Discovering regulatory binding-site modules using rule-based learning

SFF(1) AND mRRPE(1) AND PAC(1) AND SCB(1) => SimExpr(YGR280C) OR SimExpr(other) : 7 3

EXPR: (0.134) SFF (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.004) SCB (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> cytoplasm organization and biogenesis, RNA metabolism, transcription	RNA binding -> RNA binding	nucleolus -> nucleus
\|YJL138C\|	TIF2	translational initiation, regulation of translational initiation -> macromolecule biosynthesis, protein metabolism	translation initiation factor activity, RNA helicase activity -> translation factor activity\, nucleic acid binding, RNA binding	ribosome, cytoplasm -> cytoplasm, ribonucleoprotein complex	PHD1
\|YMR259C\|	NO SYMBOL				ARG80, GCR2, GTS1, HIR1, SRD1
YHR052W	CIC1	protein catabolism -> macromolecule catabolism, protein metabolism	protein binding\, bridging -> protein binding\, bridging	nucleolus, proteasome complex (sensu Eukarya) -> nucleus, cytoplasm	HAP4, MATa1
YOR078W	BUD21	processing of 20S pre-rRNA -> cytoplasm organization and biogenesis, RNA metabolism, transcription	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, MSS11, SIG1, SKO1
YBR104W	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	FKH1, FKH2
YJL109C	UTP10	processing of 20S pre-rRNA -> cytoplasm organization and biogenesis, RNA metabolism, transcription	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
YJL069C	UTP18				ABF1
YCL059C	KRR1	ribosome biogenesis, rRNA processing -> cytoplasm organization and biogenesis, RNA metabolism, transcription		nucleolus -> nucleus
\|YLR249W\|	YEF3	translational elongation -> macromolecule biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
Main:		RNA metabolism (0.50)	RNA binding (0.57)	nucleus (0.62)	ABF1 (0.29)
Score:		0.32	0.33	0.71	0.048
P-value:		3.912E-03 (rRNA processing)	1.827E-02 (snoRNA binding)	2.304E-04 (nucleolus)	1.000E+00

LYS14(1) AND mRRPE(1) AND PAC(1) => SimExpr(YGR280C) OR SimExpr(other) : 7 2

EXPR: (0.126) LYS14 (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.002)

ORF	SYMBOL	P	F	C	TF
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus
YML093W	UTP14	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
\|YMR259C\|	NO SYMBOL				ARG80, GCR2, GTS1, HIR1, SRD1
YHR052W	CIC1	protein catabolism -> catabolism, protein metabolism	protein binding\, bridging -> protein binding\, bridging	nucleolus, proteasome complex (sensu Eukarya) -> nucleus, cytoplasm	HAP4, MATa1
YJR070C	NO SYMBOL				GAT3, YAP5
YNL110C	NOP15	ribosomal large subunit biogenesis -> cell organization and biogenesis		nucleus, nucleolus -> nucleus
\|YHR128W\|	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups		CIN5
YMR290C	HAS1			nucleolus, nuclear membrane -> nucleus, endomembrane system	RAP1
YGL099W	LSG1	conjugation with cellular fusion, sporulation (sensu Saccharomyces), ribosome nucleus export -> conjugation, sporulation, cell organization and biogenesis, protein metabolism, transport, sexual reproduction	GTPase activity -> purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	cytoplasm -> cytoplasm	PHO4
Main:		cell organization and biogenesis (0.67)	RNA binding (0.40)	nucleus (0.83)	GCR2 (0.17)
Score:		0.60	0.10	0.73	0.000
P-value:		5.396E-03 (ribosome biogenesis)	9.488E-01 (RNA binding)	8.333E-05 (nucleolus)	9.462E-01 (MATa1)

STRE'(1) AND Gcr1(1) => SimExpr(YJL052W) : 5

EXPR: (0.108) STRE' (P < 0.000) Gcr1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YER177W	BMH1	pseudohyphal growth, sporulation (sensu Saccharomyces), RAS protein signal transduction, activation of MAPK (pseudohyphal growth), glycogen metabolism -> cell organization and biogenesis, sporulation, carbohydrate metabolism, signal transduction, energy derivation by oxidation of organic compounds	DNA binding -> DNA binding	nucleus -> nucleus	ACE2, GCR1, MBP1, NDD1, SWI4, SWI5
YGR254W	ENO1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphopyruvate hydratase activity -> hydro-lyase activity	phosphopyruvate hydratase complex, cytoplasm -> cytoplasm	FKH2, MSN4, PDR1, SWI5, YAP5
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 the CH-OH group of donors\, NAD or NADP as acceptor	cytoplasm -> cytoplasm	ACE2, ADR1, FKH2, HIR1, IME4, MBP1, NDD1, PHO4, RCS1, SFP1, SKN7, SWI5
YJL052W	TDH1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	glyceraldehyde 3-phosphate dehydrogenase (phosphorylating) activity -> oxidoreductase activity\, acting on the aldehyde or oxo group of donors\, NAD or NADP as acceptor	cytosol, lipid particle, cell wall -> cytoplasm, cell wall	MAC1
YOR374W	ALD4	ethanol metabolism -> alcohol metabolism	aldehyde dehydrogenase (NAD+) activity -> oxidoreductase activity\, acting on the aldehyde or oxo group of donors\, NAD or NADP as acceptor	mitochondrion -> cytoplasm	RAP1
Main:		alcohol metabolism (0.80)	oxidoreductase activity\, acting on the aldehyde or oxo group of donors\, NAD or NADP as acceptor (0.40)	cytoplasm (0.80)	SWI5 (0.60)
Score:		0.90	0.10	0.60	0.300
P-value:		1.748E-04 (monosaccharide catabolism)	3.111E-03 (oxidoreductase activity\, acting on the aldehyde or oxo group of donors\, NAD or NADP as acceptor)	5.952E-01 (cytosol)	2.493E-03 (SWI5)

MCB(1) AND PAC(1) => SimExpr(YLR049C) OR SimExpr(other) : 5 2

EXPR: (0.125) MCB (P < 0.001) PAC (P < 0.000)

