleocytoplasmic transport -> transport	chaperone activity -> chaperone activity	nucleolus -> nucleus	CUP9, MET4, RAP1
\|YIL066C\|	RNR3	DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ribonucleoside-diphosphate reductase activity -> ribonucleoside-diphosphate reductase activity	cytoplasm -> cytoplasm	RFX1, STB1
\|YFL011W\|	HXT10	hexose transport -> transport	glucose transporter activity, fructose transporter activity, mannose transporter activity, galactose transporter activity -> glucose transporter activity, fructose transporter activity, mannose transporter activity, galactose transporter activity	plasma membrane -> plasma membrane	GTS1, MBP1, RTG3
YHR089C	GAR1	rRNA modification, 35S primary transcript processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	RNA binding -> RNA binding	nucleolus, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	CBF1, FZF1
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.55)	RNA binding (0.22)	nucleus (0.60)	RAP1 (0.33)
Score:		0.42	0.03	0.60	0.083
P-value:		1.990E-04 (rRNA metabolism)	1.335E+00 (RNA binding)	1.072E-04 (nucleolus)	3.231E-01 (MET4)

PAC(1) AND SCB(1) => SimExpr(other) OR SimExpr(YDR399W) : 7 15

EXPR: (0.105) PAC (P < 0.056) SCB (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YGR159C	NSR1	ribosomal small subunit assembly and maintenance, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	single-stranded DNA binding, RNA binding -> nucleic acid binding	nucleolus, nucleus -> intracellular
YBR104W	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> intracellular, inner membrane	FKH1, FKH2
YDR399W	HPT1	purine nucleotide biosynthesis -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	hypoxanthine phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups
YLR197W	SIK1	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex, nucleus, nucleolus -> intracellular	DAL81, HAL9
YJL138C	TIF2	translational initiation, regulation of translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity, RNA helicase activity -> nucleic acid binding	ribosome, cytoplasm -> intracellular	PHD1
YNL141W	AAH1	adenine catabolism -> aromatic compound metabolism, catabolism, heterocycle metabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	adenine deaminase activity -> hydrolase activity\, acting on carbon-nitrogen (but not peptide) bonds		YFL044C
YNL112W	DBP2		RNA helicase activity -> nucleic acid binding	bud neck -> site of polarized growth (sensu Fungi)
YER001W	MNN1	N-glycan processing, O-linked glycosylation -> biosynthesis, protein metabolism	alpha-1\,3-mannosyltransferase activity -> transferase activity\, transferring glycosyl groups	Golgi apparatus -> intracellular	HAL9, MAC1, NRG1, PHD1, RLM1, SKN7, SMP1, SWI4, SWI6, YAP6
\|YIL118W\|	RHO3	exocytosis, small GTPase mediated signal transduction, establishment of cell polarity (sensu Saccharomyces), actin filament organization -> signal transduction, cell organization and biogenesis, transport	Rho small monomeric GTPase activity, signal transducer activity -> purine nucleotide binding, signal transducer activity, hydrolase activity\, acting on acid anhydrides	intracellular -> intracellular	CIN5, NRG1, PHD1, SKN7, SOK2, YAP6
\|YFR034C\|	PHO4	phosphate metabolism, cellular response to phosphate starvation -> phosphorus metabolism, response to extracellular stimulus, response to biotic stimulus	transcription factor activity -> nucleic acid binding	nucleus, cytoplasm -> intracellular
YNL292W	PUS4	tRNA modification -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pseudouridylate synthase activity -> carbon-oxygen lyase activity	mitochondrion, nucleus -> intracellular	RCS1
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> intracellular	ABF1, SWI6
YDR184C	ATC1	response to stress, polar budding -> response to stress, asexual reproduction		nucleus -> intracellular	ARO80, GLN3, SIP4, SKO1
\|YBL099W\|	ATP1	ATP synthesis coupled proton transport -> transport	hydrogen-transporting ATP synthase activity -> transporter activity	proton-transporting ATP synthase\, catalytic core (sensu Eukarya) -> intracellular, integral to membrane, inner membrane	HAP4, ROX1
\|YDR364C\|	CDC40	DNA replication, S phase of mitotic cell cycle, mRNA splicing, mitotic spindle assembly (sensu Saccharomyces) -> cytoplasm organization and biogenesis, cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, M phase	nucleic acid binding, pre-mRNA splicing factor activity -> nucleic acid binding	spliceosome complex, nuclear membrane, nuclear pore -> pore complex, intracellular, endomembrane system
YJL208C	NUC1	DNA recombination -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	endodeoxyribonuclease activity, exodeoxyribonuclease activity, ribonuclease activity -> hydrolase activity\, acting on ester bonds, nucleic acid binding	mitochondrial inner membrane -> intracellular, inner membrane
\|YIL066C\|	RNR3	DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ribonucleoside-diphosphate reductase activity -> oxidoreductase activity\, acting on CH2 groups	cytoplasm -> intracellular	RFX1, STB1
YBR034C	HMT1	peptidyl-arginine modification, mRNA-nucleus export -> protein metabolism, transport, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	protein-arginine N-methyltransferase activity -> transferase activity\, transferring one-carbon groups	nucleus -> intracellular
\|YDR076W\|	RAD55	meiotic DNA recombinase assembly, DNA recombinase assembly, double-strand break repair via synthesis-dependent strand annealing, double-strand break repair via break-induced replication, double-strand break repair via single-strand annealing -> mating-type determination, cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	protein binding -> protein binding	nucleus -> intracellular	DAL81
YMR239C	RNT1	35S primary transcript processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ribonuclease III activity -> hydrolase activity\, acting on ester bonds, nucleic acid binding	nucleolus -> intracellular
\|YML043C\|	RRN11	transcription from Pol I promoter -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA polymerase I transcription factor activity -> RNA polymerase I transcription factor activity	RNA polymerase I transcription factor complex -> intracellular	MAL13
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> nucleic acid binding	ribosome -> intracellular	INO2, INO4
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.62)	nucleic acid binding (0.42)	intracellular (0.95)	PHD1 (0.21)
Score:		0.46	0.18	0.90	0.066
P-value:		1.462E-02 (RNA modification)	7.448E-02 (RNA binding)	6.764E-03 (nucleolus)	5.851E-01 (HAL9)

CSRE(1) AND PAC(1) => SimExpr(other) OR SimExpr(YDR399W) : 3 7

mRRPE(1) AND PAC(1) => SimExpr(YDR399W) OR SimExpr(other) : 27 2

mRRPE(1) AND PAC(1) AND SCB(1) => SimExpr(YDR399W) : 11

CSRE(1) AND PAC(1) => SimExpr(other) OR SimExpr(YBR034C) : 3 7

CSRE(1) AND PAC(1) => SimExpr(other) OR SimExpr(YPL143W) : 3 7

mRRPE(1) AND PAC(1) => SimExpr(YGR159C) OR SimExpr(other) : 28 1

CSRE(1) AND PAC(1) => SimExpr(YGR159C) OR SimExpr(other) : 8 2

CSRE(1) AND PAC(1) AND SCB(1) => SimExpr(YGR159C) : 5

EXPR: (0.070) PAC (P < 0.006) SCB (P < 0.000) CSRE (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YGR159C	NSR1	ribosomal small subunit assembly and maintenance, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	single-stranded DNA binding, RNA binding -> single-stranded DNA binding, RNA binding	nucleolus, nucleus -> nucleus
YDR399W	HPT1	purine nucleotide biosynthesis -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	hypoxanthine phosphoribosyltransferase activity -> hypoxanthine phosphoribosyltransferase activity
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, SWI6
YBR034C	HMT1	peptidyl-arginine modification, mRNA-nucleus export -> protein metabolism, transport, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	protein-arginine N-methyltransferase activity -> protein-arginine N-methyltransferase activity	nucleus -> nucleus
YML043C	RRN11	transcription from Pol I promoter -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA polymerase I transcription factor activity -> RNA polymerase I transcription factor activity	RNA polymerase I transcription factor complex -> nucleus	MAL13
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (1.00)	RNA binding (0.25)	nucleus (1.00)	ABF1 (0.50)
Score:		1.00	0.00	1.00	0.000
P-value:		4.879E-03 (transcription from Pol I promoter)	6.354E-01 (transferase activity)	1.622E-03 (nucleolus)	1.397E-01 (MAL13)

mRRPE(1) AND PAC(1) AND SCB(1) => SimExpr(YGR159C) : 11

mRRPE(1) AND PAC(1) AND MCM1'(1) => SimExpr(YGR159C) : 6

EXPR: (0.074) mRRPE (P < 0.000) PAC (P < 0.011) MCM1' (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YGR159C	NSR1	ribosomal small subunit assembly and maintenance, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	single-stranded DNA binding, RNA binding -> single-stranded DNA binding, RNA binding	nucleolus, nucleus -> nucleolus, nucleus
YDR399W	HPT1	purine nucleotide biosynthesis -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	hypoxanthine phosphoribosyltransferase activity -> transferase activity\, transferring pentosyl groups
YHR128W	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring pentosyl groups		CIN5
YPL043W	NOP4	rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleolus
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> small nuclear ribonucleoprotein complex, nucleolus, ribonucleoprotein complex	ABF1, SWI6
YOR095C	RKI1	pentose-phosphate shunt -> coenzymes and prosthetic group metabolism, alcohol metabolism, water-soluble vitamin metabolism, carbohydrate metabolism, energy derivation by oxidation of organic compounds, catabolism	ribose-5-phosphate isomerase activity -> intramolecular isomerase activity\, interconverting aldoses and ketoses		FHL1, FKH2, RAP1
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.83)	transferase activity\, transferring pentosyl groups (0.40)	nucleolus (1.00)	ABF1 (0.33)
Score:		0.67	0.20	1.00	0.000
P-value:		6.463E-03 (rRNA processing)	9.418E-03 (transferase activity\, transferring pentosyl groups)	3.174E-03 (nucleolus)	1.000E+00

CSRE(1) AND LYS14(1) AND ALPHA1'(1) => SimExpr(other) OR SimExpr(YIL052C) : 2 7

SFF'(1) AND SWI5(1) AND MCB(1) => SimExpr(YDR309C) OR SimExpr(other) : 6 2

EXPR: (0.109) SFF' (P < 0.000) SWI5 (P < 0.000) MCB (P < 0.024)

ORF	SYMBOL	P	F	C	TF
YOL006C	TOP1	negative regulation of recombination within rDNA repeats, DNA topological change, DNA strand elongation, chromatin assembly/disassembly, regulation of transcription from Pol II promoter, RNA elongation from Pol II promoter, mitotic chromosome condensation, nuclear migration -> cell organization and biogenesis, cell cycle, mitotic cell cycle, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	DNA topoisomerase type I activity -> DNA topoisomerase type I activity	nucleus -> nucleus	REB1
YDR297W	SUR2	sphingolipid metabolism, sphingolipid biosynthesis -> lipid metabolism, biosynthesis	sphingosine hydroxylase activity -> sphingosine hydroxylase activity	endoplasmic reticulum -> cytoplasm	CBF1, MTH1
YDR309C	GIC2	axial budding, Rho protein signal transduction, establishment of cell polarity (sensu Saccharomyces) -> asexual reproduction, signal transduction, cell organization and biogenesis	small GTPase regulatory/interacting protein activity -> small GTPase regulatory/interacting protein activity	actin cap (sensu Saccharomyces), bud tip, shmoo tip, incipient bud site -> cell cortex, site of polarized growth (sensu Fungi), incipient bud site, cytoplasm	ASH1, HSF1, MBP1, PHD1, RLM1, SKN7, STB1, STE12, SWI4, SWI6
\|YKL042W\|	SPC42	microtubule nucleation, spindle pole body duplication (sensu Saccharomyces) -> cell organization and biogenesis, cell proliferation	structural constituent of cytoskeleton -> structural constituent of cytoskeleton	intermediate layer of spindle pole body, central plaque of spindle pole body -> cytoplasm
YIL066C	RNR3	DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ribonucleoside-diphosphate reductase activity -> ribonucleoside-diphosphate reductase activity	cytoplasm -> cytoplasm	RFX1, STB1
YMR179W	SPT21	regulation of transcription from Pol II promoter -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			MBP1, STB1, SWI4, SWI6, UGA3
YER070W	RNR1	DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ribonucleoside-diphosphate reductase activity -> ribonucleoside-diphosphate reductase activity	cytoplasm -> cytoplasm	FKH2, MBP1, REB1, SWI4, SWI6
\|YDR052C\|	DBF4	DNA replication initiation, regulation of DNA replication, protein amino acid phosphorylation -> phosphorus metabolism, cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	protein serine/threonine kinase activity -> protein serine/threonine kinase activity	nucleoplasm -> nucleus	IME4, NRG1
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.62)	ribonucleoside-diphosphate reductase activity (0.29)	cytoplasm (0.71)	SWI4 MBP1 SWI6 STB1 (0.43)
Score:		0.57	0.05	0.52	0.286
P-value:		5.078E-04 (DNA replication and chromosome cycle)	1.156E-03 (oxidoreductase activity\, acting on CH2 groups\, disulfide as acceptor)	3.629E-01 (cytoskeleton)	2.080E-03 (STB1)

Gcr1(1) AND ATRepeat(1) => SimExpr(other) OR SimExpr(YKL152C) : 2 5

EXPR: (0.114) Gcr1 (P < 0.232) ATRepeat (P < 0.013)

ORF	SYMBOL	P	F	C	TF
YGL038C	OCH1	N-linked glycoprotein maturation -> biosynthesis, protein metabolism	transferase activity\, transferring glycosyl groups, alpha-1\,6-mannosyltransferase activity -> transferase activity\, transferring glycosyl groups, alpha-1\,6-mannosyltransferase activity	Golgi cis cisterna -> cytoplasm	CRZ1, SKN7, SWI4, SWI6
\|YCL027W\|	FUS1	conjugation with cellular fusion -> conjugation, sexual reproduction		plasma membrane, shmoo tip -> plasma membrane, site of polarized growth (sensu Fungi)	DIG1, STE12
YKL152C	GPM1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphoglycerate mutase activity -> phosphoglycerate mutase activity	cytosol -> cytoplasm	GCR1, GCR2, HSF1, RAP1
YKR097W	PCK1	gluconeogenesis -> alcohol metabolism, carbohydrate metabolism, biosynthesis, energy pathways	phosphoenolpyruvate carboxykinase (ATP) activity -> phosphoenolpyruvate carboxykinase (ATP) activity	cytosol -> cytoplasm	MCM1, MTH1, SIP4, SKN7
YLR354C	TAL1	pentose-phosphate shunt -> coenzymes and prosthetic group metabolism, alcohol metabolism, water-soluble vitamin metabolism, carbohydrate metabolism, energy derivation by oxidation of organic compounds, catabolism	transaldolase activity -> transaldolase activity	cytoplasm -> cytoplasm	MBP1
YLR121C	YPS3	protein metabolism -> protein metabolism	aspartic-type endopeptidase activity -> aspartic-type endopeptidase activity	plasma membrane -> plasma membrane	CIN5, SWI4, YAP6
\|YDR263C\|	DIN7	DNA repair -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	nuclease activity -> nuclease activity	mitochondrion -> cytoplasm	FKH1, FKH2, MBP1, SWI6
Main:		alcohol metabolism (0.43)	transaldolase activity (0.17)	cytoplasm (0.71)	SWI4 MBP1 SWI6 SKN7 (0.29)
Score:		0.29	0.00	0.52	0.190
P-value:		1.851E-02 (glucose metabolism)	4.167E-01 (enzyme activity)	7.473E-01 (plasma membrane)	3.556E-01 (MBP1)

LYS14(1) AND ATRepeat(1) => SimExpr(YKL152C) OR SimExpr(other) : 5 1

EXPR: (0.098) LYS14 (P < 0.001) ATRepeat (P < 0.001)