ORF	SYMBOL	P	F	C	TF
\|YIL026C\|	IRR1	mitotic sister chromatid cohesion, colony morphology, germination (sensu Saccharomyces), cytogamy -> cell organization and biogenesis, sporulation, plasma membrane fusion, sporulation (sensu Fungi), cell proliferation, conjugation, sexual reproduction	protein binding -> protein binding	nuclear cohesin complex -> chromosome, nucleus	ABF1, MAL33, MBP1, SWI6
YPR144C	NOC4	ribosome biogenesis -> cell organization and biogenesis		nucleus -> nucleus	HIR1
YLR049C	NO SYMBOL				MBP1, SWI5
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
YDR279W	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
YOR284W	HUA2				RFX1, YAP6
\|YJR055W\|	HIT1	aerobic respiration -> energy pathways			STP2
Main:		cell organization and biogenesis (0.50)	ribonucleoside-diphosphate reductase activity (0.50)	nucleus (0.67)	MBP1 (0.43)
Score:		0.33	0.00	0.33	0.190
P-value:		5.867E-01 (DNA replication and chromosome cycle)	2.000E+00	3.799E+00 (nucleus)	1.050E-02 (MBP1)

ALPHA1'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YOR272W) OR SimExpr(other) : 36 12

EXPR: (0.133) ALPHA1' (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.001)

ORF	SYMBOL	P	F	C	TF
YNR053C	NOG2	mRNA splicing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	GTPase activity -> purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleus, nucleolus, nucleoplasm -> nucleus, nucleoplasm	ABF1, AZF1
\|YMR049C\|	ERB1	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			RTG3
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus
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
YML093W	UTP14	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
YHR196W	UTP9	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex, nucleolus, nucleus -> nucleus, ribonucleoprotein complex
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
YDR184C	ATC1	response to stress, polar budding -> response to stress, asexual reproduction		nucleus -> nucleus	ARO80, GLN3, SIP4, SKO1
YJR070C	NO SYMBOL				GAT3, YAP5
YNL308C	KRI1	ribosome biogenesis -> cell growth and/or maintenance		nucleolus -> nucleus
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
YLR276C	DBP9	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	MATa1, RCS1, RTG3, SWI5
\|YNL112W\|	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
YDR279W	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
YDR496C	PUF6				RFX1
YGL169W	SUA5	cell growth and/or maintenance -> cell growth and/or maintenance			ABF1
YOR272W	YTM1	chromosome organization and biogenesis (sensu Eukarya), ribosomal large subunit biogenesis -> cell growth and/or maintenance		nucleus, nucleolus -> nucleus	LEU3, PUT3, REB1
\|YOR359W\|	VTS1	protein-vacuolar targeting -> protein metabolism, cell growth and/or maintenance	intracellular transporter activity -> transporter activity	cytosol -> cytoplasm	RAP1
YLR002C	NOC3	DNA replication initiation, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	chromatin binding, protein binding -> DNA binding, protein binding	nucleus, nucleolus -> nucleus	HIR1, IXR1, RCS1
\|YGR162W\|	TIF4631	translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	HSF1
\|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
YHR169W	DBP8	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
\|YNL175C\|	NOP13		RNA binding -> RNA binding	nucleolus, nucleoplasm -> nucleus	INO2, INO4
\|YPR183W\|	DPM1	N-linked glycosylation, O-linked glycosylation, GPI anchor biosynthesis -> lipid biosynthesis, biosynthesis, membrane lipid metabolism, protein metabolism, lipoprotein metabolism	transferase activity\, transferring glycosyl groups, dolichyl-phosphate beta-D-mannosyltransferase activity -> transferase activity\, transferring glycosyl groups	endoplasmic reticulum, nuclear envelope-endoplasmic reticulum network -> cytoplasm, endomembrane system	SWI5
\|YHR128W\|	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups		CIN5
\|YCR090C\|	NO SYMBOL
YNL132W	KRE33
YOR078W	BUD21	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, MSS11, SIG1, SKO1
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
YGR245C	SDA1	actin cytoskeleton organization and biogenesis, start control point of mitotic cell cycle -> cell growth and/or maintenance		nucleus -> nucleus
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
\|YFR001W\|	LOC1	ribosomal large subunit biogenesis -> cell growth and/or maintenance	mRNA binding -> RNA binding	nucleus -> nucleus	ARG80, GAL4, GTS1, HAP4, HIR1, LEU3, MSN2, MSN4, RCS1, RLM1, SWI4
YBR104W	YMC2	transport -> cell growth and/or maintenance	transporter activity -> transporter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	FKH1, FKH2
YER082C	UTP7	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	CHA4
YJL109C	UTP10	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
YNR024W	NO SYMBOL
YKL014C	NO SYMBOL				ABF1
\|YER110C\|	KAP123	protein-nucleus import -> protein metabolism, cell growth and/or maintenance	protein carrier activity -> protein binding	cytoplasm, nuclear pore, nucleus -> cytoplasm, nucleus, integral to membrane, endomembrane system
YCL059C	KRR1	ribosome biogenesis, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
YNL075W	IMP4	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	rRNA primary transcript binding -> RNA binding	small nucleolar ribonucleoprotein complex, small nuclear ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	USV1
YCR072C	NO SYMBOL				YFL044C
YAL059W	ECM1	cell wall organization and biogenesis -> cell growth and/or maintenance			MOT3
YGL099W	LSG1	conjugation with cellular fusion, sporulation (sensu Saccharomyces), ribosome nucleus export -> conjugation, protein metabolism, cell growth and/or maintenance, sexual reproduction	GTPase activity -> purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	cytoplasm -> cytoplasm	PHO4
YCR016W	NO SYMBOL
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
\|YPR010C\|	RPA135	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	ROX1, SIG1
YDR449C	UTP6	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	FHL1, GAT3, HIR2, RAP1, RGM1, YAP5
YLR222C	UTP13	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1
Main:		cell growth and/or maintenance (0.81)	RNA binding (0.61)	nucleus (0.82)	ABF1 (0.18)
Score:		0.75	0.39	0.71	0.068
P-value:		4.375E-19 (ribosome biogenesis)	6.431E-09 (snoRNA binding)	7.397E-20 (nucleolus)	1.000E+00

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

EXPR: (0.099) mRRPE (P < 0.000) PAC (P < 0.000) CSRE (P < 0.000)