ORF	SYMBOL	P	F	C	TF
YGL038C	OCH1	N-linked glycoprotein maturation -> biosynthesis, protein metabolism	transferase activity\, transferring glycosyl groups, alpha-1\,6-mannosyltransferase activity -> transferase activity\, transferring glycosyl groups, alpha-1\,6-mannosyltransferase activity	Golgi cis cisterna -> cytoplasm	CRZ1, SKN7, SWI4, SWI6
YLR153C	ACS2	acetyl-CoA biosynthesis -> biosynthesis, coenzymes and prosthetic group metabolism, organic acid metabolism	acetate-CoA ligase activity -> acetate-CoA ligase activity	cytosol -> cytoplasm
YDR226W	ADK1	cell proliferation -> cell proliferation	adenylate kinase activity -> adenylate kinase activity	cytoplasm, mitochondrial intermembrane space -> cytoplasm	PUT3
YKL152C	GPM1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphoglycerate mutase activity -> phosphoglycerate mutase activity	cytosol -> cytoplasm	GCR1, GCR2, HSF1, RAP1
YDL048C	STP4				HIR2
\|YBR115C\|	LYS2	lysine biosynthesis\, aminoadipic pathway -> amine metabolism, amino acid and derivative metabolism, organic acid metabolism, biosynthesis	aminoadipate-semialdehyde dehydrogenase activity -> aminoadipate-semialdehyde dehydrogenase activity	cytoplasm -> cytoplasm	DAL81, GCN4
Main:		biosynthesis (0.80)	adenylate kinase activity (0.20)	cytoplasm (1.00)	GCR2 (0.20)
Score:		0.60	0.00	1.00	0.000
P-value:		3.970E-01 (biosynthesis)	5.543E-01 (enzyme activity)	1.341E+00 (cytosol)	6.676E-01 (CRZ1)

CSRE(1) AND RAP1(1) => SimExpr(YKL152C) OR SimExpr(other) : 8 3

CSRE(1) AND RAP1(1) AND SFF(1) => SimExpr(YKL152C) : 6

EXPR: (0.075) SFF (P < 0.000) CSRE (P < 0.000) RAP1 (P < 0.005)

ORF	SYMBOL	P	F	C	TF
YGR214W	RPS0A	protein biosynthesis, ribosomal small subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosol, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, ribosome	FHL1, RAP1
YJR145C	RPS4A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya), cytoplasm -> cytosol, cytoplasm, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, ribosome	ACE2, CIN5, FHL1, INO4, MTH1, RAP1, YAP6
YLR344W	RPL26A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, RAP1
YKL152C	GPM1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphoglycerate mutase activity -> phosphoglycerate mutase activity	cytosol -> cytosol	GCR1, GCR2, HSF1, RAP1
YGR254W	ENO1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphopyruvate hydratase activity -> phosphopyruvate hydratase activity	phosphopyruvate hydratase complex, cytoplasm -> cytosol, cytoplasm	FKH2, MSN4, PDR1, SWI5, YAP5
YNL069C	RPL16B	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, GAT3, PDR1, RAP1, RGM1, YAP5
Main:		biosynthesis (1.00)	structural constituent of ribosome (0.67)	cytosol (1.00)	RAP1 (0.83)
Score:		1.00	0.40	1.00	0.733
P-value:		1.366E-02 (biosynthesis)	5.227E-03 (structural constituent of ribosome)	1.572E-04 (cytosol)	5.499E-04 (RAP1)

CSRE(1) AND RAP1(1) AND SFF'(1) => SimExpr(YKL152C) : 7

EXPR: (0.078) SFF' (P < 0.000) CSRE (P < 0.000) RAP1 (P < 0.006)

ORF	SYMBOL	P	F	C	TF
YGL147C	RPL9A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, MBP1, RAP1, SWI4
YGR214W	RPS0A	protein biosynthesis, ribosomal small subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosol, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, ribosome	FHL1, RAP1
YJR145C	RPS4A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya), cytoplasm -> cytosol, cytoplasm, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, ribosome	ACE2, CIN5, FHL1, INO4, MTH1, RAP1, YAP6
YLR344W	RPL26A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, RAP1
YKL152C	GPM1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphoglycerate mutase activity -> phosphoglycerate mutase activity	cytosol -> cytosol	GCR1, GCR2, HSF1, RAP1
YGR254W	ENO1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphopyruvate hydratase activity -> phosphopyruvate hydratase activity	phosphopyruvate hydratase complex, cytoplasm -> cytosol, cytoplasm	FKH2, MSN4, PDR1, SWI5, YAP5
YNL069C	RPL16B	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, GAT3, PDR1, RAP1, RGM1, YAP5
Main:		biosynthesis (1.00)	structural constituent of ribosome (0.71)	cytosol (1.00)	RAP1 (0.86)
Score:		1.00	0.48	1.00	0.762
P-value:		3.801E-03 (biosynthesis)	5.957E-04 (structural constituent of ribosome)	2.278E-05 (cytosol)	6.256E-05 (RAP1)

CSRE(1) AND RAP1(1) => SimExpr(other) OR SimExpr(YNL069C) : 2 9

CSRE(1) AND RAP1(1) AND SWI5(1) => SimExpr(YNL069C) : 5

EXPR: (0.065) SWI5 (P < 0.000) CSRE (P < 0.002) RAP1 (P < 0.143)

ORF	SYMBOL	P	F	C	TF
YDR450W	RPS18A	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, small ribosomal subunit	FHL1, GAT3, HIR2, RAP1, RGM1, YAP5
YJR145C	RPS4A	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya), cytoplasm -> cytosolic ribosome (sensu Eukarya), cytoplasm, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, small ribosomal subunit	ACE2, CIN5, FHL1, INO4, MTH1, RAP1, YAP6
YLR344W	RPL26A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), large ribosomal subunit	FHL1, RAP1
YOR213C	SAS5	chromatin silencing at telomere -> chromatin silencing at telomere	acetyltransferase activity -> acetyltransferase activity	nuclear chromosome\, telomeric region, nuclear chromatin -> nuclear chromosome\, telomeric region, nuclear chromatin	GRF10(Pho2), SUM1
YNL069C	RPL16B	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), large ribosomal subunit	FHL1, GAT3, PDR1, RAP1, RGM1, YAP5
Main:		protein biosynthesis (0.80)	structural constituent of ribosome (0.80)	cytosolic ribosome (sensu Eukarya) (0.80)	FHL1 RAP1 (0.80)
Score:		0.60	0.60	0.60	0.600
P-value:		1.692E-02 (protein biosynthesis)	1.631E-03 (structural constituent of ribosome)	1.479E-03 (cytosolic ribosome (sensu Eukarya))	9.113E-04 (FHL1)

RAP1(1) => SimExpr(other) OR SimExpr(YLR344W) : 15 36

EXPR: (0.103) RAP1 (P < 0.584)

ORF	SYMBOL	P	F	C	TF
\|YMR013C\|	SEC59	protein-ER targeting, protein amino acid glycosylation -> cell organization and biogenesis, biosynthesis, protein modification, protein metabolism, transport	dolichol kinase activity -> transferase activity\, transferring phosphorus-containing groups	membrane -> membrane	FHL1, NDD1, RAP1, RLM1, RME1
YOL121C	RPS19A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	AZF1, FHL1, GCR1, GCR2, HAL9, MET31, MOT3, PDR1, RAP1, ROX1, RPH1, SMP1, YAP6, ZAP1
\|YLR452C\|	SST2	signal transduction, adaptation to pheromone during conjugation with cellular fusion -> signal transduction, conjugation, perception of external stimulus, sexual reproduction, response to abiotic stimulus	GTPase activator activity -> small GTPase regulatory/interacting protein activity	plasma membrane -> membrane	DIG1, FHL1, RAP1, STE12
\|YLR208W\|	SEC13	nonselective vesicle assembly, ER to Golgi transport, ER-associated protein catabolism -> macromolecule catabolism, transport, protein metabolism		cytoplasm, COPII vesicle coat, nuclear pore, extrinsic to plasma membrane -> nucleus, cytoplasm, membrane coat, membrane
\|YEL056W\|	HAT2	chromatin assembly/disassembly, chromatin silencing at telomere -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	H3/H4 histone acetyltransferase activity -> transferase activity\, transferring acyl groups	cytoplasm, nucleus -> cytoplasm, nucleus	GAL4
\|YBL022C\|	PIM1	proteolysis and peptidolysis, response to heat -> catabolism, response to abiotic stimulus, protein metabolism	ATP-dependent peptidase activity -> peptidase activity	mitochondrial matrix -> cytoplasm	RAP1
\|YBR117C\|	TKL2	pentose-phosphate shunt -> coenzymes and prosthetic group metabolism, alcohol metabolism, water-soluble vitamin metabolism, carbohydrate metabolism, energy derivation by oxidation of organic compounds, catabolism	transketolase activity -> transferase activity\, transferring aldehyde or ketonic groups		FHL1, RAP1
YKR057W	RPS21A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ABF1, FHL1
\|YHL038C\|	CBP2	RNA splicing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pre-mRNA splicing factor activity -> RNA binding	mitochondrion -> cytoplasm	RAP1
YDL130W	RPP1B	protein biosynthesis, translational elongation -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAL4, RAP1, RFX1
YKL006W	RPL14A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, GRF10(Pho2), GTS1, RAP1
YGL147C	RPL9A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, MBP1, RAP1, SWI4
YLR441C	RPS1A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1, YAP5
YLR146C	SPE4	pantothenate biosynthesis, spermine biosynthesis -> biosynthesis, amine metabolism, coenzymes and prosthetic group metabolism, amino acid and derivative metabolism, secondary metabolism	spermine synthase activity -> transferase activity\, transferring alkyl or aryl (other than methyl) groups
YBR181C	RPS6B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya), cytoplasm -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, MAL13, RAP1, RGM1
YGR214W	RPS0A	protein biosynthesis, ribosomal small subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YJR123W	RPS5	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GRF10(Pho2), HSF1, MSN4, YAP1
YDL136W	RPL35B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, INO4, MSS11, RAP1
YDR450W	RPS18A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, HIR2, RAP1, RGM1, YAP5
YOR369C	RPS12	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ARG80, FHL1, FKH2, LEU3, NDD1, PDR1, RME1, SMP1, YAP6
YPL131W	RPL5	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1
YJR145C	RPS4A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya), cytoplasm -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ACE2, CIN5, FHL1, INO4, MTH1, RAP1, YAP6
YBL087C	RPL23A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, IXR1, MSS11, PDR1, RAP1, SMP1, SOK2
\|YDR406W\|	PDR15	transport -> transport	ATP-binding cassette (ABC) transporter activity -> purine nucleotide binding, primary active transporter activity, hydrolase activity\, acting on acid anhydrides	integral to membrane -> membrane
YBR118W	TEF2	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YLR061W	RPL22A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	BAS1, FHL1, HIR1, PDR1, RAP1, RCS1, RME1, ZAP1
YDR418W	RPL12B	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, SMP1
YLR344W	RPL26A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YKL152C	GPM1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphoglycerate mutase activity -> intramolecular transferase activity	cytosol -> cytoplasm	GCR1, GCR2, HSF1, RAP1
YNL302C	RPS19B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, RAP1
\|YMR231W\|	PEP5	nonselective vesicle docking, homotypic vacuole fusion (non-autophagic), Golgi to endosome transport, late endosome to vacuole transport -> cell organization and biogenesis, transport, vesicle-mediated transport		vacuolar membrane (sensu Fungi) -> cytoplasm, vacuole	ARG81, DOT6, HAL9, HAP2, MCM1, YAP1
YGL030W	RPL30	protein biosynthesis, rRNA processing, mRNA splicing, regulation of translation -> cell organization and biogenesis, biosynthesis, transcription, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya), cytoplasm -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1, SFP1
\|YER047C\|	SAP1				MSS11
YIL018W	RPL2B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, SWI5, YAP5
\|YGR254W\|	ENO1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphopyruvate hydratase activity -> carbon-oxygen lyase activity	phosphopyruvate hydratase complex, cytoplasm -> cytoplasm	FKH2, MSN4, PDR1, SWI5, YAP5
YKR092C	SRP40	nucleocytoplasmic transport -> transport	chaperone activity -> chaperone activity	nucleolus -> nucleus	CUP9, MET4, RAP1
YGL076C	RPL7A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex
YER074W	RPS24A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, SMP1, YAP5
YBR048W	RPS11B	protein biosynthesis, ribosomal small subunit assembly and maintenance, regulation of translational fidelity -> cell organization and biogenesis, biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	GAL4, HAP4, LEU3, MET31, MSN1
YJR139C	HOM6	homoserine biosynthesis, methionine metabolism, threonine metabolism -> amine metabolism, sulfur metabolism, biosynthesis, amino acid and derivative metabolism, organic acid metabolism	homoserine dehydrogenase activity -> oxidoreductase activity\, acting on CH-OH group of donors		HMS1, RAP1
\|YBR295W\|	PCA1	copper ion homeostasis -> cell homeostasis	P-type ATPase activity -> purine nucleotide binding, primary active transporter activity, cation transporter activity, hydrolase activity\, acting on acid anhydrides	membrane -> membrane	GAL4, SMP1
YKL180W	RPL17A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya), cytoplasm -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1
\|YBL093C\|	ROX3	transcription from Pol II promoter -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA polymerase II transcription mediator activity -> general RNA polymerase II transcription factor activity	mediator complex, nucleus -> nucleus	FHL1, RAP1
YGR085C	RPL11B	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, MIG1
YOR213C	SAS5	chromatin silencing at telomere -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	acetyltransferase activity -> transferase activity\, transferring acyl groups	nuclear chromosome\, telomeric region, nuclear chromatin -> chromosome, nuclear chromosome	GRF10(Pho2), SUM1
\|YMR224C\|	MRE11	DNA repair, double-strand break repair via nonhomologous end-joining, meiotic DNA double-strand break formation, meiotic DNA double-strand break processing, double-strand break repair via break-induced replication -> DNA metabolism, cell proliferation, catabolism	endonuclease activity, 3'-5' exonuclease activity, protein binding -> hydrolase activity\, acting on ester bonds, protein binding	nucleus -> nucleus	RAP1
\|YMR193W\|	MRPL24	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	mitochondrial large ribosomal subunit -> cytoplasm, ribonucleoprotein complex	ARO80, HAP4, HAP5, LEU3, MET31, RTG1, RTG3, STE12, STP1, UGA3
YHL033C	RPL8A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
YPL090C	RPS6A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, INO4, RAP1, YAP5
YNL069C	RPL16B	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, YAP5
Main:		biosynthesis (0.74)	structural constituent of ribosome (0.62)	cytoplasm (0.83)	RAP1 (0.70)
Score:		0.64	0.39	0.70	0.659
P-value:		5.960E-15 (protein biosynthesis)	4.524E-20 (structural constituent of ribosome)	3.720E-22 (cytosolic ribosome (sensu Eukarya))	1.617E-27 (FHL1)

RAP1(1) AND ALPHA1'(1) => SimExpr(other) OR SimExpr(YLR344W) : 9 20

EXPR: (0.105) ALPHA1' (P < 0.000) RAP1 (P < 0.639)