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
YGR245C	SDA1	actin cytoskeleton organization and biogenesis, start control point of mitotic cell cycle -> cell organization and biogenesis, cell proliferation		nucleus -> nucleus
YDR399W	HPT1	purine nucleotide biosynthesis -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	hypoxanthine phosphoribosyltransferase activity -> hypoxanthine phosphoribosyltransferase activity
YPR010C	RPA135	transcription from Pol I promoter -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	DNA-directed RNA polymerase activity -> DNA-directed RNA polymerase activity	DNA-directed RNA polymerase I complex -> nucleus	ROX1, SIG1
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
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.80)	RNA binding (0.33)	nucleus (1.00)	ABF1 (0.50)
Score:		0.80	0.00	1.00	0.000
P-value:		7.627E-03 (transcription from Pol I promoter)	7.516E-01 (transferase activity)	3.882E-03 (nucleolus)	2.427E-01 (SIG1)

ECB(1) AND MCB(1) => SimExpr(YML027W) OR SimExpr(other) : 5 2

EXPR: (0.117) ECB (P < 0.000) MCB (P < 0.024)

ORF	SYMBOL	P	F	C	TF
YCL024W	KCC4	septin checkpoint, protein amino acid phosphorylation, bud growth, axial budding, septin ring assembly -> cell cycle, phosphate metabolism, budding, septin ring assembly, protein modification	protein kinase activity -> protein kinase activity	bud neck -> bud neck	ASH1, CIN5, DAL81, HSF1, MET4, PHD1, RAP1, STP1, STP2
\|YMR102C\|	NO SYMBOL
YNR028W	CPR8		peptidyl-prolyl cis-trans isomerase activity -> peptidyl-prolyl cis-trans isomerase activity		ASH1, DIG1, MCM1
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
YDR507C	GIN4	septin checkpoint, protein amino acid phosphorylation, bud growth, axial budding, septin ring assembly -> cell cycle, phosphate metabolism, budding, septin ring assembly, protein modification	protein kinase activity -> protein kinase activity	bud neck -> bud neck	GRF10(Pho2), GTS1, MBP1, MCM1, SWI4, SWI6
\|YGR189C\|	CRH1			cell wall, incipient bud site -> cell wall, incipient bud site	GRF10(Pho2), MBP1, RLM1, STE12, SWI4, SWI5
YML027W	YOX1	negative regulation of transcription from Pol II promoter\, mitotic, regulation of mitotic cell cycle -> regulation of transcription, M phase, transcription, cell cycle	specific transcriptional repressor activity, DNA binding -> specific transcriptional repressor activity, DNA binding	nucleus -> nucleus	MBP1, SWI4, SWI6
Main:		cell cycle (1.00)	protein kinase activity (0.40)	nucleus (0.40)	SWI4 MBP1 (0.67)
Score:		1.00	0.10	0.20	0.667
P-value:		3.093E-04 (septin checkpoint)	3.615E-01 (protein kinase activity)	1.114E-01 (bud neck)	4.457E-04 (ASH1)

ALPHA1(1) AND SWI5(1) AND MCB(1) => SimExpr(YML027W) OR SimExpr(other) : 7 3

EXPR: (0.118) SWI5 (P < 0.000) MCB (P < 0.012) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YKR077W	NO SYMBOL
\|YLR049C\|	NO SYMBOL				MBP1, SWI5
YDR134C	NO SYMBOL				ASH1, NRG1, SOK2, SWI4
\|YJR030C\|	NO SYMBOL				MBP1, PHO4, RTG1, SWI6
\|YER132C\|	PMD1	sporulation -> sporulation			SMP1
YPR185W	APG13	protein-vacuolar targeting, autophagy -> organelle organization and biogenesis, autophagy, intracellular protein transport, protein metabolism	protein binding -> protein binding	extrinsic to membrane -> extrinsic to membrane	MET4, SWI6
YFR027W	ECO1	sister chromatid cohesion, DNA replication, DNA repair -> DNA replication and chromosome cycle, DNA repair, mitotic cell cycle, DNA metabolism	acetyltransferase activity -> acetyltransferase activity	nuclear chromatin -> chromosome, nucleus
YMR076C	PDS5	mitotic sister chromatid cohesion, mitotic chromosome condensation -> DNA replication and chromosome cycle, M phase, mitotic cell cycle	structural molecule activity -> structural molecule activity	condensed nuclear chromosome -> chromosome, nucleus	FKH2, MBP1, SWI6
YML027W	YOX1	negative regulation of transcription from Pol II promoter\, mitotic, regulation of mitotic cell cycle -> mitotic cell cycle, M phase, regulation of transcription, nuclear division, transcription\, DNA-dependent, regulation of cell cycle	specific transcriptional repressor activity, DNA binding -> specific transcriptional repressor activity, DNA binding	nucleus -> nucleus	MBP1, SWI4, SWI6
YMR179W	SPT21	regulation of transcription from Pol II promoter -> regulation of transcription, transcription\, DNA-dependent			MBP1, STB1, SWI4, SWI6, UGA3
Main:		mitotic cell cycle (0.50)	DNA binding (0.25)	nucleus (0.75)	MBP1 SWI6 (0.62)
Score:		0.27	0.00	0.50	0.571
P-value:		1.053E-02 (sister chromatid cohesion)	2.575E+00 (binding)	2.915E-01 (nuclear chromosome)	4.452E-05 (SWI6)

MCM1(1) AND ALPHA1(1) AND MCB(1) => SimExpr(YML027W) OR SimExpr(other) : 5 1

EXPR: (0.102) MCB (P < 0.008) MCM1 (P < 0.000) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YKR077W	NO SYMBOL
YCL024W	KCC4	septin checkpoint, protein amino acid phosphorylation, bud growth, axial budding, septin ring assembly -> cell cycle, phosphate metabolism, budding, septin ring assembly, protein modification	protein kinase activity -> protein kinase activity	bud neck -> bud neck	ASH1, CIN5, DAL81, HSF1, MET4, PHD1, RAP1, STP1, STP2
YNR028W	CPR8		peptidyl-prolyl cis-trans isomerase activity -> peptidyl-prolyl cis-trans isomerase activity		ASH1, DIG1, MCM1
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
\|YGR189C\|	CRH1			cell wall, incipient bud site -> cell wall, incipient bud site	GRF10(Pho2), MBP1, RLM1, STE12, SWI4, SWI5
YML027W	YOX1	negative regulation of transcription from Pol II promoter\, mitotic, regulation of mitotic cell cycle -> regulation of transcription, M phase, transcription, cell cycle	specific transcriptional repressor activity, DNA binding -> specific transcriptional repressor activity, DNA binding	nucleus -> nucleus	MBP1, SWI4, SWI6
Main:		cell cycle (1.00)	DNA binding (0.25)	nucleus (0.50)	SWI4 ASH1 MBP1 (0.60)
Score:		1.00	0.00	0.17	0.600
P-value:		1.856E-01 (regulation of cell cycle)	3.367E-01 (transcription regulator activity)	3.369E+00 (nucleus)	2.445E-04 (ASH1)