ORF	SYMBOL	P	F	C	TF
\|YMR013C\|	SEC59	protein-ER targeting, protein amino acid glycosylation -> cell organization and biogenesis, biosynthesis, protein modification, protein metabolism, transport	dolichol kinase activity -> transferase activity\, transferring phosphorus-containing groups	membrane -> membrane	FHL1, NDD1, RAP1, RLM1, RME1
YOL121C	RPS19A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	AZF1, FHL1, GCR1, GCR2, HAL9, MET31, MOT3, PDR1, RAP1, ROX1, RPH1, SMP1, YAP6, ZAP1
\|YEL056W\|	HAT2	chromatin assembly/disassembly, chromatin silencing at telomere -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	H3/H4 histone acetyltransferase activity -> transferase activity\, transferring acyl groups	cytoplasm, nucleus -> cytoplasm, nucleus	GAL4
\|YBL022C\|	PIM1	proteolysis and peptidolysis, response to heat -> catabolism, response to abiotic stimulus, protein metabolism	ATP-dependent peptidase activity -> peptidase activity	mitochondrial matrix -> cytoplasm	RAP1
\|YBR117C\|	TKL2	pentose-phosphate shunt -> coenzymes and prosthetic group metabolism, alcohol metabolism, water-soluble vitamin metabolism, carbohydrate metabolism, energy derivation by oxidation of organic compounds, catabolism	transketolase activity -> transferase activity\, transferring aldehyde or ketonic groups		FHL1, RAP1
\|YHL038C\|	CBP2	RNA splicing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pre-mRNA splicing factor activity -> RNA binding	mitochondrion -> cytoplasm	RAP1
YDL130W	RPP1B	protein biosynthesis, translational elongation -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAL4, RAP1, RFX1
YLR146C	SPE4	pantothenate biosynthesis, spermine biosynthesis -> biosynthesis, amine metabolism, coenzymes and prosthetic group metabolism, amino acid and derivative metabolism, secondary metabolism	spermine synthase activity -> transferase activity\, transferring alkyl or aryl (other than methyl) groups
YBR181C	RPS6B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya), cytoplasm -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, MAL13, RAP1, RGM1
YGR214W	RPS0A	protein biosynthesis, ribosomal small subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YJR123W	RPS5	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GRF10(Pho2), HSF1, MSN4, YAP1
YDL136W	RPL35B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, INO4, MSS11, RAP1
YOR369C	RPS12	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ARG80, FHL1, FKH2, LEU3, NDD1, PDR1, RME1, SMP1, YAP6
YPL131W	RPL5	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1
YBR118W	TEF2	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YLR061W	RPL22A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	BAS1, FHL1, HIR1, PDR1, RAP1, RCS1, RME1, ZAP1
YDR418W	RPL12B	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, SMP1
YLR344W	RPL26A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, RAP1
\|YMR231W\|	PEP5	nonselective vesicle docking, homotypic vacuole fusion (non-autophagic), Golgi to endosome transport, late endosome to vacuole transport -> cell organization and biogenesis, transport, vesicle-mediated transport		vacuolar membrane (sensu Fungi) -> cytoplasm, vacuole	ARG81, DOT6, HAL9, HAP2, MCM1, YAP1
\|YER047C\|	SAP1				MSS11
\|YGR254W\|	ENO1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphopyruvate hydratase activity -> carbon-oxygen lyase activity	phosphopyruvate hydratase complex, cytoplasm -> cytoplasm	FKH2, MSN4, PDR1, SWI5, YAP5
YGL076C	RPL7A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex
YER074W	RPS24A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, SMP1, YAP5
YBR048W	RPS11B	protein biosynthesis, ribosomal small subunit assembly and maintenance, regulation of translational fidelity -> cell organization and biogenesis, biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	GAL4, HAP4, LEU3, MET31, MSN1
\|YBR295W\|	PCA1	copper ion homeostasis -> cell homeostasis	P-type ATPase activity -> purine nucleotide binding, primary active transporter activity, cation transporter activity, hydrolase activity\, acting on acid anhydrides	membrane -> membrane	GAL4, SMP1
YKL180W	RPL17A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya), cytoplasm -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1
YOR213C	SAS5	chromatin silencing at telomere -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	acetyltransferase activity -> transferase activity\, transferring acyl groups	nuclear chromosome\, telomeric region, nuclear chromatin -> chromosome, nuclear chromosome	GRF10(Pho2), SUM1
YHL033C	RPL8A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1
YPL090C	RPS6A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, INO4, RAP1, YAP5
Main:		biosynthesis (0.75)	structural constituent of ribosome (0.63)	cytoplasm (0.88)	FHL1 (0.67)
Score:		0.67	0.40	0.78	0.590
P-value:		2.231E-08 (protein biosynthesis)	4.607E-11 (structural constituent of ribosome)	1.179E-12 (cytosolic ribosome (sensu Eukarya))	1.850E-14 (FHL1)

RAP1(1) AND SWI5(1) => SimExpr(other) OR SimExpr(YLR344W) : 6 14

EXPR: (0.100) SWI5 (P < 0.000) RAP1 (P < 0.475)

ORF	SYMBOL	P	F	C	TF
\|YMR013C\|	SEC59	protein-ER targeting, protein amino acid glycosylation -> cell organization and biogenesis, biosynthesis, protein modification, protein metabolism, transport	dolichol kinase activity -> dolichol kinase activity	membrane -> membrane	FHL1, NDD1, RAP1, RLM1, RME1
\|YLR452C\|	SST2	signal transduction, adaptation to pheromone during conjugation with cellular fusion -> signal transduction, conjugation, perception of external stimulus, sexual reproduction, response to abiotic stimulus	GTPase activator activity -> GTPase activator activity	plasma membrane -> membrane	DIG1, FHL1, RAP1, STE12
\|YEL056W\|	HAT2	chromatin assembly/disassembly, chromatin silencing at telomere -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	H3/H4 histone acetyltransferase activity -> acetyltransferase activity	cytoplasm, nucleus -> cytoplasm, nucleus	GAL4
YKL006W	RPL14A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, GRF10(Pho2), GTS1, RAP1
YLR441C	RPS1A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1, YAP5
YBR181C	RPS6B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya), cytoplasm -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, MAL13, RAP1, RGM1
YDR450W	RPS18A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, HIR2, RAP1, RGM1, YAP5
YOR369C	RPS12	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ARG80, FHL1, FKH2, LEU3, NDD1, PDR1, RME1, SMP1, YAP6
YJR145C	RPS4A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya), cytoplasm -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ACE2, CIN5, FHL1, INO4, MTH1, RAP1, YAP6
YBL087C	RPL23A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, IXR1, MSS11, PDR1, RAP1, SMP1, SOK2
\|YDR406W\|	PDR15	transport -> transport	ATP-binding cassette (ABC) transporter activity -> ATPase activity, P-P-bond-hydrolysis-driven transporter activity, hydrolase activity\, acting on acid anhydrides\, catalyzing transmembrane movement of substances	integral to membrane -> membrane
YLR344W	RPL26A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YGL030W	RPL30	protein biosynthesis, rRNA processing, mRNA splicing, regulation of translation -> cell organization and biogenesis, biosynthesis, transcription, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya), cytoplasm -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1, SFP1
YKR092C	SRP40	nucleocytoplasmic transport -> transport	chaperone activity -> chaperone activity	nucleolus -> nucleus	CUP9, MET4, RAP1
YER074W	RPS24A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, SMP1, YAP5
\|YBR295W\|	PCA1	copper ion homeostasis -> cell homeostasis	P-type ATPase activity -> ATPase activity, P-P-bond-hydrolysis-driven transporter activity, cation transporter activity, hydrolase activity\, acting on acid anhydrides\, catalyzing transmembrane movement of substances	membrane -> membrane	GAL4, SMP1
YOR213C	SAS5	chromatin silencing at telomere -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	acetyltransferase activity -> acetyltransferase activity	nuclear chromosome\, telomeric region, nuclear chromatin -> chromosome, nuclear chromosome	GRF10(Pho2), SUM1
\|YMR224C\|	MRE11	DNA repair, double-strand break repair via nonhomologous end-joining, meiotic DNA double-strand break formation, meiotic DNA double-strand break processing, double-strand break repair via break-induced replication -> DNA metabolism, cell proliferation, catabolism	endonuclease activity, 3'-5' exonuclease activity, protein binding -> endonuclease activity, 3'-5' exonuclease activity, protein binding	nucleus -> nucleus	RAP1
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
YNL069C	RPL16B	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, YAP5
Main:		biosynthesis (0.65)	structural constituent of ribosome (0.55)	cytoplasm (0.65)	RAP1 (0.74)
Score:		0.45	0.30	0.46	0.637
P-value:		1.090E-05 (protein biosynthesis)	2.358E-06 (structural constituent of ribosome)	1.313E-07 (cytosolic ribosome (sensu Eukarya))	1.232E-10 (FHL1)

RAP1(1) AND MCM1'(1) => SimExpr(other) OR SimExpr(YLR344W) : 5 16

EXPR: (0.090) MCM1' (P < 0.000) RAP1 (P < 0.115)

ORF	SYMBOL	P	F	C	TF
\|YLR452C\|	SST2	signal transduction, adaptation to pheromone during conjugation with cellular fusion -> signal transduction, conjugation, perception of external stimulus, sexual reproduction, response to abiotic stimulus	GTPase activator activity -> small GTPase regulatory/interacting protein activity	plasma membrane -> plasma membrane	DIG1, FHL1, RAP1, STE12
\|YBR117C\|	TKL2	pentose-phosphate shunt -> coenzymes and prosthetic group metabolism, alcohol metabolism, water-soluble vitamin metabolism, carbohydrate metabolism, energy derivation by oxidation of organic compounds, catabolism	transketolase activity -> transferase activity\, transferring aldehyde or ketonic groups		FHL1, RAP1
\|YHL038C\|	CBP2	RNA splicing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pre-mRNA splicing factor activity -> RNA binding	mitochondrion -> cytoplasm	RAP1
YDL130W	RPP1B	protein biosynthesis, translational elongation -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAL4, RAP1, RFX1
YKL006W	RPL14A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, GRF10(Pho2), GTS1, RAP1
YGL147C	RPL9A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, MBP1, RAP1, SWI4
YLR146C	SPE4	pantothenate biosynthesis, spermine biosynthesis -> biosynthesis, amine metabolism, coenzymes and prosthetic group metabolism, amino acid and derivative metabolism, secondary metabolism	spermine synthase activity -> transferase activity\, transferring alkyl or aryl (other than methyl) groups
YGR214W	RPS0A	protein biosynthesis, ribosomal small subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YDR450W	RPS18A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, HIR2, RAP1, RGM1, YAP5
YLR061W	RPL22A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	BAS1, FHL1, HIR1, PDR1, RAP1, RCS1, RME1, ZAP1
YLR344W	RPL26A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YKL152C	GPM1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphoglycerate mutase activity -> intramolecular transferase activity	cytosol -> cytoplasm	GCR1, GCR2, HSF1, RAP1
YGL030W	RPL30	protein biosynthesis, rRNA processing, mRNA splicing, regulation of translation -> cell organization and biogenesis, biosynthesis, transcription, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya), cytoplasm -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1, SFP1
YIL018W	RPL2B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, SWI5, YAP5
\|YGR254W\|	ENO1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphopyruvate hydratase activity -> carbon-oxygen lyase activity	phosphopyruvate hydratase complex, cytoplasm -> cytoplasm	FKH2, MSN4, PDR1, SWI5, YAP5
YER074W	RPS24A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, SMP1, YAP5
YJR139C	HOM6	homoserine biosynthesis, methionine metabolism, threonine metabolism -> amine metabolism, sulfur metabolism, biosynthesis, amino acid and derivative metabolism, organic acid metabolism	homoserine dehydrogenase activity -> oxidoreductase activity\, acting on CH-OH group of donors		HMS1, RAP1
\|YBL093C\|	ROX3	transcription from Pol II promoter -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA polymerase II transcription mediator activity -> general RNA polymerase II transcription factor activity	mediator complex, nucleus -> nucleus	FHL1, RAP1
YGR085C	RPL11B	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, MIG1
YPL090C	RPS6A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, INO4, RAP1, YAP5
YNL069C	RPL16B	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, YAP5
Main:		biosynthesis (0.81)	structural constituent of ribosome (0.62)	cytoplasm (0.89)	RAP1 (0.90)
Score:		0.68	0.39	0.78	0.916
P-value:		2.807E-05 (biosynthesis)	5.563E-09 (structural constituent of ribosome)	5.032E-10 (cytosolic ribosome (sensu Eukarya))	1.578E-15 (RAP1)

CSRE(1) AND RAP1(1) => SimExpr(other) OR SimExpr(YLR344W) : 2 9

RAP1(1) AND SCB(1) => SimExpr(YLR344W) OR SimExpr(other) : 8 1

EXPR: (0.084) SCB (P < 0.000) RAP1 (P < 0.119)

ORF	SYMBOL	P	F	C	TF
\|YLR208W\|	SEC13	nonselective vesicle assembly, ER to Golgi transport, ER-associated protein catabolism -> vesicle-mediated transport, intracellular transport, macromolecule catabolism, secretory pathway, protein metabolism		cytoplasm, COPII vesicle coat, nuclear pore, extrinsic to plasma membrane -> nucleus, extrinsic to membrane, cytoplasm, membrane coat, integral to membrane, endomembrane system, plasma membrane
YOR369C	RPS12	protein biosynthesis -> macromolecule biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ARG80, FHL1, FKH2, LEU3, NDD1, PDR1, RME1, SMP1, YAP6
YPL131W	RPL5	protein biosynthesis, ribosomal large subunit assembly and maintenance -> macromolecule biosynthesis, cytoplasm organization and biogenesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1
YBL087C	RPL23A	protein biosynthesis -> macromolecule biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, IXR1, MSS11, PDR1, RAP1, SMP1, SOK2
YBR118W	TEF2	translational elongation -> macromolecule biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YLR344W	RPL26A	protein biosynthesis -> macromolecule biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YGR085C	RPL11B	protein biosynthesis, ribosomal large subunit assembly and maintenance -> macromolecule biosynthesis, cytoplasm organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, MIG1
YHL033C	RPL8A	protein biosynthesis -> macromolecule biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1
YLR249W	YEF3	translational elongation -> macromolecule biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
Main:		protein metabolism (1.00)	structural constituent of ribosome (0.75)	cytoplasm (1.00)	FHL1 (0.88)
Score:		1.00	0.57	1.00	0.750
P-value:		2.819E-05 (protein biosynthesis)	2.238E-04 (structural constituent of ribosome)	1.586E-06 (ribosome)	1.471E-06 (FHL1)

RAP1(1) AND SWI5(1) AND MCM1'(1) => SimExpr(YLR344W) OR SimExpr(other) : 6 1

EXPR: (0.070) SWI5 (P < 0.000) MCM1' (P < 0.000) RAP1 (P < 0.030)

ORF	SYMBOL	P	F	C	TF
\|YLR452C\|	SST2	signal transduction, adaptation to pheromone during conjugation with cellular fusion -> signal transduction, adaptation to pheromone during conjugation with cellular fusion	GTPase activator activity -> GTPase activator activity	plasma membrane -> plasma membrane	DIG1, FHL1, RAP1, STE12
YKL006W	RPL14A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), large ribosomal subunit	FHL1, GAT3, GRF10(Pho2), GTS1, RAP1
YDR450W	RPS18A	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, small ribosomal subunit	FHL1, GAT3, HIR2, RAP1, RGM1, YAP5
YLR344W	RPL26A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), large ribosomal subunit	FHL1, RAP1
YGL030W	RPL30	protein biosynthesis, rRNA processing, mRNA splicing, regulation of translation -> protein biosynthesis, rRNA processing, mRNA splicing, regulation of translation	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya), cytoplasm -> cytosolic ribosome (sensu Eukarya), cytoplasm, large ribosomal subunit	FHL1, GAT3, RAP1, SFP1
YER074W	RPS24A	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, small ribosomal subunit	FHL1, GAT3, PDR1, RAP1, RGM1, SMP1, YAP5
YNL069C	RPL16B	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), large ribosomal subunit	FHL1, GAT3, PDR1, RAP1, RGM1, YAP5
Main:		protein biosynthesis (0.86)	structural constituent of ribosome (0.86)	cytosolic ribosome (sensu Eukarya) (0.86)	RAP1 FHL1 (1.00)
Score:		0.71	0.71	0.71	1.000
P-value:		5.608E-04 (protein biosynthesis)	1.504E-05 (structural constituent of ribosome)	8.648E-06 (cytosolic ribosome (sensu Eukarya))	3.457E-08 (FHL1)

RAP1(1) AND ALPHA1'(1) AND MCM1'(1) => SimExpr(other) OR SimExpr(YLR344W) : 3 7

EXPR: (0.092) ALPHA1' (P < 0.000) MCM1' (P < 0.000) RAP1 (P < 0.281)