MCM1(1) AND ECB(1) AND MCB(1) => SimExpr(YML027W) OR SimExpr(other) : 5 1

EXPR: (0.111) ECB (P < 0.000) MCB (P < 0.028) MCM1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YCL024W	KCC4	septin checkpoint, protein amino acid phosphorylation, bud growth, axial budding, septin ring assembly -> cell cycle, phosphate metabolism, budding, septin ring assembly, protein modification	protein kinase activity -> protein kinase activity	bud neck -> bud neck	ASH1, CIN5, DAL81, HSF1, MET4, PHD1, RAP1, STP1, STP2
YNR028W	CPR8		peptidyl-prolyl cis-trans isomerase activity -> peptidyl-prolyl cis-trans isomerase activity		ASH1, DIG1, MCM1
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
YDR507C	GIN4	septin checkpoint, protein amino acid phosphorylation, bud growth, axial budding, septin ring assembly -> cell cycle, phosphate metabolism, budding, septin ring assembly, protein modification	protein kinase activity -> protein kinase activity	bud neck -> bud neck	GRF10(Pho2), GTS1, MBP1, MCM1, SWI4, SWI6
\|YGR189C\|	CRH1			cell wall, incipient bud site -> cell wall, incipient bud site	GRF10(Pho2), MBP1, RLM1, STE12, SWI4, SWI5
YML027W	YOX1	negative regulation of transcription from Pol II promoter\, mitotic, regulation of mitotic cell cycle -> regulation of transcription, M phase, transcription, cell cycle	specific transcriptional repressor activity, DNA binding -> specific transcriptional repressor activity, DNA binding	nucleus -> nucleus	MBP1, SWI4, SWI6
Main:		cell cycle (1.00)	protein kinase activity (0.40)	nucleus (0.40)	SWI4 MBP1 (0.67)
Score:		1.00	0.10	0.20	0.667
P-value:		2.209E-04 (septin checkpoint)	2.664E-01 (protein kinase activity)	8.080E-02 (bud neck)	2.055E-04 (MBP1)

MCM1(1) AND SFF'(1) AND STE12(1) AND MCM1'(1) => SimExpr(YDR309C) OR SimExpr(other) : 6 2

EXPR: (0.114) SFF' (P < 0.000) STE12 (P < 0.001) MCM1' (P < 0.000) MCM1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
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
\|YHR023W\|	MYO1	cytokinesis, response to osmotic stress, axial budding -> cell proliferation, response to abiotic stimulus, asexual reproduction	microfilament motor activity -> microfilament motor activity	contractile ring (sensu Saccharomyces) -> site of polarized growth (sensu Fungi), cell cortex, cytoplasm
YKR013W	PRY2				SWI4, SWI6
YNL053W	MSG5	adaptation to pheromone during conjugation with cellular fusion -> conjugation, perception of external stimulus, sexual reproduction, response to abiotic stimulus	prenylated protein tyrosine phosphatase activity -> prenylated protein tyrosine phosphatase activity		DIG1, FKH1, MCM1
YJL157C	FAR1	signal transduction during conjugation with cellular fusion, cell cycle arrest -> signal transduction, cell proliferation, conjugation, perception of external stimulus, sexual reproduction, response to abiotic stimulus	cyclin-dependent protein kinase inhibitor activity -> cyclin-dependent protein kinase inhibitor activity	cytoplasm, nucleus -> cytoplasm, nucleus	MCM1
YGR146C	NO SYMBOL				HSF1
\|YAR018C\|	KIN3	chromosome segregation -> cell proliferation	protein kinase activity -> protein kinase activity		FKH2, MCM1, MSS11, NDD1
YHR005C	GPA1	signal transduction during conjugation with cellular fusion -> signal transduction, conjugation, perception of external stimulus, sexual reproduction, response to abiotic stimulus	heterotrimeric G-protein GTPase activity -> heterotrimeric G-protein GTPase activity	heterotrimeric G-protein complex, plasma membrane -> extrinsic to membrane, plasma membrane	DIG1, IXR1, MCM1, PHD1, SOK2, STE12
Main:		response to abiotic stimulus (0.67)	heterotrimeric G-protein GTPase activity (0.17)	cytoplasm (0.75)	MCM1 (0.57)
Score:		0.73	0.00	0.50	0.429
P-value:		2.435E-04 (reproduction)	1.759E+00 (hydrolase activity)	2.090E-01 (cell cortex)	1.848E-03 (MCM1)

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

EXPR: (0.072) SFF (P < 0.000) SWI5 (P < 0.000) SCB (P < 0.000) RAP1 (P < 0.003)

ORF	SYMBOL	P	F	C	TF
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
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
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
YMR194W	RPL36A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	ARG80, ARO80, BAS1, CUP9, FHL1, HAL9, HAP4, HAP5, HMS1, MET31, NRG1, RAP1, RCS1, RME1, STP2
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:		1.576E-04 (protein biosynthesis)	5.237E-04 (structural constituent of ribosome)	4.219E-05 (ribosome)	1.522E-04 (FHL1)

RAP1(1) AND SFF'(1) AND SWI5(1) AND SCB(1) => SimExpr(YLR344W) : 5

EXPR: (0.072) SFF' (P < 0.000) SWI5 (P < 0.000) SCB (P < 0.000) RAP1 (P < 0.001)

ORF	SYMBOL	P	F	C	TF
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
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
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
YMR194W	RPL36A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	ARG80, ARO80, BAS1, CUP9, FHL1, HAL9, HAP4, HAP5, HMS1, MET31, NRG1, RAP1, RCS1, RME1, STP2
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:		1.576E-04 (protein biosynthesis)	5.237E-04 (structural constituent of ribosome)	4.219E-05 (ribosome)	1.522E-04 (FHL1)

ALPHA1(1) AND SFF(1) AND PDR(1) AND ATRepeat(1) => SimExpr(YLR121C) OR SimExpr(other) : 5 2

EXPR: (0.125) SFF (P < 0.000) PDR (P < 0.003) ATRepeat (P < 0.001) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YGL197W	MDS3	sporulation -> sporulation		cytoplasm -> cytoplasm	MTH1
YOR153W	PDR5	drug transport, response to drug -> transport, response to abiotic stimulus	xenobiotic-transporting ATPase activity -> xenobiotic-transporting ATPase activity	plasma membrane -> plasma membrane	YAP6
YER062C	HOR2	carbohydrate metabolism, response to osmotic stress, glycerol biosynthesis -> carbohydrate metabolism, response to abiotic stimulus, alcohol metabolism, energy derivation by oxidation of organic compounds, glycerol ether metabolism, lipid metabolism, biosynthesis	glycerol-1-phosphatase activity -> glycerol-1-phosphatase activity		MTH1
\|YDR226W\|	ADK1	cell proliferation -> cell proliferation	adenylate kinase activity -> adenylate kinase activity	cytoplasm, mitochondrial intermembrane space -> cytoplasm	PUT3
\|YDL048C\|	STP4				HIR2
YOR273C	TPO4	polyamine transport -> transport	spermine transporter activity, spermidine transporter activity -> spermine transporter activity, spermidine transporter activity	plasma membrane, vacuolar membrane -> plasma membrane, cytoplasm	ARO80, BAS1, FZF1, HIR1, IME4, NRG1, PDR1, PHO4, SFP1, SKN7, STP1
YLR121C	YPS3	protein metabolism -> protein metabolism	aspartic-type endopeptidase activity -> aspartic-type endopeptidase activity	plasma membrane -> plasma membrane	CIN5, SWI4, YAP6
Main:		response to abiotic stimulus (0.33)	adenylate kinase activity (0.20)	cytoplasm (0.60)	MTH1 YAP6 (0.29)
Score:		0.13	0.00	0.60	0.095
P-value:		3.758E-01 (response to abiotic stimulus)	5.825E-01 (hydrolase activity)	8.418E-02 (plasma membrane)	1.381E-01 (MTH1)

mRRPE(1) AND PAC(1) AND MCM1'(1) => SimExpr(YGL029W) OR SimExpr(other) : 13 5

EXPR: (0.133) mRRPE (P < 0.000) PAC (P < 0.007) MCM1' (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YMR049C	ERB1	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			RTG3
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus
YML125C	NO SYMBOL				MAL13, MSN4, NDD1, RME1, SWI5
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
YML093W	UTP14	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
\|YBR267W\|	NO SYMBOL
YPL043W	NOP4	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
YGL169W	SUA5	cell growth and/or maintenance -> cell growth and/or maintenance			ABF1
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
\|YIL122W\|	POG1	re-entry into mitotic cell cycle after pheromone arrest -> cell growth and/or maintenance, conjugation, perception of external stimulus, sexual reproduction, response to abiotic stimulus	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> nucleus	ASH1, CIN5, NRG1, RLM1, SMP1, YAP6
\|YHR128W\|	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups		CIN5
YER082C	UTP7	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	CHA4
YCR016W	NO SYMBOL
\|YDR399W\|	HPT1	purine nucleotide biosynthesis -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	hypoxanthine phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups
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
YDR365C	NO SYMBOL				ABF1, MSS11, YJL206C
Main:		cell growth and/or maintenance (0.77)	RNA binding (0.56)	nucleus (1.00)	ABF1 (0.30)
Score:		0.79	0.31	1.00	0.133
P-value:		5.573E-07 (rRNA processing)	4.411E-02 (transferase activity\, transferring pentosyl groups)	2.809E-05 (nucleolus)	1.000E+00

ALPHA1'(1) AND mRRPE(1) AND PAC(1) AND MCM1'(1) => SimExpr(YGL029W) OR SimExpr(other) : 9 2

EXPR: (0.122) ALPHA1' (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.004) MCM1' (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YMR049C	ERB1	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			RTG3
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> cell growth and/or maintenance, 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 growth and/or maintenance, 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
YML093W	UTP14	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleolus, ribonucleoprotein complex
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleolus
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
YGL169W	SUA5	cell growth and/or maintenance -> cell growth and/or maintenance			ABF1
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
\|YHR128W\|	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups		CIN5
YER082C	UTP7	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleolus, ribonucleoprotein complex	CHA4
YCR016W	NO SYMBOL
Main:		cell growth and/or maintenance (0.78)	RNA binding (0.60)	nucleolus (1.00)	ABF1 SWI6 (0.29)
Score:		0.75	0.30	1.00	0.095
P-value:		6.837E-06 (rRNA processing)	1.946E-02 (snoRNA binding)	3.270E-04 (nucleolus)	4.564E-01 (SWI6)

SFF'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YGL029W) OR SimExpr(other) : 33 14