ORF	SYMBOL	P	F	C	TF
\|YBR117C\|	TKL2	pentose-phosphate shunt -> coenzymes and prosthetic group metabolism, alcohol metabolism, water-soluble vitamin metabolism, carbohydrate metabolism, energy derivation by oxidation of organic compounds, catabolism	transketolase activity -> transferase activity\, transferring aldehyde or ketonic groups		FHL1, RAP1
\|YHL038C\|	CBP2	RNA splicing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pre-mRNA splicing factor activity -> RNA binding	mitochondrion -> cytoplasm	RAP1
YDL130W	RPP1B	protein biosynthesis, translational elongation -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAL4, RAP1, RFX1
YLR146C	SPE4	pantothenate biosynthesis, spermine biosynthesis -> biosynthesis, amine metabolism, coenzymes and prosthetic group metabolism, amino acid and derivative metabolism, secondary metabolism	spermine synthase activity -> transferase activity\, transferring alkyl or aryl (other than methyl) groups
YGR214W	RPS0A	protein biosynthesis, ribosomal small subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YLR061W	RPL22A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	BAS1, FHL1, HIR1, PDR1, RAP1, RCS1, RME1, ZAP1
YLR344W	RPL26A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, RAP1
\|YGR254W\|	ENO1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphopyruvate hydratase activity -> carbon-oxygen lyase activity	phosphopyruvate hydratase complex, cytoplasm -> cytoplasm	FKH2, MSN4, PDR1, SWI5, YAP5
YER074W	RPS24A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, SMP1, YAP5
YPL090C	RPS6A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, INO4, RAP1, YAP5
Main:		biosynthesis (0.80)	structural constituent of ribosome (0.60)	cytoplasm (1.00)	RAP1 (0.89)
Score:		0.67	0.36	1.00	0.861
P-value:		2.315E-02 (biosynthesis)	4.690E-04 (structural constituent of ribosome)	2.195E-04 (cytosolic ribosome (sensu Eukarya))	2.612E-06 (RAP1)

CSRE(1) AND RAP1(1) AND SWI5(1) => SimExpr(YLR344W) : 5

RAP1(1) AND ALPHA1'(1) AND SCB(1) => SimExpr(YLR344W) : 5

EXPR: (0.069) ALPHA1' (P < 0.000) SCB (P < 0.000) RAP1 (P < 0.053)

ORF	SYMBOL	P	F	C	TF
YOR369C	RPS12	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosol, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, ribosome	ARG80, FHL1, FKH2, LEU3, NDD1, PDR1, RME1, SMP1, YAP6
YPL131W	RPL5	protein biosynthesis, ribosomal large subunit assembly and maintenance -> protein biosynthesis, ribosome biogenesis and assembly	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, GAT3, RAP1
YBR118W	TEF2	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation elongation factor activity	ribosome -> ribosome	FHL1, RAP1
YLR344W	RPL26A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, RAP1
YHL033C	RPL8A	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1
Main:		protein biosynthesis (1.00)	structural constituent of ribosome (0.80)	ribosome (1.00)	FHL1 (1.00)
Score:		1.00	0.60	1.00	1.000
P-value:		5.595E-04 (protein biosynthesis)	1.631E-03 (structural constituent of ribosome)	1.672E-04 (ribosome)	8.831E-06 (FHL1)

RAP1(1) AND SFF'(1) AND SCB(1) => SimExpr(YLR344W) : 8

EXPR: (0.076) SFF' (P < 0.000) SCB (P < 0.000) RAP1 (P < 0.050)

ORF	SYMBOL	P	F	C	TF
YOR369C	RPS12	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosol, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, ribosome	ARG80, FHL1, FKH2, LEU3, NDD1, PDR1, RME1, SMP1, YAP6
YPL131W	RPL5	protein biosynthesis, ribosomal large subunit assembly and maintenance -> protein biosynthesis, ribosome biogenesis and assembly	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, GAT3, RAP1
YBL087C	RPL23A	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, IXR1, MSS11, PDR1, RAP1, SMP1, SOK2
YBR118W	TEF2	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation elongation factor activity	ribosome -> ribosome	FHL1, RAP1
YLR344W	RPL26A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, RAP1
YGR085C	RPL11B	protein biosynthesis, ribosomal large subunit assembly and maintenance -> protein biosynthesis, ribosome biogenesis and assembly	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, MIG1
YHL033C	RPL8A	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1
YLR249W	YEF3	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation elongation factor activity	ribosome -> ribosome	INO2, INO4
Main:		protein biosynthesis (1.00)	structural constituent of ribosome (0.75)	ribosome (1.00)	FHL1 (0.88)
Score:		1.00	0.57	1.00	0.750
P-value:		3.588E-06 (protein biosynthesis)	8.006E-05 (structural constituent of ribosome)	1.941E-07 (ribosome)	3.438E-07 (FHL1)

MCB(1) AND SCB(1) => SimExpr(YCR065W) OR SimExpr(other) : 10 4

EXPR: (0.106) MCB (P < 0.070) SCB (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YNL082W	PMS1	mismatch repair, meiosis -> DNA metabolism, cell proliferation	ATPase activity, ATP binding, DNA binding -> purine nucleotide binding, DNA binding, hydrolase activity\, acting on acid anhydrides	nuclear chromosome -> chromosome, nucleus	MTH1
YGL225W	VRG4	nucleotide-sugar transport, N-linked glycosylation, lipid glycosylation -> transport, biosynthesis, lipid metabolism, protein metabolism	nucleotide-sugar transporter activity -> nucleotide-sugar transporter activity	Golgi apparatus -> cytoplasm
YOL006C	TOP1	negative regulation of recombination within rDNA repeats, DNA topological change, DNA strand elongation, chromatin assembly/disassembly, regulation of transcription from Pol II promoter, RNA elongation from Pol II promoter, mitotic chromosome condensation, nuclear migration -> cell organization and biogenesis, cell cycle, mitotic cell cycle, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	DNA topoisomerase type I activity -> other isomerase activity	nucleus -> nucleus	REB1
YCR065W	HCM1	spindle assembly, transcription initiation from Pol II promoter -> cell organization and biogenesis, cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> nucleus	ASH1, HSF1, MBP1, NDD1, PHD1, ROX1, STB1, SWI4
YDR211W	GCD6	translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity -> translation factor activity\, nucleic acid binding	ribosome, eukaryotic translation initiation factor 2B complex -> cytoplasm, ribonucleoprotein complex	HSF1
\|YDR297W\|	SUR2	sphingolipid metabolism, sphingolipid biosynthesis -> lipid metabolism, biosynthesis	sphingosine hydroxylase activity -> sphingosine hydroxylase activity	endoplasmic reticulum -> cytoplasm	CBF1, MTH1
\|YKL042W\|	SPC42	microtubule nucleation, spindle pole body duplication (sensu Saccharomyces) -> cell organization and biogenesis, cell proliferation	structural constituent of cytoskeleton -> structural constituent of cytoskeleton	intermediate layer of spindle pole body, central plaque of spindle pole body -> cytoplasm
YBL035C	POL12	DNA replication\, priming, DNA replication initiation, lagging strand elongation -> cell proliferation, cell cycle, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	alpha DNA polymerase activity -> transferase activity\, transferring phosphorus-containing groups	alpha DNA polymerase\:primase complex -> nucleus	MBP1
YIL066C	RNR3	DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ribonucleoside-diphosphate reductase activity -> oxidoreductase activity\, acting on CH2 groups	cytoplasm -> cytoplasm	RFX1, STB1
YBR088C	POL30	leading strand elongation, lagging strand elongation, mutagenesis, base-excision repair, nucleotide-excision repair, mismatch repair, postreplication repair -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, mitotic cell cycle	DNA polymerase processivity factor activity -> transferase activity\, transferring phosphorus-containing groups	replication fork -> nucleus
\|YGR085C\|	RPL11B	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, MIG1
\|YML012W\|	ERV25	ER to Golgi transport -> transport, vesicle-mediated transport		COPII-coated vesicle -> cytoplasm	ABF1
YER070W	RNR1	DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ribonucleoside-diphosphate reductase activity -> oxidoreductase activity\, acting on CH2 groups	cytoplasm -> cytoplasm	FKH2, MBP1, REB1, SWI4, SWI6
YDR052C	DBF4	DNA replication initiation, regulation of DNA replication, protein amino acid phosphorylation -> phosphorus metabolism, cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	protein serine/threonine kinase activity -> transferase activity\, transferring phosphorus-containing groups	nucleoplasm -> nucleus	IME4, NRG1
Main:		cell proliferation (0.57)	transferase activity\, transferring phosphorus-containing groups (0.23)	cytoplasm (0.57)	MBP1 (0.27)
Score:		0.53	0.05	0.47	0.127
P-value:		4.340E-06 (DNA replication and chromosome cycle)	7.486E-03 (oxidoreductase activity\, acting on CH2 groups\, disulfide as acceptor)	4.996E-02 (replication fork)	1.745E-01 (MBP1)

ALPHA1'(1) AND MCB(1) AND SCB(1) => SimExpr(YCR065W) OR SimExpr(other) : 5 2

EXPR: (0.090) ALPHA1' (P < 0.000) MCB (P < 0.018) SCB (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YGL225W	VRG4	nucleotide-sugar transport, N-linked glycosylation, lipid glycosylation -> transport, biosynthesis, lipid metabolism, protein metabolism	nucleotide-sugar transporter activity -> nucleotide-sugar transporter activity	Golgi apparatus -> cytoplasm
YOL006C	TOP1	negative regulation of recombination within rDNA repeats, DNA topological change, DNA strand elongation, chromatin assembly/disassembly, regulation of transcription from Pol II promoter, RNA elongation from Pol II promoter, mitotic chromosome condensation, nuclear migration -> cell organization and biogenesis, cell cycle, mitotic cell cycle, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	DNA topoisomerase type I activity -> DNA topoisomerase type I activity	nucleus -> nucleus	REB1
YCR065W	HCM1	spindle assembly, transcription initiation from Pol II promoter -> cell organization and biogenesis, cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> nucleus	ASH1, HSF1, MBP1, NDD1, PHD1, ROX1, STB1, SWI4
\|YDR297W\|	SUR2	sphingolipid metabolism, sphingolipid biosynthesis -> lipid metabolism, biosynthesis	sphingosine hydroxylase activity -> sphingosine hydroxylase activity	endoplasmic reticulum -> cytoplasm	CBF1, MTH1
\|YKL042W\|	SPC42	microtubule nucleation, spindle pole body duplication (sensu Saccharomyces) -> cell organization and biogenesis, cell proliferation	structural constituent of cytoskeleton -> structural constituent of cytoskeleton	intermediate layer of spindle pole body, central plaque of spindle pole body -> cytoplasm
YIL066C	RNR3	DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ribonucleoside-diphosphate reductase activity -> ribonucleoside-diphosphate reductase activity	cytoplasm -> cytoplasm	RFX1, STB1
YER070W	RNR1	DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ribonucleoside-diphosphate reductase activity -> ribonucleoside-diphosphate reductase activity	cytoplasm -> cytoplasm	FKH2, MBP1, REB1, SWI4, SWI6
Main:		cell proliferation (0.57)	ribonucleoside-diphosphate reductase activity (0.29)	cytoplasm (0.71)	SWI4 STB1 REB1 MBP1 (0.40)
Score:		0.52	0.05	0.52	0.300
P-value:		6.514E-03 (DNA replication and chromosome cycle)	8.678E-04 (oxidoreductase activity\, acting on CH2 groups\, disulfide as acceptor)	2.431E+00 (intracellular)	5.032E-02 (STB1)

ALPHA1(1) AND ALPHA1'(1) AND MCB(1) => SimExpr(YCR065W) OR SimExpr(other) : 5 2

EXPR: (0.096) ALPHA1' (P < 0.000) MCB (P < 0.043) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YGL225W	VRG4	nucleotide-sugar transport, N-linked glycosylation, lipid glycosylation -> transport, biosynthesis, lipid metabolism, protein metabolism	nucleotide-sugar transporter activity -> nucleotide-sugar transporter activity	Golgi apparatus -> cytoplasm
YDR097C	MSH6	mismatch repair -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, cell proliferation	ATPase activity, ATP binding, DNA binding -> ATPase activity, ATP binding, DNA binding	nucleus -> nucleus	DOT6, MBP1, SWI6
YOL006C	TOP1	negative regulation of recombination within rDNA repeats, DNA topological change, DNA strand elongation, chromatin assembly/disassembly, regulation of transcription from Pol II promoter, RNA elongation from Pol II promoter, mitotic chromosome condensation, nuclear migration -> cell organization and biogenesis, cell cycle, mitotic cell cycle, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	DNA topoisomerase type I activity -> DNA topoisomerase type I activity	nucleus -> nucleus	REB1
YCR065W	HCM1	spindle assembly, transcription initiation from Pol II promoter -> cell organization and biogenesis, cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> nucleus	ASH1, HSF1, MBP1, NDD1, PHD1, ROX1, STB1, SWI4
\|YLR430W\|	SEN1	35S primary transcript processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ATP dependent RNA helicase activity -> RNA helicase activity, ATPase activity	nucleolus -> nucleus	ARG80, GTS1, HAP5, RTG3, SIP4
\|YER047C\|	SAP1				MSS11
YNL233W	BNI4	cytokinesis -> cell proliferation	protein binding -> protein binding	contractile ring (sensu Saccharomyces) -> site of polarized growth (sensu Fungi), cell cortex, cytoplasm	PHO4
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.67)	ATPase activity (0.33)	nucleus (0.67)	MBP1 (0.33)
Score:		0.53	0.07	0.47	0.067
P-value:		1.178E-01 (cell proliferation)	6.480E-01 (ATP binding)	9.201E-01 (nucleus)	3.556E-01 (MBP1)

MCM1(1) AND MCB(1) => SimExpr(YCR065W) : 6

EXPR: (0.092) MCB (P < 0.032) MCM1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YGR109C	CLB6	regulation of CDK activity, G1/S transition of mitotic cell cycle, premeiotic DNA synthesis -> cell cycle, mitotic cell cycle, DNA metabolism	cyclin-dependent protein kinase\, regulator activity -> cyclin-dependent protein kinase\, regulator activity		MBP1, STB1, SWI4, SWI6
YCR065W	HCM1	spindle assembly, transcription initiation from Pol II promoter -> cytoplasm organization and biogenesis, cell cycle, transcription	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> nucleus	ASH1, HSF1, MBP1, NDD1, PHD1, ROX1, STB1, SWI4
YDR309C	GIC2	axial budding, Rho protein signal transduction, establishment of cell polarity (sensu Saccharomyces) -> budding, intracellular signaling cascade, cytoplasm organization and biogenesis	small GTPase regulatory/interacting protein activity -> small GTPase regulatory/interacting protein activity	actin cap (sensu Saccharomyces), bud tip, shmoo tip, incipient bud site -> cell cortex, site of polarized growth (sensu Fungi), incipient bud site, cytoplasm	ASH1, HSF1, MBP1, PHD1, RLM1, SKN7, STB1, STE12, SWI4, SWI6
YIL066C	RNR3	DNA replication -> cell cycle, DNA metabolism	ribonucleoside-diphosphate reductase activity -> ribonucleoside-diphosphate reductase activity	cytoplasm -> cytoplasm	RFX1, STB1
YNR028W	CPR8		peptidyl-prolyl cis-trans isomerase activity -> peptidyl-prolyl cis-trans isomerase activity		ASH1, DIG1, MCM1
YGL163C	RAD54	double-strand break repair via synthesis-dependent strand annealing, heteroduplex formation, double-strand break repair via break-induced replication, telomerase-independent telomere maintenance, double-strand break repair via single-strand annealing, chromatin modeling -> mating-type switching/recombination, chromosome organization and biogenesis (sensu Eukarya), DNA repair, response to DNA damage, DNA metabolism	DNA supercoiling activity, DNA dependent ATPase activity -> DNA supercoiling activity, DNA dependent ATPase activity	nucleus -> nucleus
Main:		DNA metabolism (0.60)	peptidyl-prolyl cis-trans isomerase activity (0.17)	cytoplasm (0.50)	STB1 (0.80)
Score:		0.60	0.00	0.33	0.800
P-value:		2.557E-01 (DNA metabolism)	1.199E+00 (enzyme activity)	3.742E+00 (nucleus)	5.347E-06 (STB1)

STE12(1) AND MCB(1) => SimExpr(YCR065W) : 5

EXPR: (0.085) STE12 (P < 0.000) MCB (P < 0.013)