EXPR: (0.138) SFF' (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YNR053C	NOG2	mRNA splicing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	GTPase activity -> purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleus, nucleolus, nucleoplasm -> nucleus, nucleoplasm	ABF1, AZF1
YML125C	NO SYMBOL				MAL13, MSN4, NDD1, RME1, SWI5
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
YDR101C	ARX1	ribosomal large subunit biogenesis -> cell organization and biogenesis		nucleoplasm, cytoplasm -> nucleus, cytoplasm	IXR1, RFX1
YNL308C	KRI1	ribosome biogenesis -> cell organization and biogenesis		nucleolus -> nucleus
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
\|YOR359W\|	VTS1	protein-vacuolar targeting -> cell organization and biogenesis, protein metabolism, transport	intracellular transporter activity -> transporter activity	cytosol -> cytoplasm	RAP1
\|YER002W\|	NOP16	ribosomal large subunit biogenesis -> cell organization and biogenesis		nucleolus, nucleus -> nucleus	IME4, NDD1, RTG3, UGA3
\|YPR183W\|	DPM1	N-linked glycosylation, O-linked glycosylation, GPI anchor biosynthesis -> lipid biosynthesis, biosynthesis, membrane lipid metabolism, protein metabolism, lipoprotein metabolism	transferase activity\, transferring glycosyl groups, dolichyl-phosphate beta-D-mannosyltransferase activity -> transferase activity\, transferring glycosyl groups	endoplasmic reticulum, nuclear envelope-endoplasmic reticulum network -> cytoplasm, endomembrane system	SWI5
YKL056C	NO SYMBOL
YOR078W	BUD21	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, MSS11, SIG1, SKO1
YGR245C	SDA1	actin cytoskeleton organization and biogenesis, start control point of mitotic cell cycle -> cell organization and biogenesis, cell proliferation		nucleus -> nucleus
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
YJL109C	UTP10	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
\|YJL069C\|	UTP18				ABF1
YKL014C	NO SYMBOL				ABF1
\|YER110C\|	KAP123	protein-nucleus import -> protein metabolism, transport	protein carrier activity -> transporter activity	cytoplasm, nuclear pore, nucleus -> cytoplasm, nucleus, integral to membrane, endomembrane system
YCL059C	KRR1	ribosome biogenesis, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
YNL075W	IMP4	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	rRNA primary transcript binding -> RNA binding	small nucleolar ribonucleoprotein complex, small nuclear ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	USV1
\|YCR072C\|	NO SYMBOL				YFL044C
YCR016W	NO SYMBOL
\|YLR249W\|	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
YDR449C	UTP6	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	FHL1, GAT3, HIR2, RAP1, RGM1, YAP5
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus
YGR187C	HGH1				ABF1, HAP3, HIR1, RCS1, RTG1
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
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
YHR052W	CIC1	protein catabolism -> catabolism, protein metabolism	protein binding\, bridging -> protein binding\, bridging	nucleolus, proteasome complex (sensu Eukarya) -> nucleus, cytoplasm	HAP4, MATa1
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
YLR276C	DBP9	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	MATa1, RCS1, RTG3, SWI5
YNL112W	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
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
YLR129W	DIP2	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ZMS1
\|YHR169W\|	DBP8	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
\|YNR046W\|	NO SYMBOL				ABF1
\|YIL122W\|	POG1	re-entry into mitotic cell cycle after pheromone arrest -> cell proliferation, conjugation, perception of external stimulus, sexual reproduction, response to abiotic stimulus	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> nucleus	ASH1, CIN5, NRG1, RLM1, SMP1, YAP6
\|YCR090C\|	NO SYMBOL
YNL132W	KRE33
\|YEL026W\|	SNU13	mRNA splicing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	pre-mRNA splicing factor activity -> RNA binding	small nucleolar ribonucleoprotein complex, nucleolus, small nuclear ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
\|YBR104W\|	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	FKH1, FKH2
YNR024W	NO SYMBOL
YMR290C	HAS1			nucleolus, nuclear membrane -> nucleus, endomembrane system	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
YDL063C	NO SYMBOL				HAL9, HAP2, MOT3
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
YGR145W	ENP2
YLR222C	UTP13	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1
Main:		cell organization and biogenesis (0.67)	RNA binding (0.58)	nucleus (0.81)	ABF1 (0.27)
Score:		0.53	0.37	0.75	0.108
P-value:		1.799E-12 (ribosome biogenesis)	1.162E-04 (RNA helicase activity)	1.235E-15 (nucleolus)	6.251E-01 (ABF1)

SFF(1) AND mRRPE(1) AND PAC(1) => SimExpr(YGL029W) OR SimExpr(other) : 26 11

EXPR: (0.133) SFF (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YNR053C	NOG2	mRNA splicing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	GTPase activity -> purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleus, nucleolus, nucleoplasm -> nucleus, nucleoplasm	ABF1, AZF1
YML125C	NO SYMBOL				MAL13, MSN4, NDD1, RME1, SWI5
YDR101C	ARX1	ribosomal large subunit biogenesis -> cell organization and biogenesis		nucleoplasm, cytoplasm -> nucleus, cytoplasm	IXR1, RFX1
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
YDR496C	PUF6				RFX1
\|YOR359W\|	VTS1	protein-vacuolar targeting -> cell organization and biogenesis, protein metabolism, transport	intracellular transporter activity -> transporter activity	cytosol -> cytoplasm	RAP1
\|YPR183W\|	DPM1	N-linked glycosylation, O-linked glycosylation, GPI anchor biosynthesis -> lipid biosynthesis, biosynthesis, membrane lipid metabolism, protein metabolism, lipoprotein metabolism	transferase activity\, transferring glycosyl groups, dolichyl-phosphate beta-D-mannosyltransferase activity -> transferase activity\, transferring glycosyl groups	endoplasmic reticulum, nuclear envelope-endoplasmic reticulum network -> cytoplasm, endomembrane system	SWI5
YOR078W	BUD21	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, MSS11, SIG1, SKO1
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
YJL109C	UTP10	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
\|YJL069C\|	UTP18				ABF1
YKL014C	NO SYMBOL				ABF1
\|YER110C\|	KAP123	protein-nucleus import -> protein metabolism, transport	protein carrier activity -> transporter activity	cytoplasm, nuclear pore, nucleus -> cytoplasm, nucleus, integral to membrane, endomembrane system
YCL059C	KRR1	ribosome biogenesis, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
\|YCR072C\|	NO SYMBOL				YFL044C
YCR016W	NO SYMBOL
\|YLR249W\|	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
YDR449C	UTP6	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	FHL1, GAT3, HIR2, RAP1, RGM1, YAP5
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus
YGR187C	HGH1				ABF1, HAP3, HIR1, RCS1, RTG1
YML093W	UTP14	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
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
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
\|YMR259C\|	NO SYMBOL				ARG80, GCR2, GTS1, HIR1, SRD1
YHR052W	CIC1	protein catabolism -> catabolism, protein metabolism	protein binding\, bridging -> protein binding\, bridging	nucleolus, proteasome complex (sensu Eukarya) -> nucleus, cytoplasm	HAP4, MATa1
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
YLR276C	DBP9	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	MATa1, RCS1, RTG3, SWI5
\|YHR169W\|	DBP8	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
\|YCR090C\|	NO SYMBOL
\|YBR104W\|	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	FKH1, FKH2
YNR024W	NO SYMBOL
YMR290C	HAS1			nucleolus, nuclear membrane -> nucleus, endomembrane system	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
YDL063C	NO SYMBOL				HAL9, HAP2, MOT3
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
YGR145W	ENP2
YLR222C	UTP13	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1
Main:		cell organization and biogenesis (0.64)	RNA binding (0.58)	nucleus (0.78)	ABF1 (0.24)
Score:		0.55	0.39	0.77	0.093
P-value:		1.430E-08 (rRNA processing)	1.059E-04 (snoRNA binding)	3.690E-11 (nucleolus)	1.000E+00

ALPHA1'(1) AND SFF'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YGL029W) OR SimExpr(other) : 21 8

EXPR: (0.136) ALPHA1' (P < 0.000) SFF' (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.001)

ORF	SYMBOL	P	F	C	TF
YNR053C	NOG2	mRNA splicing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	GTPase activity -> purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleus, nucleolus, nucleoplasm -> nucleus, nucleoplasm	ABF1, AZF1
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
YNL308C	KRI1	ribosome biogenesis -> cell organization and biogenesis		nucleolus -> nucleus
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
\|YOR359W\|	VTS1	protein-vacuolar targeting -> cell organization and biogenesis, protein metabolism, transport	intracellular transporter activity -> transporter activity	cytosol -> cytoplasm	RAP1
\|YPR183W\|	DPM1	N-linked glycosylation, O-linked glycosylation, GPI anchor biosynthesis -> lipid biosynthesis, biosynthesis, membrane lipid metabolism, protein metabolism, lipoprotein metabolism	transferase activity\, transferring glycosyl groups, dolichyl-phosphate beta-D-mannosyltransferase activity -> transferase activity\, transferring glycosyl groups	endoplasmic reticulum, nuclear envelope-endoplasmic reticulum network -> cytoplasm, endomembrane system	SWI5
YOR078W	BUD21	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, MSS11, SIG1, SKO1
YGR245C	SDA1	actin cytoskeleton organization and biogenesis, start control point of mitotic cell cycle -> cell organization and biogenesis, cell proliferation		nucleus -> nucleus
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
YJL109C	UTP10	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
YKL014C	NO SYMBOL				ABF1
\|YER110C\|	KAP123	protein-nucleus import -> protein metabolism, transport	protein carrier activity -> transporter activity	cytoplasm, nuclear pore, nucleus -> cytoplasm, nucleus, integral to membrane, endomembrane system
YCL059C	KRR1	ribosome biogenesis, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
YNL075W	IMP4	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	rRNA primary transcript binding -> RNA binding	small nucleolar ribonucleoprotein complex, small nuclear ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	USV1
\|YCR072C\|	NO SYMBOL				YFL044C
YCR016W	NO SYMBOL
YDR449C	UTP6	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	FHL1, GAT3, HIR2, RAP1, RGM1, YAP5
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
YLR276C	DBP9	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	MATa1, RCS1, RTG3, SWI5
YNL112W	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
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
\|YHR169W\|	DBP8	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
\|YCR090C\|	NO SYMBOL
YNL132W	KRE33
\|YBR104W\|	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	FKH1, FKH2
YNR024W	NO SYMBOL
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
YLR222C	UTP13	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1
Main:		cell organization and biogenesis (0.75)	RNA binding (0.62)	nucleus (0.80)	ABF1 (0.31)
Score:		0.64	0.42	0.66	0.150
P-value:		4.294E-10 (rRNA processing)	9.168E-04 (snoRNA binding)	7.110E-12 (nucleolus)	1.000E+00

SFF'(1) AND mRRPE(1) AND PAC(1) AND MCM1'(1) => SimExpr(YGL029W) OR SimExpr(other) : 6 2

EXPR: (0.132) SFF' (P < 0.000) mRRPE (P < 0.008) PAC (P < 0.034) MCM1' (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YML125C	NO SYMBOL				MAL13, MSN4, NDD1, RME1, SWI5
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> rRNA modification, rRNA processing		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, SWI6
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
YCR016W	NO SYMBOL
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> rRNA processing, snRNA processing	RNA binding -> RNA binding	nucleolus -> nucleus
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis, rRNA processing		nucleolus -> nucleus
YOR095C	RKI1	pentose-phosphate shunt -> glucose catabolism, main pathways of carbohydrate metabolism, nicotinamide metabolism	ribose-5-phosphate isomerase activity -> ribose-5-phosphate isomerase activity		FHL1, FKH2, RAP1
\|YIL122W\|	POG1	re-entry into mitotic cell cycle after pheromone arrest -> re-entry into mitotic cell cycle, conjugation with cellular fusion, response to pheromone	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> nucleus	ASH1, CIN5, NRG1, RLM1, SMP1, YAP6
Main:		rRNA processing (0.60)	RNA binding (0.33)	nucleus (1.00)	RLM1 SWI6 (0.40)
Score:		0.30	0.00	1.00	0.200
P-value:		2.861E-02 (rRNA processing)	2.000E+00	1.986E-02 (nucleolus)	2.636E-01 (RLM1)

SFF(1) AND mRRPE(1) AND PAC(1) AND MCM1'(1) => SimExpr(YGL029W) OR SimExpr(other) : 5 1

EXPR: (0.112) SFF (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.003) MCM1' (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YML125C	NO SYMBOL				MAL13, MSN4, NDD1, RME1, SWI5
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
YCR016W	NO SYMBOL
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> rRNA processing, snRNA processing	RNA binding -> RNA binding	nucleolus -> nucleolus
YML093W	UTP14	processing of 20S pre-rRNA -> rRNA processing	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleolus, ribonucleoprotein complex
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis, rRNA processing		nucleolus -> nucleolus
Main:		rRNA processing (1.00)	RNA binding (1.00)	nucleolus (1.00)	GCR2 (0.50)
Score:		1.00	1.00	1.00	0.000
P-value:		1.011E-02 (rRNA processing)	3.853E-01 (RNA binding)	7.533E-03 (nucleolus)	3.288E-01 (THI2)

ALPHA1'(1) AND SFF'(1) AND mRRPE(1) AND PAC(1) AND MCM1'(1) => SimExpr(YGL029W) OR SimExpr(other) : 5 1

EXPR: (0.116) ALPHA1' (P < 0.000) SFF' (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.009) MCM1' (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> rRNA modification, rRNA processing		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> small nuclear ribonucleoprotein complex, nucleolus, ribonucleoprotein complex	ABF1, SWI6
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
YCR016W	NO SYMBOL
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> rRNA processing, snRNA processing	RNA binding -> RNA binding	nucleolus -> nucleolus
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis, rRNA processing		nucleolus -> nucleolus
YOR095C	RKI1	pentose-phosphate shunt -> glucose catabolism, main pathways of carbohydrate metabolism, nicotinamide metabolism	ribose-5-phosphate isomerase activity -> ribose-5-phosphate isomerase activity		FHL1, FKH2, RAP1
Main:		rRNA processing (0.75)	RNA binding (0.50)	nucleolus (1.00)	SWI6 (0.67)
Score:		0.50	0.00	1.00	0.333
P-value:		1.071E-02 (rRNA processing)	2.000E+00	7.533E-03 (nucleolus)	1.047E-01 (SWI6)