ORF	SYMBOL	P	F	C	TF
YCR065W	HCM1	spindle assembly, transcription initiation from Pol II promoter -> cell organization and biogenesis, cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> nucleus	ASH1, HSF1, MBP1, NDD1, PHD1, ROX1, STB1, SWI4
YDR309C	GIC2	axial budding, Rho protein signal transduction, establishment of cell polarity (sensu Saccharomyces) -> asexual reproduction, signal transduction, cell organization and biogenesis	small GTPase regulatory/interacting protein activity -> small GTPase regulatory/interacting protein activity	actin cap (sensu Saccharomyces), bud tip, shmoo tip, incipient bud site -> cell cortex, site of polarized growth (sensu Fungi), incipient bud site, cytoplasm	ASH1, HSF1, MBP1, PHD1, RLM1, SKN7, STB1, STE12, SWI4, SWI6
YJR043C	POL32	leading strand elongation, lagging strand elongation, mutagenesis, base-excision repair, nucleotide-excision repair, mismatch repair, postreplication repair -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, mitotic cell cycle	delta DNA polymerase activity -> delta DNA polymerase activity	delta DNA polymerase complex, nucleus -> cytoplasm, nucleus	MOT3, RTS2
YNL233W	BNI4	cytokinesis -> cell proliferation	protein binding -> protein binding	contractile ring (sensu Saccharomyces) -> site of polarized growth (sensu Fungi), cell cortex, cytoplasm	PHO4
YPR135W	CTF4	DNA dependent DNA replication, DNA repair -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, cell proliferation	DNA binding -> DNA binding	nucleus -> nucleus	BAS1, DIG1, FZF1
Main:		cell proliferation (0.80)	DNA binding (0.20)	cytoplasm (0.60)	SWI4 STB1 ASH1 HSF1 PHD1 MBP1 (0.40)
Score:		0.70	0.00	0.60	0.100
P-value:		1.957E-02 (cell proliferation)	1.354E+00 (binding)	5.936E-02 (cell cortex)	2.046E-02 (ASH1)

HAP234(1) AND ALPHA1'(1) => SimExpr(YBL099W) OR SimExpr(other) : 9 4

EXPR: (0.111) ALPHA1' (P < 0.000) HAP234 (P < 0.122)

ORF	SYMBOL	P	F	C	TF
YLR304C	ACO1	tricarboxylic acid cycle, citrate metabolism, glutamate biosynthesis, propionate metabolism -> carbohydrate metabolism, amine metabolism, organic acid metabolism, energy pathways, amino acid and derivative metabolism, biosynthesis	aconitate hydratase activity -> aconitate hydratase activity	cytosol, mitochondrial matrix -> cytoplasm	CIN5, YAP6
YOR136W	IDH2	tricarboxylic acid cycle, isocitrate metabolism, glutamate biosynthesis -> carbohydrate metabolism, amine metabolism, organic acid metabolism, energy pathways, amino acid and derivative metabolism, biosynthesis	isocitrate dehydrogenase (NAD+) activity -> isocitrate dehydrogenase activity	mitochondrial matrix, mitochondrion -> cytoplasm	MET4
\|YCR069W\|	CPR4		peptidyl-prolyl cis-trans isomerase activity -> peptidyl-prolyl cis-trans isomerase activity	membrane -> membrane	SKO1
\|YBR118W\|	TEF2	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YLR038C	COX12	cytochrome c oxidase biogenesis -> protein metabolism	cytochrome c oxidase activity -> heme-copper terminal oxidase activity, oxidoreductase activity\, acting on heme group of donors\, oxygen as acceptor, primary active transporter activity, hydrogen ion transporter activity	respiratory chain complex IV (sensu Eukarya) -> cytoplasm, respiratory chain complex IV, membrane	HAP4
YEL024W	RIP1	aerobic respiration, oxidative phosphorylation\, ubiquinone to cytochrome c -> energy pathways, electron transport, phosphorus metabolism	ubiquinol-cytochrome c reductase activity -> oxidoreductase activity\, acting on diphenols and related substances as donors\, cytochrome as acceptor, primary active transporter activity, hydrogen ion transporter activity	respiratory chain complex III (sensu Eukarya) -> cytoplasm, respiratory chain complex III, membrane	CBF1, HAP2, HAP4
\|YMR280C\|	CAT8	gluconeogenesis, positive regulation of transcription from Pol II promoter -> alcohol metabolism, monosaccharide metabolism, carbohydrate metabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, biosynthesis, energy pathways	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> nucleus	ABF1, REB1
YBL099W	ATP1	ATP synthesis coupled proton transport -> transport	hydrogen-transporting ATP synthase activity -> hydrogen ion transporter activity	proton-transporting ATP synthase\, catalytic core (sensu Eukarya) -> cytoplasm, proton-transporting ATP synthase complex, membrane	HAP4, ROX1
YPR145W	ASN1	asparagine biosynthesis -> amine metabolism, amino acid and derivative metabolism, organic acid metabolism, biosynthesis	asparagine synthase (glutamine-hydrolyzing) activity -> asparagine synthase (glutamine-hydrolyzing) activity		DAL81, GCN4, GLN3, MET4, RAP1, SUM1
YKL141W	SDH3	oxidative phosphorylation\, succinate to ubiquinone, tricarboxylic acid cycle -> electron transport, carbohydrate metabolism, phosphorus metabolism, energy pathways	succinate dehydrogenase activity -> succinate dehydrogenase activity	respiratory chain complex II (sensu Eukarya) -> cytoplasm, respiratory chain complex II, succinate dehydrogenase complex (ubiquinone), membrane
YML028W	TSA1	response to oxidative stress, regulation of redox homeostasis -> oxygen and reactive oxygen species metabolism, cell homeostasis, response to biotic stimulus	thioredoxin peroxidase activity -> thioredoxin peroxidase activity	cytoplasm -> cytoplasm	MBP1, NDD1, SKN7, YAP1
YOR187W	TUF1	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	mitochondrial matrix, mitochondrial ribosome -> cytoplasm, ribonucleoprotein complex	HAP4, REB1
\|YHR018C\|	ARG4	arginine biosynthesis -> amine metabolism, nitrogen metabolism, amino acid and derivative metabolism, organic acid metabolism, biosynthesis	argininosuccinate lyase activity -> argininosuccinate lyase activity	cytosol -> cytoplasm	GCN4, INO2
Main:		biosynthesis (0.58)	hydrogen ion transporter activity (0.23)	cytoplasm (0.83)	HAP4 (0.33)
Score:		0.45	0.05	0.74	0.152
P-value:		1.352E-03 (tricarboxylic acid cycle)	2.089E-02 (hydrogen ion transporter activity)	5.530E-03 (mitochondrial electron transport chain)	2.211E-03 (HAP4)

RAP1(1) => SimExpr(other) OR SimExpr(YGR085C) : 16 35

RAP1(1) AND SCB(1) => SimExpr(YGR085C) OR SimExpr(other) : 8 1

RAP1(1) AND SFF'(1) AND SCB(1) => SimExpr(YGR085C) : 8

RAP1(1) AND ALPHA1(1) AND SCB(1) => SimExpr(YGR085C) : 5

EXPR: (0.059) SCB (P < 0.000) RAP1 (P < 0.074) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YPL131W	RPL5	protein biosynthesis, ribosomal large subunit assembly and maintenance -> protein biosynthesis, ribosome biogenesis and assembly	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, GAT3, RAP1
YBL087C	RPL23A	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, IXR1, MSS11, PDR1, RAP1, SMP1, SOK2
YGR085C	RPL11B	protein biosynthesis, ribosomal large subunit assembly and maintenance -> protein biosynthesis, ribosome biogenesis and assembly	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, MIG1
YHL033C	RPL8A	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1
YLR249W	YEF3	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation elongation factor activity	ribosome -> ribosome	INO2, INO4
Main:		protein biosynthesis (1.00)	structural constituent of ribosome (0.80)	ribosome (1.00)	FHL1 (0.80)
Score:		1.00	0.60	1.00	0.600
P-value:		1.119E-03 (protein biosynthesis)	1.398E-03 (structural constituent of ribosome)	1.008E-04 (cytosolic large ribosomal subunit (sensu Eukarya))	7.160E-04 (FHL1)

mRRPE(1) AND PAC(1) => SimExpr(YOR095C) OR SimExpr(other) : 26 3

SFF'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YOR095C) OR SimExpr(other) : 9 2

EXPR: (0.094) SFF' (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.015)

ORF	SYMBOL	P	F	C	TF
\|YGL016W\|	KAP122	protein-nucleus import, response to drug -> response to abiotic stimulus, protein metabolism, transport	protein carrier activity -> transporter activity	cytoplasm, nuclear pore -> cytoplasm, nucleus, integral to membrane, endomembrane system	MSN2
YBR104W	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	FKH1, FKH2
YJL033W	HCA4	35S primary transcript processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ATP dependent RNA helicase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleus	HIR2, USV1
YJL138C	TIF2	translational initiation, regulation of translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity, RNA helicase activity -> translation factor activity\, nucleic acid binding, RNA binding	ribosome, cytoplasm -> cytoplasm, ribonucleoprotein complex	PHD1
YER110C	KAP123	protein-nucleus import -> protein metabolism, transport	protein carrier activity -> transporter activity	cytoplasm, nuclear pore, nucleus -> cytoplasm, nucleus, integral to membrane, endomembrane system
YNL112W	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
\|YNL292W\|	PUS4	tRNA modification -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pseudouridylate synthase activity -> carbon-oxygen lyase activity	mitochondrion, nucleus -> cytoplasm, nucleus	RCS1
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, SWI6
YOR095C	RKI1	pentose-phosphate shunt -> coenzymes and prosthetic group metabolism, alcohol metabolism, water-soluble vitamin metabolism, carbohydrate metabolism, energy derivation by oxidation of organic compounds, catabolism	ribose-5-phosphate isomerase activity -> intramolecular isomerase activity		FHL1, FKH2, RAP1
YGL078C	DBP3	ribosomal large subunit assembly and maintenance, 35S primary transcript processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ATP dependent RNA helicase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleus
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.40)	RNA binding (0.40)	cytoplasm (0.60)	FKH2 (0.25)
Score:		0.31	0.22	0.64	0.036
P-value:		1.087E-02 (35S primary transcript processing)	9.534E-05 (RNA helicase activity)	6.271E-02 (nucleolus)	5.897E-01 (FKH2)

RAP1(1) AND SCB(1) => SimExpr(YBR118W) OR SimExpr(other) : 8 1

RAP1(1) AND SFF'(1) AND SCB(1) => SimExpr(YBR118W) : 8

RAP1(1) AND ALPHA1'(1) AND SCB(1) => SimExpr(YBR118W) : 5

RAP1(1) AND SWI5(1) => SimExpr(other) OR SimExpr(YER074W) : 6 14

RAP1(1) AND SWI5(1) AND MCM1'(1) => SimExpr(YER074W) OR SimExpr(other) : 6 1

RAP1(1) AND ALPHA1(1) AND SWI5(1) => SimExpr(other) OR SimExpr(YER074W) : 2 6

EXPR: (0.106) SWI5 (P < 0.002) RAP1 (P < 0.729) ALPHA1 (P < 0.001)

ORF	SYMBOL	P	F	C	TF
\|YMR013C\|	SEC59	protein-ER targeting, protein amino acid glycosylation -> cytoplasm organization and biogenesis, macromolecule biosynthesis, intracellular transport, secretory pathway, protein modification, glycoprotein metabolism, protein metabolism, protein transport	dolichol kinase activity -> dolichol kinase activity	membrane -> membrane	FHL1, NDD1, RAP1, RLM1, RME1
YKL006W	RPL14A	protein biosynthesis -> macromolecule biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, GRF10(Pho2), GTS1, RAP1
YBL087C	RPL23A	protein biosynthesis -> macromolecule biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, IXR1, MSS11, PDR1, RAP1, SMP1, SOK2
YKR092C	SRP40	nucleocytoplasmic transport -> intracellular transport	chaperone activity -> chaperone activity	nucleolus -> nucleus	CUP9, MET4, RAP1
YER074W	RPS24A	protein biosynthesis -> macromolecule biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, SMP1, YAP5
YOR213C	SAS5	chromatin silencing at telomere -> nuclear organization and biogenesis, gene silencing, DNA metabolism, transcription	acetyltransferase activity -> acetyltransferase activity	nuclear chromosome\, telomeric region, nuclear chromatin -> chromosome, nuclear chromosome	GRF10(Pho2), SUM1
\|YMR224C\|	MRE11	DNA repair, double-strand break repair via nonhomologous end-joining, meiotic DNA double-strand break formation, meiotic DNA double-strand break processing, double-strand break repair via break-induced replication -> DNA recombination, cell cycle, catabolism, DNA metabolism	endonuclease activity, 3'-5' exonuclease activity, protein binding -> endonuclease activity, 3'-5' exonuclease activity, protein binding	nucleus -> nucleus	RAP1
YLR249W	YEF3	translational elongation -> macromolecule biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
Main:		protein metabolism (0.62)	structural constituent of ribosome (0.38)	cytoplasm (0.50)	RAP1 (0.75)
Score:		0.43	0.11	0.25	0.571
P-value:		3.994E-02 (protein biosynthesis)	1.967E-01 (structural constituent of ribosome)	8.363E-02 (ribosome)	2.439E-04 (RAP1)

RAP1(1) => SimExpr(other) OR SimExpr(YGL076C) : 15 36

RAP1(1) AND SCB(1) => SimExpr(YHL033C) OR SimExpr(other) : 8 1

RAP1(1) AND ALPHA1'(1) AND SCB(1) => SimExpr(YHL033C) : 5

RAP1(1) AND ALPHA1(1) AND SCB(1) => SimExpr(YHL033C) : 5

RAP1(1) AND SFF'(1) AND SCB(1) => SimExpr(YHL033C) : 8

RAP1(1) => SimExpr(other) OR SimExpr(YOR369C) : 16 35

RAP1(1) AND SFF(1) => SimExpr(other) OR SimExpr(YOR369C) : 9 22

EXPR: (0.093) SFF (P < 0.000) RAP1 (P < 0.313)

ORF	SYMBOL	P	F	C	TF
YOL121C	RPS19A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	AZF1, FHL1, GCR1, GCR2, HAL9, MET31, MOT3, PDR1, RAP1, ROX1, RPH1, SMP1, YAP6, ZAP1
\|YLR452C\|	SST2	signal transduction, adaptation to pheromone during conjugation with cellular fusion -> signal transduction, conjugation, perception of external stimulus, sexual reproduction, response to abiotic stimulus	GTPase activator activity -> GTPase activator activity	plasma membrane -> membrane	DIG1, FHL1, RAP1, STE12
\|YLR208W\|	SEC13	nonselective vesicle assembly, ER to Golgi transport, ER-associated protein catabolism -> macromolecule catabolism, transport, protein metabolism		cytoplasm, COPII vesicle coat, nuclear pore, extrinsic to plasma membrane -> nucleus, cytoplasm, membrane coat, membrane
YKR057W	RPS21A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ABF1, FHL1
YKL006W	RPL14A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, GRF10(Pho2), GTS1, RAP1
YLR441C	RPS1A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1, YAP5
\|YLR146C\|	SPE4	pantothenate biosynthesis, spermine biosynthesis -> biosynthesis, amine metabolism, coenzymes and prosthetic group metabolism, amino acid and derivative metabolism, secondary metabolism	spermine synthase activity -> spermine synthase activity
YGR214W	RPS0A	protein biosynthesis, ribosomal small subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YJR123W	RPS5	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GRF10(Pho2), HSF1, MSN4, YAP1
YOR369C	RPS12	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ARG80, FHL1, FKH2, LEU3, NDD1, PDR1, RME1, SMP1, YAP6
YPL131W	RPL5	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1
YJR145C	RPS4A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya), cytoplasm -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ACE2, CIN5, FHL1, INO4, MTH1, RAP1, YAP6
YBL087C	RPL23A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, IXR1, MSS11, PDR1, RAP1, SMP1, SOK2
\|YDR406W\|	PDR15	transport -> transport	ATP-binding cassette (ABC) transporter activity -> ATPase activity\, coupled to transmembrane movement of substances, P-P-bond-hydrolysis-driven transporter activity	integral to membrane -> membrane
YLR061W	RPL22A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	BAS1, FHL1, HIR1, PDR1, RAP1, RCS1, RME1, ZAP1
YDR418W	RPL12B	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, SMP1
YLR344W	RPL26A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YKL152C	GPM1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphoglycerate mutase activity -> phosphoglycerate mutase activity	cytosol -> cytoplasm	GCR1, GCR2, HSF1, RAP1
\|YMR231W\|	PEP5	nonselective vesicle docking, homotypic vacuole fusion (non-autophagic), Golgi to endosome transport, late endosome to vacuole transport -> cell organization and biogenesis, transport, vesicle-mediated transport		vacuolar membrane (sensu Fungi) -> cytoplasm, vacuole	ARG81, DOT6, HAL9, HAP2, MCM1, YAP1
\|YGR254W\|	ENO1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphopyruvate hydratase activity -> phosphopyruvate hydratase activity	phosphopyruvate hydratase complex, cytoplasm -> cytoplasm	FKH2, MSN4, PDR1, SWI5, YAP5
YKR092C	SRP40	nucleocytoplasmic transport -> transport	chaperone activity -> chaperone activity	nucleolus -> nucleus	CUP9, MET4, RAP1
YER074W	RPS24A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, SMP1, YAP5
YJR139C	HOM6	homoserine biosynthesis, methionine metabolism, threonine metabolism -> amine metabolism, sulfur metabolism, biosynthesis, amino acid and derivative metabolism, organic acid metabolism	homoserine dehydrogenase activity -> homoserine dehydrogenase activity		HMS1, RAP1
\|YBR295W\|	PCA1	copper ion homeostasis -> cell homeostasis	P-type ATPase activity -> ATPase activity\, coupled to transmembrane movement of substances, P-P-bond-hydrolysis-driven transporter activity, cation transporter activity	membrane -> membrane	GAL4, SMP1
YKL180W	RPL17A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya), cytoplasm -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1
\|YBL093C\|	ROX3	transcription from Pol II promoter -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA polymerase II transcription mediator activity -> RNA polymerase II transcription mediator activity	mediator complex, nucleus -> nucleus	FHL1, RAP1
YGR085C	RPL11B	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, MIG1
\|YMR224C\|	MRE11	DNA repair, double-strand break repair via nonhomologous end-joining, meiotic DNA double-strand break formation, meiotic DNA double-strand break processing, double-strand break repair via break-induced replication -> DNA metabolism, cell proliferation, catabolism	endonuclease activity, 3'-5' exonuclease activity, protein binding -> endonuclease activity, 3'-5' exonuclease activity, protein binding	nucleus -> nucleus	RAP1
YHL033C	RPL8A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
YNL069C	RPL16B	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, YAP5
Main:		biosynthesis (0.74)	structural constituent of ribosome (0.62)	cytoplasm (0.79)	FHL1 (0.71)
Score:		0.61	0.38	0.65	0.725
P-value:		9.552E-08 (protein biosynthesis)	1.976E-11 (structural constituent of ribosome)	2.499E-13 (cytosolic ribosome (sensu Eukarya))	1.196E-16 (FHL1)

RAP1(1) AND SFF'(1) => SimExpr(other) OR SimExpr(YOR369C) : 12 27

EXPR: (0.098) SFF' (P < 0.000) RAP1 (P < 0.534)

ORF	SYMBOL	P	F	C	TF
\|YMR013C\|	SEC59	protein-ER targeting, protein amino acid glycosylation -> cell organization and biogenesis, biosynthesis, protein modification, protein metabolism, transport	dolichol kinase activity -> dolichol kinase activity	membrane -> membrane	FHL1, NDD1, RAP1, RLM1, RME1
YOL121C	RPS19A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	AZF1, FHL1, GCR1, GCR2, HAL9, MET31, MOT3, PDR1, RAP1, ROX1, RPH1, SMP1, YAP6, ZAP1
\|YLR452C\|	SST2	signal transduction, adaptation to pheromone during conjugation with cellular fusion -> signal transduction, conjugation, perception of external stimulus, sexual reproduction, response to abiotic stimulus	GTPase activator activity -> GTPase activator activity	plasma membrane -> membrane	DIG1, FHL1, RAP1, STE12
\|YBL022C\|	PIM1	proteolysis and peptidolysis, response to heat -> catabolism, response to abiotic stimulus, protein metabolism	ATP-dependent peptidase activity -> ATP-dependent peptidase activity	mitochondrial matrix -> cytoplasm	RAP1
\|YBR117C\|	TKL2	pentose-phosphate shunt -> coenzymes and prosthetic group metabolism, alcohol metabolism, water-soluble vitamin metabolism, carbohydrate metabolism, energy derivation by oxidation of organic compounds, catabolism	transketolase activity -> transketolase activity		FHL1, RAP1
YKR057W	RPS21A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ABF1, FHL1
YKL006W	RPL14A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, GRF10(Pho2), GTS1, RAP1
YGL147C	RPL9A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, MBP1, RAP1, SWI4
YLR441C	RPS1A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1, YAP5
\|YLR146C\|	SPE4	pantothenate biosynthesis, spermine biosynthesis -> biosynthesis, amine metabolism, coenzymes and prosthetic group metabolism, amino acid and derivative metabolism, secondary metabolism	spermine synthase activity -> spermine synthase activity
YGR214W	RPS0A	protein biosynthesis, ribosomal small subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YJR123W	RPS5	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GRF10(Pho2), HSF1, MSN4, YAP1
YDL136W	RPL35B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, INO4, MSS11, RAP1
YOR369C	RPS12	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ARG80, FHL1, FKH2, LEU3, NDD1, PDR1, RME1, SMP1, YAP6
YPL131W	RPL5	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1
YJR145C	RPS4A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya), cytoplasm -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ACE2, CIN5, FHL1, INO4, MTH1, RAP1, YAP6
YBL087C	RPL23A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, IXR1, MSS11, PDR1, RAP1, SMP1, SOK2
\|YDR406W\|	PDR15	transport -> transport	ATP-binding cassette (ABC) transporter activity -> ATPase activity\, coupled to transmembrane movement of substances, P-P-bond-hydrolysis-driven transporter activity	integral to membrane -> membrane
YBR118W	TEF2	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YLR061W	RPL22A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	BAS1, FHL1, HIR1, PDR1, RAP1, RCS1, RME1, ZAP1
YDR418W	RPL12B	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, SMP1
YLR344W	RPL26A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YKL152C	GPM1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphoglycerate mutase activity -> phosphoglycerate mutase activity	cytosol -> cytoplasm	GCR1, GCR2, HSF1, RAP1
\|YMR231W\|	PEP5	nonselective vesicle docking, homotypic vacuole fusion (non-autophagic), Golgi to endosome transport, late endosome to vacuole transport -> cell organization and biogenesis, transport, vesicle-mediated transport		vacuolar membrane (sensu Fungi) -> cytoplasm, vacuole	ARG81, DOT6, HAL9, HAP2, MCM1, YAP1
\|YGR254W\|	ENO1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphopyruvate hydratase activity -> phosphopyruvate hydratase activity	phosphopyruvate hydratase complex, cytoplasm -> cytoplasm	FKH2, MSN4, PDR1, SWI5, YAP5
YKR092C	SRP40	nucleocytoplasmic transport -> transport	chaperone activity -> chaperone activity	nucleolus -> nucleus	CUP9, MET4, RAP1
YGL076C	RPL7A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex
YER074W	RPS24A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, SMP1, YAP5
YBR048W	RPS11B	protein biosynthesis, ribosomal small subunit assembly and maintenance, regulation of translational fidelity -> cell organization and biogenesis, biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	GAL4, HAP4, LEU3, MET31, MSN1
YJR139C	HOM6	homoserine biosynthesis, methionine metabolism, threonine metabolism -> amine metabolism, sulfur metabolism, biosynthesis, amino acid and derivative metabolism, organic acid metabolism	homoserine dehydrogenase activity -> homoserine dehydrogenase activity		HMS1, RAP1
\|YBR295W\|	PCA1	copper ion homeostasis -> cell homeostasis	P-type ATPase activity -> ATPase activity\, coupled to transmembrane movement of substances, P-P-bond-hydrolysis-driven transporter activity, cation transporter activity	membrane -> membrane	GAL4, SMP1
YKL180W	RPL17A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya), cytoplasm -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1
\|YBL093C\|	ROX3	transcription from Pol II promoter -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA polymerase II transcription mediator activity -> RNA polymerase II transcription mediator activity	mediator complex, nucleus -> nucleus	FHL1, RAP1
YGR085C	RPL11B	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, MIG1
\|YMR224C\|	MRE11	DNA repair, double-strand break repair via nonhomologous end-joining, meiotic DNA double-strand break formation, meiotic DNA double-strand break processing, double-strand break repair via break-induced replication -> DNA metabolism, cell proliferation, catabolism	endonuclease activity, 3'-5' exonuclease activity, protein binding -> endonuclease activity, 3'-5' exonuclease activity, protein binding	nucleus -> nucleus	RAP1
\|YMR193W\|	MRPL24	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	mitochondrial large ribosomal subunit -> cytoplasm, ribonucleoprotein complex	ARO80, HAP4, HAP5, LEU3, MET31, RTG1, RTG3, STE12, STP1, UGA3
YHL033C	RPL8A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
YNL069C	RPL16B	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, YAP5
Main:		biosynthesis (0.77)	structural constituent of ribosome (0.61)	cytoplasm (0.81)	RAP1 FHL1 (0.69)
Score:		0.65	0.36	0.66	0.692
P-value:		4.025E-12 (protein biosynthesis)	4.923E-15 (structural constituent of ribosome)	3.389E-16 (cytosolic ribosome (sensu Eukarya))	3.885E-21 (FHL1)

RAP1(1) AND SWI5(1) => SimExpr(other) OR SimExpr(YOR369C) : 6 14

RAP1(1) AND SCB(1) => SimExpr(YOR369C) OR SimExpr(other) : 8 1

RAP1(1) AND SFF'(1) AND SCB(1) => SimExpr(YOR369C) : 8

RAP1(1) AND ALPHA1'(1) AND SCB(1) => SimExpr(YOR369C) : 5

RAP1(1) AND mRRPE(1) => SimExpr(other) OR SimExpr(YDL130W) : 2 5

EXPR: (0.098) mRRPE (P < 0.004) RAP1 (P < 0.375)

ORF	SYMBOL	P	F	C	TF
\|YMR013C\|	SEC59	protein-ER targeting, protein amino acid glycosylation -> cell organization and biogenesis, biosynthesis, protein modification, protein metabolism, transport	dolichol kinase activity -> dolichol kinase activity	membrane -> membrane	FHL1, NDD1, RAP1, RLM1, RME1
YOL121C	RPS19A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosol, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, ribosome	AZF1, FHL1, GCR1, GCR2, HAL9, MET31, MOT3, PDR1, RAP1, ROX1, RPH1, SMP1, YAP6, ZAP1
YDL130W	RPP1B	protein biosynthesis, translational elongation -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, GAL4, RAP1, RFX1
\|YLR146C\|	SPE4	pantothenate biosynthesis, spermine biosynthesis -> biosynthesis, amine metabolism, coenzymes and prosthetic group metabolism, amino acid and derivative metabolism, secondary metabolism	spermine synthase activity -> spermine synthase activity
YGL030W	RPL30	protein biosynthesis, rRNA processing, mRNA splicing, regulation of translation -> cell organization and biogenesis, biosynthesis, transcription, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya), cytoplasm -> cytosol, cytoplasm, ribosome	FHL1, GAT3, RAP1, SFP1
YBR048W	RPS11B	protein biosynthesis, ribosomal small subunit assembly and maintenance, regulation of translational fidelity -> cell organization and biogenesis, biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosol, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, ribosome	GAL4, HAP4, LEU3, MET31, MSN1
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> ribosome	INO2, INO4
Main:		biosynthesis (1.00)	structural constituent of ribosome (0.57)	ribosome (0.83)	RAP1 FHL1 (0.67)
Score:		1.00	0.29	0.67	0.533
P-value:		9.347E-04 (protein biosynthesis)	8.551E-03 (structural constituent of ribosome)	3.979E-03 (ribosome)	1.076E-02 (FHL1)

RAP1(1) => SimExpr(other) OR SimExpr(YPL131W) : 16 35

RAP1(1) AND SCB(1) => SimExpr(YPL131W) OR SimExpr(other) : 8 1

RAP1(1) AND ALPHA1(1) AND SCB(1) => SimExpr(YPL131W) : 5

RAP1(1) AND SFF'(1) AND SCB(1) => SimExpr(YPL131W) : 8

RAP1(1) AND ALPHA1'(1) AND SCB(1) => SimExpr(YPL131W) : 5

RAP1(1) => SimExpr(other) OR SimExpr(YBR181C) : 16 35

RAP1(1) AND SWI5(1) => SimExpr(other) OR SimExpr(YBR181C) : 6 14

RAP1(1) => SimExpr(other) OR SimExpr(YGL030W) : 15 36

RAP1(1) AND mRRPE(1) => SimExpr(other) OR SimExpr(YGL030W) : 1 6

RAP1(1) AND ALPHA1(1) AND SFF(1) => SimExpr(other) OR SimExpr(YLR061W) : 4 13

EXPR: (0.093) SFF (P < 0.000) RAP1 (P < 0.452) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YKR057W	RPS21A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ABF1, FHL1
YKL006W	RPL14A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, GRF10(Pho2), GTS1, RAP1
YPL131W	RPL5	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1
YBL087C	RPL23A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, IXR1, MSS11, PDR1, RAP1, SMP1, SOK2
YLR061W	RPL22A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	BAS1, FHL1, HIR1, PDR1, RAP1, RCS1, RME1, ZAP1
YKL152C	GPM1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphoglycerate mutase activity -> phosphoglycerate mutase activity	cytosol -> cytoplasm	GCR1, GCR2, HSF1, RAP1
\|YMR231W\|	PEP5	nonselective vesicle docking, homotypic vacuole fusion (non-autophagic), Golgi to endosome transport, late endosome to vacuole transport -> cell organization and biogenesis, transport, vesicle-mediated transport		vacuolar membrane (sensu Fungi) -> cytoplasm, vacuole	ARG81, DOT6, HAL9, HAP2, MCM1, YAP1
\|YGR254W\|	ENO1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphopyruvate hydratase activity -> phosphopyruvate hydratase activity	phosphopyruvate hydratase complex, cytoplasm -> cytoplasm	FKH2, MSN4, PDR1, SWI5, YAP5
YKR092C	SRP40	nucleocytoplasmic transport -> transport	chaperone activity -> chaperone activity	nucleolus -> nucleus	CUP9, MET4, RAP1
YER074W	RPS24A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, SMP1, YAP5
YJR139C	HOM6	homoserine biosynthesis, methionine metabolism, threonine metabolism -> amine metabolism, sulfur metabolism, biosynthesis, amino acid and derivative metabolism, organic acid metabolism	homoserine dehydrogenase activity -> homoserine dehydrogenase activity		HMS1, RAP1
YKL180W	RPL17A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya), cytoplasm -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1
\|YBL093C\|	ROX3	transcription from Pol II promoter -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA polymerase II transcription mediator activity -> RNA polymerase II transcription mediator activity	mediator complex, nucleus -> nucleus	FHL1, RAP1
YGR085C	RPL11B	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, MIG1
\|YMR224C\|	MRE11	DNA repair, double-strand break repair via nonhomologous end-joining, meiotic DNA double-strand break formation, meiotic DNA double-strand break processing, double-strand break repair via break-induced replication -> DNA metabolism, cell proliferation, catabolism	endonuclease activity, 3'-5' exonuclease activity, protein binding -> endonuclease activity, 3'-5' exonuclease activity, protein binding	nucleus -> nucleus	RAP1
YHL033C	RPL8A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
Main:		biosynthesis (0.76)	structural constituent of ribosome (0.56)	cytoplasm (0.81)	RAP1 (0.65)
Score:		0.61	0.30	0.68	0.603
P-value:		1.244E-03 (protein biosynthesis)	1.776E-05 (structural constituent of ribosome)	5.236E-06 (cytosolic ribosome (sensu Eukarya))	2.239E-07 (FHL1)

RAP1(1) => SimExpr(other) OR SimExpr(YOL121C) : 15 36

RAP1(1) AND SFF(1) => SimExpr(other) OR SimExpr(YOL121C) : 8 23

RAP1(1) AND mRRPE(1) => SimExpr(other) OR SimExpr(YOL121C) : 1 6

RAP1(1) => SimExpr(other) OR SimExpr(YKL006W) : 15 36

RAP1(1) AND SWI5(1) => SimExpr(other) OR SimExpr(YKL006W) : 6 14

RAP1(1) AND MCM1'(1) => SimExpr(other) OR SimExpr(YKL006W) : 5 16

RAP1(1) AND ALPHA1(1) => SimExpr(other) OR SimExpr(YKL006W) : 7 17

EXPR: (0.099) RAP1 (P < 0.739) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
\|YMR013C\|	SEC59	protein-ER targeting, protein amino acid glycosylation -> cell organization and biogenesis, biosynthesis, protein modification, protein metabolism, transport	dolichol kinase activity -> dolichol kinase activity	membrane -> membrane	FHL1, NDD1, RAP1, RLM1, RME1
\|YBR117C\|	TKL2	pentose-phosphate shunt -> coenzymes and prosthetic group metabolism, alcohol metabolism, water-soluble vitamin metabolism, carbohydrate metabolism, energy derivation by oxidation of organic compounds, catabolism	transketolase activity -> transketolase activity		FHL1, RAP1
YKR057W	RPS21A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ABF1, FHL1
YDL130W	RPP1B	protein biosynthesis, translational elongation -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAL4, RAP1, RFX1
YKL006W	RPL14A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, GRF10(Pho2), GTS1, RAP1
YPL131W	RPL5	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1
YBL087C	RPL23A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, IXR1, MSS11, PDR1, RAP1, SMP1, SOK2
YLR061W	RPL22A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	BAS1, FHL1, HIR1, PDR1, RAP1, RCS1, RME1, ZAP1
YKL152C	GPM1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphoglycerate mutase activity -> phosphoglycerate mutase activity	cytosol -> cytoplasm	GCR1, GCR2, HSF1, RAP1
\|YMR231W\|	PEP5	nonselective vesicle docking, homotypic vacuole fusion (non-autophagic), Golgi to endosome transport, late endosome to vacuole transport -> cell organization and biogenesis, transport, vesicle-mediated transport		vacuolar membrane (sensu Fungi) -> cytoplasm, vacuole	ARG81, DOT6, HAL9, HAP2, MCM1, YAP1
\|YER047C\|	SAP1				MSS11
YIL018W	RPL2B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, SWI5, YAP5
\|YGR254W\|	ENO1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphopyruvate hydratase activity -> phosphopyruvate hydratase activity	phosphopyruvate hydratase complex, cytoplasm -> cytoplasm	FKH2, MSN4, PDR1, SWI5, YAP5
YKR092C	SRP40	nucleocytoplasmic transport -> transport	chaperone activity -> chaperone activity	nucleolus -> nucleus	CUP9, MET4, RAP1
YER074W	RPS24A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, SMP1, YAP5
YBR048W	RPS11B	protein biosynthesis, ribosomal small subunit assembly and maintenance, regulation of translational fidelity -> cell organization and biogenesis, biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	GAL4, HAP4, LEU3, MET31, MSN1
YJR139C	HOM6	homoserine biosynthesis, methionine metabolism, threonine metabolism -> amine metabolism, sulfur metabolism, biosynthesis, amino acid and derivative metabolism, organic acid metabolism	homoserine dehydrogenase activity -> homoserine dehydrogenase activity		HMS1, RAP1
YKL180W	RPL17A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya), cytoplasm -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1
\|YBL093C\|	ROX3	transcription from Pol II promoter -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA polymerase II transcription mediator activity -> RNA polymerase II transcription mediator activity	mediator complex, nucleus -> nucleus	FHL1, RAP1
YGR085C	RPL11B	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, MIG1
YOR213C	SAS5	chromatin silencing at telomere -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	acetyltransferase activity -> acetyltransferase activity	nuclear chromosome\, telomeric region, nuclear chromatin -> chromosome, nuclear chromosome	GRF10(Pho2), SUM1
\|YMR224C\|	MRE11	DNA repair, double-strand break repair via nonhomologous end-joining, meiotic DNA double-strand break formation, meiotic DNA double-strand break processing, double-strand break repair via break-induced replication -> DNA metabolism, cell proliferation, catabolism	endonuclease activity, 3'-5' exonuclease activity, protein binding -> endonuclease activity, 3'-5' exonuclease activity, protein binding	nucleus -> nucleus	RAP1
YHL033C	RPL8A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
Main:		biosynthesis (0.74)	structural constituent of ribosome (0.55)	cytoplasm (0.76)	RAP1 (0.62)
Score:		0.60	0.29	0.59	0.536
P-value:		3.678E-05 (protein biosynthesis)	7.440E-07 (structural constituent of ribosome)	1.053E-07 (cytosolic ribosome (sensu Eukarya))	1.895E-10 (FHL1)

RAP1(1) AND SWI5(1) AND MCM1'(1) => SimExpr(YKL006W) OR SimExpr(other) : 6 1

RAP1(1) AND ALPHA1(1) AND SWI5(1) => SimExpr(other) OR SimExpr(YKL006W) : 2 6

RAP1(1) AND SFF(1) AND SWI5(1) => SimExpr(YLR441C) OR SimExpr(other) : 10 4

RAP1(1) AND mRRPE(1) => SimExpr(other) OR SimExpr(YBR048W) : 1 6

mRRPE(1) AND PAC(1) => SimExpr(YLR249W) OR SimExpr(other) : 27 2

mRRPE(1) AND PAC(1) AND SCB(1) => SimExpr(YLR249W) OR SimExpr(other) : 10 1

mRRPE(1) AND SWI5(1) AND PAC(1) => SimExpr(YLR249W) OR SimExpr(other) : 6 1

EXPR: (0.085) mRRPE (P < 0.003) SWI5 (P < 0.000) PAC (P < 0.022)

ORF	SYMBOL	P	F	C	TF
\|YGL016W\|	KAP122	protein-nucleus import, response to drug -> response to abiotic stimulus, protein metabolism, transport	protein carrier activity -> protein carrier activity	cytoplasm, nuclear pore -> cytoplasm, nucleus, integral to membrane, endomembrane system	MSN2
YDR399W	HPT1	purine nucleotide biosynthesis -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	hypoxanthine phosphoribosyltransferase activity -> hypoxanthine phosphoribosyltransferase activity
YMR229C	RRP5	rRNA processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding, snoRNA binding -> RNA binding, snoRNA binding	nucleolus, nucleolus organizer complex -> nucleus	FHL1, RAP1
YJR002W	MPP10	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nucleolar ribonucleoprotein complex, small nuclear ribonucleoprotein complex, nucleolus, nucleus -> nucleus, ribonucleoprotein complex
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, SWI6
YHR089C	GAR1	rRNA modification, 35S primary transcript processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	RNA binding -> RNA binding	nucleolus, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	CBF1, FZF1
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.71)	RNA binding (0.40)	nucleus (0.83)	ABF1 (0.20)
Score:		0.57	0.10	0.93	0.000
P-value:		3.512E-05 (rRNA modification)	4.289E-01 (nucleic acid binding)	2.184E-05 (small nucleolar ribonucleoprotein complex)	2.685E-01 (MSN2)

RAP1(1) AND SCB(1) => SimExpr(YLR249W) OR SimExpr(other) : 8 1

RAP1(1) AND mRRPE(1) => SimExpr(other) OR SimExpr(YLR249W) : 1 6

RAP1(1) AND ALPHA1(1) AND SFF(1) AND SWI5(1) => SimExpr(YLR249W) OR SimExpr(other) : 5 1

EXPR: (0.088) SFF (P < 0.000) SWI5 (P < 0.000) RAP1 (P < 0.106) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YKL006W	RPL14A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, GRF10(Pho2), GTS1, RAP1
YBL087C	RPL23A	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, IXR1, MSS11, PDR1, RAP1, SMP1, SOK2
YKR092C	SRP40	nucleocytoplasmic transport -> nucleocytoplasmic transport	chaperone activity -> chaperone activity	nucleolus -> nucleus	CUP9, MET4, RAP1
YER074W	RPS24A	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, SMP1, YAP5
\|YMR224C\|	MRE11	DNA repair, double-strand break repair via nonhomologous end-joining, meiotic DNA double-strand break formation, meiotic DNA double-strand break processing, double-strand break repair via break-induced replication -> mitotic recombination, M phase, DNA catabolism, DNA recombination, DNA repair	endonuclease activity, 3'-5' exonuclease activity, protein binding -> endonuclease activity, 3'-5' exonuclease activity, protein binding	nucleus -> nucleus	RAP1
YLR249W	YEF3	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
Main:		protein biosynthesis (0.67)	structural constituent of ribosome (0.50)	cytoplasm (0.67)	RAP1 (0.83)
Score:		0.40	0.20	0.47	0.667
P-value:		5.607E-02 (protein biosynthesis)	5.977E-02 (structural constituent of ribosome)	2.140E-02 (ribosome)	5.176E-04 (RAP1)

ALPHA1(1) AND mRRPE(1) AND PAC(1) => SimExpr(YLR249W) : 7

EXPR: (0.092) mRRPE (P < 0.012) PAC (P < 0.045) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YJL033W	HCA4	35S primary transcript processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ATP dependent RNA helicase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleus	HIR2, USV1
YMR229C	RRP5	rRNA processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding, snoRNA binding -> RNA binding	nucleolus, nucleolus organizer complex -> nucleus	FHL1, RAP1
YJR002W	MPP10	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nucleolar ribonucleoprotein complex, small nuclear ribonucleoprotein complex, nucleolus, nucleus -> nucleus, ribonucleoprotein complex
YHR128W	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups		CIN5
YOR095C	RKI1	pentose-phosphate shunt -> coenzymes and prosthetic group metabolism, alcohol metabolism, water-soluble vitamin metabolism, carbohydrate metabolism, energy derivation by oxidation of organic compounds, catabolism	ribose-5-phosphate isomerase activity -> intramolecular isomerase activity		FHL1, FKH2, RAP1
YMR239C	RNT1	35S primary transcript processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ribonuclease III activity -> hydrolase activity\, acting on ester bonds, RNA binding	nucleolus -> nucleus
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.71)	RNA binding (0.50)	nucleus (0.80)	RAP1 FHL1 (0.40)
Score:		0.52	0.20	0.70	0.100
P-value:		2.713E-04 (rRNA processing)	7.534E-02 (RNA binding)	1.842E-04 (nucleolus)	5.170E-01 (USV1)

RAP1(1) AND ALPHA1(1) AND SCB(1) => SimExpr(YLR249W) : 5

RAP1(1) AND SFF'(1) AND SCB(1) => SimExpr(YLR249W) : 8

RAP1(1) AND mRRPE(1) => SimExpr(other) OR SimExpr(YLR146C) : 2 5

RAP1(1) AND SCB(1) => SimExpr(YBL087C) OR SimExpr(other) : 8 1

RAP1(1) AND ALPHA1(1) AND SCB(1) => SimExpr(YBL087C) : 5

RAP1(1) AND SFF'(1) AND SCB(1) => SimExpr(YBL087C) : 8

ndt80(MSE)(1) AND SWI5(1) => SimExpr(YPR122W) OR SimExpr(other) : 7 2

EXPR: (0.108) ndt80(MSE) (P < 0.061) SWI5 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YPR122W	AXL1	axial budding, bud site selection, conjugation with cellular fusion, peptide pheromone maturation -> asexual reproduction, conjugation, protein metabolism, cell proliferation, cell organization and biogenesis, sexual reproduction	metalloendopeptidase activity -> metalloendopeptidase activity	integral to membrane, bud neck, shmoo tip -> integral to membrane, site of polarized growth (sensu Fungi)	CIN5
YER155C	BEM2	cell wall organization and biogenesis, bud growth, small GTPase mediated signal transduction, establishment of cell polarity (sensu Saccharomyces), actin cytoskeleton organization and biogenesis, microtubule cytoskeleton organization and biogenesis -> asexual reproduction, signal transduction, cell organization and biogenesis, organelle organization and biogenesis	signal transducer activity -> signal transducer activity	intracellular -> intracellular
YGL116W	CDC20	mitotic spindle elongation, ubiquitin-dependent protein catabolism, mitotic metaphase/anaphase transition, mitotic chromosome segregation, cyclin catabolism -> cell organization and biogenesis, catabolism, cell proliferation, cell cycle, protein metabolism	enzyme activator activity -> enzyme activator activity	anaphase-promoting complex -> intracellular	DIG1, FKH2, INO2, INO4, IXR1, MCM1, NDD1
YFR023W	PES4	DNA dependent DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			DIG1, FKH1, FKH2, GLN3, HAP3, MCM1, MSN2, RIM101, RLM1, RTG3, STE12, SUM1, THI2, YAP1
YMR001C	CDC5	DNA dependent DNA replication, protein amino acid phosphorylation -> phosphorus metabolism, cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	protein serine/threonine kinase activity -> protein serine/threonine kinase activity	nucleus, spindle pole, bud neck -> intracellular, site of polarized growth (sensu Fungi)	NDD1, REB1, SWI6
\|YHL043W\|	ECM34	cell wall organization and biogenesis -> cell organization and biogenesis
YMR280C	CAT8	gluconeogenesis, positive regulation of transcription from Pol II promoter -> alcohol metabolism, monosaccharide metabolism, carbohydrate metabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, biosynthesis, energy pathways	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> intracellular	ABF1, REB1
YKL104C	GFA1	cell wall chitin biosynthesis -> cell organization and biogenesis, biosynthesis, polysaccharide metabolism, carbohydrate metabolism	glucosamine-fructose-6-phosphate aminotransferase (isomerizing) activity -> glucosamine-fructose-6-phosphate aminotransferase (isomerizing) activity		REB1
\|YJR007W\|	SUI2	translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity -> translation initiation factor activity	ribosome, cytoplasm -> intracellular	GLN3, HAP3, HIR1, RCS1
Main:		cell organization and biogenesis (0.56)	metalloendopeptidase activity (0.14)	intracellular (0.83)	REB1 (0.43)
Score:		0.64	0.00	0.73	0.286
P-value:		1.445E-01 (external encapsulating structure organization and biogenesis)	1.561E+00 (transferase activity)	1.713E-01 (bud neck)	1.744E-01 (REB1)

ALPHA1(1) AND ndt80(MSE)(1) AND SWI5(1) => SimExpr(YPR122W) : 5

EXPR: (0.090) ndt80(MSE) (P < 0.025) SWI5 (P < 0.000) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YPR122W	AXL1	axial budding, bud site selection, conjugation with cellular fusion, peptide pheromone maturation -> asexual reproduction, conjugation, protein metabolism, cell proliferation, cell organization and biogenesis, sexual reproduction	metalloendopeptidase activity -> metalloendopeptidase activity	integral to membrane, bud neck, shmoo tip -> integral to membrane, site of polarized growth (sensu Fungi)	CIN5
YGL116W	CDC20	mitotic spindle elongation, ubiquitin-dependent protein catabolism, mitotic metaphase/anaphase transition, mitotic chromosome segregation, cyclin catabolism -> cell organization and biogenesis, catabolism, cell proliferation, cell cycle, protein metabolism	enzyme activator activity -> enzyme activator activity	anaphase-promoting complex -> nucleus, ubiquitin ligase complex	DIG1, FKH2, INO2, INO4, IXR1, MCM1, NDD1
YFR023W	PES4	DNA dependent DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			DIG1, FKH1, FKH2, GLN3, HAP3, MCM1, MSN2, RIM101, RLM1, RTG3, STE12, SUM1, THI2, YAP1
YMR001C	CDC5	DNA dependent DNA replication, protein amino acid phosphorylation -> phosphorus metabolism, cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	protein serine/threonine kinase activity -> protein serine/threonine kinase activity	nucleus, spindle pole, bud neck -> nucleus, cytoplasm, site of polarized growth (sensu Fungi)	NDD1, REB1, SWI6
YMR280C	CAT8	gluconeogenesis, positive regulation of transcription from Pol II promoter -> alcohol metabolism, monosaccharide metabolism, carbohydrate metabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, biosynthesis, energy pathways	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> nucleus	ABF1, REB1
Main:		cell proliferation (0.80)	metalloendopeptidase activity (0.25)	nucleus (0.75)	FKH2 NDD1 MCM1 REB1 DIG1 (0.40)
Score:		0.80	0.00	0.67	0.300
P-value:		2.055E-02 (cell proliferation)	2.543E+00 (enzyme activity)	4.566E-02 (bud neck)	7.290E-02 (DIG1)

ALPHA1(1) AND ALPHA2(1) AND ALPHA1'(1) AND mRRPE(1) => SimExpr(YER131W) OR SimExpr(other) : 5 2

EXPR: (0.112) ALPHA2 (P < 0.006) ALPHA1' (P < 0.009) mRRPE (P < 0.187) ALPHA1 (P < 0.008)

ORF	SYMBOL	P	F	C	TF
YDR023W	SES1	amino acid activation -> biosynthesis, protein metabolism	serine-tRNA ligase activity -> serine-tRNA ligase activity	cytoplasm -> cytoplasm	GRF10(Pho2), MOT3
YJL033W	HCA4	35S primary transcript processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ATP dependent RNA helicase activity -> ATP dependent RNA helicase activity	nucleolus -> nucleus	HIR2, USV1
\|YHR128W\|	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> uracil phosphoribosyltransferase activity		CIN5
YNL111C	CYB5	sterol biosynthesis -> alcohol metabolism, biosynthesis, lipid metabolism	electron transporter activity -> electron transporter activity	microsome -> membrane fraction	ABF1, GCR2, GTS1, NRG1, REB1, ROX1
YER131W	RPS26B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YBR048W	RPS11B	protein biosynthesis, ribosomal small subunit assembly and maintenance, regulation of translational fidelity -> cell organization and biogenesis, biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	GAL4, HAP4, LEU3, MET31, MSN1
\|YBR294W\|	SUL1	sulfate transport -> transport	sulfate transporter activity -> sulfate transporter activity	plasma membrane -> plasma membrane	STB1
Main:		biosynthesis (0.71)	structural constituent of ribosome (0.29)	cytoplasm (0.50)	GCR2 (0.14)
Score:		0.57	0.05	0.20	0.000
P-value:		3.036E-01 (biosynthesis)	6.853E-01 (structural constituent of ribosome)	1.945E-01 (cytosolic small ribosomal subunit (sensu Eukarya))	6.785E-01 (MSN1)

LYS14(1) AND ATRepeat(1) => SimExpr(YDR226W) OR SimExpr(other) : 5 1

mRRPE(1) AND PAC(1) => SimExpr(YMR239C) OR SimExpr(other) : 26 3

mRRPE(1) AND PAC(1) AND SCB(1) => SimExpr(YMR239C) : 11

ALPHA1'(1) AND MCB(1) AND SCB(1) => SimExpr(other) OR SimExpr(YGL225W) : 2 5

ALPHA1(1) AND mRRPE(1) AND PAC(1) => SimExpr(YJL033W) OR SimExpr(other) : 6 1

ALPHA1'(1) AND SFF(1) AND RPN4(1) => SimExpr(other) OR SimExpr(YOR362C) : 3 9

EXPR: (0.114) ALPHA1' (P < 0.000) SFF (P < 0.000) RPN4 (P < 0.140)

ORF	SYMBOL	P	F	C	TF
YDR394W	RPT3	ubiquitin-dependent protein catabolism -> macromolecule catabolism, protein metabolism	ATPase activity, endopeptidase activity -> purine nucleotide binding, peptidase activity, hydrolase activity\, acting on acid anhydrides	proteasome regulatory particle (sensu Eukarya), proteasome regulatory particle\, base subcomplex (sensu Eukarya) -> cytosol, endoplasmic reticulum, nucleus	RTG1
YDL126C	CDC48	ubiquitin-dependent protein catabolism, nonselective vesicle fusion, cell cycle, apoptosis, protein transport, ER-associated protein catabolism -> secretory pathway, cell cycle, programmed cell death, protein transport, macromolecule catabolism, vesicle-mediated transport, protein metabolism	ATPase activity -> purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleus, microsome, endoplasmic reticulum, cytosol -> nucleus, vesicular fraction, endoplasmic reticulum, cytosol	DAL82, MAL33, SWI4
\|YER109C\|	FLO8	pseudohyphal growth, invasive growth -> cellular morphogenesis	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus, cytoplasm -> nucleus, cytoplasm
\|YGR184C\|	UBR1	protein polyubiquitination, protein monoubiquitination -> macromolecule catabolism, protein modification, protein metabolism	ubiquitin-protein ligase activity -> ligase activity\, forming carbon-nitrogen bonds	proteasome complex (sensu Eukarya) -> cytosol, endoplasmic reticulum, nucleus	HMS1, REB1, RIM101
YER012W	PRE1	ubiquitin-dependent protein catabolism, response to stress, sporulation (sensu Saccharomyces) -> macromolecule catabolism, response to stress, sporulation (sensu Fungi), protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya), nucleus -> cytosol, nucleus, endoplasmic reticulum
YOR362C	PRE10	ubiquitin-dependent protein catabolism -> macromolecule catabolism, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya) -> cytosol, endoplasmic reticulum, nucleus
\|YGR124W\|	ASN2	asparagine biosynthesis -> amine biosynthesis, amine metabolism, amino acid and derivative metabolism, carboxylic acid metabolism	asparagine synthase (glutamine-hydrolyzing) activity -> ligase activity\, forming carbon-nitrogen bonds		ASH1, ROX1
YNL012W	SPO1	meiosis -> cell cycle	phospholipase activity -> hydrolase activity\, acting on ester bonds	nucleus -> nucleus	ARO80, SRD1
YML092C	PRE8	ubiquitin-dependent protein catabolism -> macromolecule catabolism, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya) -> cytosol, endoplasmic reticulum, nucleus
YGL201C	MCM6	DNA unwinding, DNA replication initiation -> cell cycle, DNA metabolism	chromatin binding, ATP dependent DNA helicase activity -> DNA binding, adenyl nucleotide binding, hydrolase activity\, acting on acid anhydrides	cytoplasm, nucleus, pre-replicative complex -> cytoplasm, nucleus, nucleoplasm	MCM1
YOL038W	PRE6	ubiquitin-dependent protein catabolism -> macromolecule catabolism, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya) -> cytosol, endoplasmic reticulum, nucleus
YMR100W	MUB1	regulation of budding -> budding
Main:		macromolecule catabolism (0.58)	peptidase activity (0.45)	nucleus (1.00)	SWI4 (0.17)
Score:		0.36	0.25	1.00	0.000
P-value:		6.617E-07 (ubiquitin-dependent protein catabolism)	6.074E-06 (endopeptidase activity)	2.116E-08 (proteasome complex (sensu Eukarya))	7.267E-01 (MAL33)

ALPHA1(1) AND ALPHA1'(1) AND MCB(1) => SimExpr(YDR097C) OR SimExpr(other) : 5 2

ABF1(1) AND SFF(1) AND mRRPE(1) => SimExpr(YLR293C) OR SimExpr(other) : 8 3

EXPR: (0.107) ABF1 (P < 0.000) SFF (P < 0.000) mRRPE (P < 0.035)

ORF	SYMBOL	P	F	C	TF
\|YAR019C\|	CDC15	cytokinesis, regulation of exit from mitosis, protein amino acid phosphorylation -> phosphorus metabolism, cell proliferation, mitotic cell cycle, protein metabolism	protein kinase activity -> transferase activity\, transferring phosphorus-containing groups	spindle pole body -> cytoplasm	PHO4
\|YAL016W\|	TPD3	protein biosynthesis, actin filament organization, mitotic spindle checkpoint, bud growth, protein amino acid dephosphorylation -> biosynthesis, cell organization and biogenesis, asexual reproduction, phosphorus metabolism, cell proliferation, cell cycle, protein metabolism	protein phosphatase type 2A activity -> hydrolase activity\, acting on ester bonds	protein phosphatase type 2A complex, bud neck, nucleus, cytoplasm, shmoo tip, bud tip, spindle pole body -> protein phosphatase type 2A complex, nucleus, site of polarized growth (sensu Fungi), site of polarized growth (sensu Saccharomyces), cytoplasm, microtubule organizing center	ABF1
YER110C	KAP123	protein-nucleus import -> protein metabolism, transport	protein carrier activity -> protein carrier activity	cytoplasm, nuclear pore, nucleus -> cytoplasm, nucleus, integral to membrane, endomembrane system
YNL292W	PUS4	tRNA modification -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pseudouridylate synthase activity -> carbon-oxygen lyase activity	mitochondrion, nucleus -> cytoplasm, nucleus	RCS1
YDR172W	SUP35	translational termination -> biosynthesis, protein metabolism	translation release factor activity -> translation factor activity\, nucleic acid binding	cytosol -> cytoplasm	ABF1, ZMS1
YNL111C	CYB5	sterol biosynthesis -> alcohol metabolism, biosynthesis, lipid metabolism	electron transporter activity -> electron transporter activity	microsome -> membrane fraction	ABF1, GCR2, GTS1, NRG1, REB1, ROX1
YGR282C	BGL2	cell wall organization and biogenesis -> cell organization and biogenesis	glucan 1\,3-beta-glucosidase activity -> hydrolase activity\, acting on glycosyl bonds	cell wall -> cell wall	ABF1, CIN5, SMP1
YDR385W	EFT2	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	ABF1, FHL1, INO4
YLR293C	GSP1	nucleocytoplasmic transport, nuclear organization and biogenesis, rRNA processing -> transport, cell organization and biogenesis, RNA metabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RAN small monomeric GTPase activity -> purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	cytoplasm, nucleus -> cytoplasm, nucleus	ABF1
YMR308C	PSE1	mRNA-nucleus export -> transport, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	protein carrier activity -> protein carrier activity	nucleus, cytoplasm -> nucleus, cytoplasm	SWI4
\|YJL159W\|	HSP150	cell wall organization and biogenesis -> cell organization and biogenesis	structural constituent of cell wall -> structural constituent of cell wall	cell wall -> cell wall	ACE2, HIR2, MCM1, RLM1, SWI5
Main:		protein metabolism (0.45)	protein carrier activity (0.18)	cytoplasm (0.73)	ABF1 (0.60)
Score:		0.44	0.04	0.53	0.333
P-value:		7.051E-02 (nucleocytoplasmic transport)	1.280E-02 (protein carrier activity)	1.747E-01 (spindle pole body)	1.106E-03 (ABF1)

ABF1(1) AND PAC(1) => SimExpr(YJL050W) : 5

EXPR: (0.078) ABF1 (P < 0.000) PAC (P < 0.007)

ORF	SYMBOL	P	F	C	TF
YLR197W	SIK1	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> RNA processing, ribosome biogenesis and assembly, rRNA metabolism, transcription\, DNA-dependent		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex, nucleus, nucleolus -> nucleus, ribonucleoprotein complex	DAL81, HAL9
YER110C	KAP123	protein-nucleus import -> intracellular protein transport, nucleocytoplasmic transport, protein metabolism	protein carrier activity -> protein carrier activity	cytoplasm, nuclear pore, nucleus -> cytoplasm, nucleus, integral to membrane, endomembrane system
YNL112W	DBP2		RNA helicase activity -> RNA helicase activity	bud neck -> site of polarized growth (sensu Fungi)
YNL292W	PUS4	tRNA modification -> RNA processing, tRNA metabolism	pseudouridylate synthase activity -> pseudouridylate synthase activity	mitochondrion, nucleus -> cytoplasm, nucleus	RCS1
YJL050W	MTR4	35S primary transcript processing -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent	ATP dependent RNA helicase activity -> RNA helicase activity, ATP dependent helicase activity, RNA dependent ATPase activity	nucleolus -> nucleus
Main:		RNA processing (0.75)	RNA helicase activity (0.50)	nucleus (0.80)	RCS1 (0.50)
Score:		0.50	0.17	0.60	0.000
P-value:		8.295E-03 (RNA modification)	1.022E-02 (RNA helicase activity)	6.316E-02 (nucleolus)	1.521E-01 (HAL9)

SFF(1) AND RPN4(1) => SimExpr(other) OR SimExpr(YNL012W) : 5 12

EXPR: (0.117) SFF (P < 0.000) RPN4 (P < 0.173)

ORF	SYMBOL	P	F	C	TF
YDR394W	RPT3	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	ATPase activity, endopeptidase activity -> purine nucleotide binding, peptidase activity, hydrolase activity\, acting on acid anhydrides	proteasome regulatory particle (sensu Eukarya), proteasome regulatory particle\, base subcomplex (sensu Eukarya) -> cytoplasm, nucleus	RTG1
YDL126C	CDC48	ubiquitin-dependent protein catabolism, nonselective vesicle fusion, cell cycle, apoptosis, protein transport, ER-associated protein catabolism -> cell proliferation, cell death, macromolecule catabolism, transport, protein metabolism	ATPase activity -> purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleus, microsome, endoplasmic reticulum, cytosol -> nucleus, membrane fraction, cytoplasm	DAL82, MAL33, SWI4
\|YER109C\|	FLO8	pseudohyphal growth, invasive growth -> cell organization and biogenesis	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus, cytoplasm -> nucleus, cytoplasm
\|YGR184C\|	UBR1	protein polyubiquitination, protein monoubiquitination -> catabolism, protein metabolism	ubiquitin-protein ligase activity -> ligase activity\, forming carbon-nitrogen bonds	proteasome complex (sensu Eukarya) -> cytoplasm, nucleus	HMS1, REB1, RIM101
YER012W	PRE1	ubiquitin-dependent protein catabolism, response to stress, sporulation (sensu Saccharomyces) -> catabolism, response to stress, sporulation, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya), nucleus -> nucleus, cytoplasm
YOR362C	PRE10	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya) -> cytoplasm, nucleus
YIL075C	RPN2	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	receptor activity, endopeptidase activity -> receptor activity, peptidase activity	proteasome regulatory particle (sensu Eukarya) -> cytoplasm, nucleus	MSS11, REB1, SFL1
\|YGR124W\|	ASN2	asparagine biosynthesis -> amine metabolism, amino acid and derivative metabolism, organic acid metabolism, biosynthesis	asparagine synthase (glutamine-hydrolyzing) activity -> ligase activity\, forming carbon-nitrogen bonds		ASH1, ROX1
YFR050C	PRE4	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya) -> cytoplasm, nucleus	MTH1, REB1
\|YNL251C\|	NRD1	nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleus -> nucleus	ABF1, MAC1
\|YKL135C\|	APL2	vesicle-mediated transport -> transport	clathrin binding -> clathrin binding	AP-1 adaptor complex -> cytoplasmic vesicle, cytoplasm	ABF1, DOT6
YNL012W	SPO1	meiosis -> cell proliferation	phospholipase activity -> hydrolase activity\, acting on ester bonds	nucleus -> nucleus	ARO80, SRD1
YGR286C	BIO2	biotin biosynthesis -> biosynthesis, coenzymes and prosthetic group metabolism, vitamin metabolism, heterocycle metabolism, organic acid metabolism, sulfur metabolism	biotin synthase activity -> transferase activity\, transferring sulfur-containing groups
YML092C	PRE8	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya) -> cytoplasm, nucleus
YGL201C	MCM6	DNA unwinding, DNA replication initiation -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	chromatin binding, ATP dependent DNA helicase activity -> DNA binding, adenyl nucleotide binding, hydrolase activity\, acting on acid anhydrides	cytoplasm, nucleus, pre-replicative complex -> cytoplasm, nucleus	MCM1
YOL038W	PRE6	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya) -> cytoplasm, nucleus
YMR100W	MUB1	regulation of budding -> asexual reproduction
Main:		protein metabolism (0.53)	peptidase activity (0.44)	nucleus (0.93)	REB1 (0.30)
Score:		0.31	0.21	0.98	0.089
P-value:		2.455E-08 (ubiquitin-dependent protein catabolism)	1.712E-08 (endopeptidase activity)	3.549E-11 (proteasome complex (sensu Eukarya))	8.044E-01 (REB1)

SWI5(1) AND PAC(1) => SimExpr(YHR089C) OR SimExpr(other) : 8 3

mRRPE(1) AND PAC(1) => SimExpr(YHR089C) OR SimExpr(other) : 28 1

mRRPE(1) AND PAC(1) => SimExpr(YPL043W) OR SimExpr(other) : 28 1

mRRPE(1) AND PAC(1) AND MCM1'(1) => SimExpr(YPL043W) : 6

AVERAGE SCORES:

P
  SCORE: 0.621 (Part of genes covered by "Main": 0.729) (No. rules=52/52)
  P-VALUE: 0.635
F
  SCORE: 0.230 (Part of genes covered by "Main": 0.457) (No. rules=52/52)
  P-VALUE: 0.538
C
  SCORE: 0.692 (Part of genes covered by "Main": 0.795) (No. rules=52/52)
  P-VALUE: 0.596
TF
  SCORE: 0.409 (Part of genes covered by "Main": 0.553) (No. rules=50/52)
  P-VALUE: 0.520
EXPRESSION: 0.462 (52)

Discovering regulatory binding-site modules using rule-based learning

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