ALPHA1(1) AND ALPHA1'(1) AND SFF'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YGL029W) OR SimExpr(other) : 6 3

EXPR: (0.134) ALPHA1' (P < 0.000) SFF' (P < 0.000) mRRPE (P < 0.007) PAC (P < 0.029) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
\|YPR183W\|	DPM1	N-linked glycosylation, O-linked glycosylation, GPI anchor biosynthesis -> protein amino acid glycosylation, phosphoinositide biosynthesis, protein lipidation, phosphoinositide metabolism	transferase activity\, transferring glycosyl groups, dolichyl-phosphate beta-D-mannosyltransferase activity -> transferase activity\, transferring glycosyl groups	endoplasmic reticulum, nuclear envelope-endoplasmic reticulum network -> endoplasmic reticulum, nuclear envelope-endoplasmic reticulum network	SWI5
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
YJL109C	UTP10	processing of 20S pre-rRNA -> rRNA processing	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleolus, ribonucleoprotein complex
YNL075W	IMP4	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> rRNA modification, rRNA processing	rRNA primary transcript binding -> RNA binding	small nucleolar ribonucleoprotein complex, small nuclear ribonucleoprotein complex -> nucleolus, small nuclear ribonucleoprotein complex, ribonucleoprotein complex	USV1
\|YCR072C\|	NO SYMBOL				YFL044C
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis, rRNA processing		nucleolus -> nucleolus
YOR095C	RKI1	pentose-phosphate shunt -> glucose catabolism, main pathways of carbohydrate metabolism, nicotinamide metabolism	ribose-5-phosphate isomerase activity -> intramolecular isomerase activity		FHL1, FKH2, RAP1
\|YHR169W\|	DBP8	35S primary transcript processing -> rRNA processing	ATP dependent RNA helicase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleolus
YJL033W	HCA4	35S primary transcript processing -> rRNA processing	ATP dependent RNA helicase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleolus	HIR2, USV1
Main:		rRNA processing (0.71)	RNA binding (0.67)	nucleolus (0.83)	USV1 (0.33)
Score:		0.48	0.40	0.67	0.067
P-value:		6.428E-05 (rRNA processing)	2.135E-02 (ATP dependent RNA helicase activity)	9.523E-05 (nucleolus)	5.402E-02 (USV1)

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

EXPR: (0.100) SCB (P < 0.000) RAP1 (P < 0.027) 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
\|YPR080W\|	TEF1	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation elongation factor activity	ribosome -> ribosome	FHL1, PDR1, RAP1, YAP5
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
YLR249W	YEF3	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation elongation factor activity	ribosome -> ribosome	INO2, INO4
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
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 (0.67)	ribosome (1.00)	FHL1 (0.83)
Score:		1.00	0.47	1.00	0.667
P-value:		3.792E-05 (protein biosynthesis)	1.921E-03 (structural constituent of ribosome)	3.416E-06 (ribosome)	2.721E-06 (FHL1)

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

EXPR: (0.086) SFF (P < 0.000) SCB (P < 0.000) RAP1 (P < 0.008) 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
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
YLR249W	YEF3	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation elongation factor activity	ribosome -> ribosome	INO2, INO4
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
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 (0.80)
Score:		1.00	0.60	1.00	0.600
P-value:		3.152E-04 (protein biosynthesis)	4.489E-04 (structural constituent of ribosome)	2.344E-05 (cytosolic large ribosomal subunit (sensu Eukarya))	6.441E-05 (FHL1)

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

EXPR: (0.086) SFF' (P < 0.000) SCB (P < 0.000) RAP1 (P < 0.010) 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
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
YLR249W	YEF3	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation elongation factor activity	ribosome -> ribosome	INO2, INO4
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
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 (0.80)
Score:		1.00	0.60	1.00	0.600
P-value:		3.152E-04 (protein biosynthesis)	4.489E-04 (structural constituent of ribosome)	2.344E-05 (cytosolic large ribosomal subunit (sensu Eukarya))	6.441E-05 (FHL1)

mRRPE(1) AND PAC(1) => SimExpr(YNL110C) OR SimExpr(other) : 68 22

EXPR: (0.132) mRRPE (P < 0.000) PAC (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YNR053C	NOG2	mRNA splicing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	GTPase activity -> purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleus, nucleolus, nucleoplasm -> nucleus, nucleoplasm	ABF1, AZF1
YML125C	NO SYMBOL				MAL13, MSN4, NDD1, RME1, SWI5
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
YDR184C	ATC1	response to stress, polar budding -> response to stress, asexual reproduction		nucleus -> nucleus	ARO80, GLN3, SIP4, SKO1
\|YJR070C\|	NO SYMBOL				GAT3, YAP5
YDR101C	ARX1	ribosomal large subunit biogenesis -> cell growth and/or maintenance		nucleoplasm, cytoplasm -> nucleus, cytoplasm	IXR1, RFX1
YBR267W	NO SYMBOL
YPL043W	NOP4	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus
YNL308C	KRI1	ribosome biogenesis -> cell growth and/or maintenance		nucleolus -> nucleus
YDR279W	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
YDR496C	PUF6				RFX1
YKL172W	EBP2	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus	ABF1, FZF1, RFX1
YMR014W	BUD22	bud site selection -> cell growth and/or maintenance		nucleus -> nucleus	CUP9, HAL9, HIR2, LEU3, NDD1, RLM1, ROX1, SMP1, YAP6
YGL169W	SUA5	cell growth and/or maintenance -> cell growth and/or maintenance			ABF1
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
YOR272W	YTM1	chromosome organization and biogenesis (sensu Eukarya), ribosomal large subunit biogenesis -> cell growth and/or maintenance		nucleus, nucleolus -> nucleus	LEU3, PUT3, REB1
\|YOR359W\|	VTS1	protein-vacuolar targeting -> protein metabolism, cell growth and/or maintenance	intracellular transporter activity -> transporter activity	cytosol -> cytoplasm	RAP1
YER002W	NOP16	ribosomal large subunit biogenesis -> cell growth and/or maintenance		nucleolus, nucleus -> nucleus	IME4, NDD1, RTG3, UGA3
YLR002C	NOC3	DNA replication initiation, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	chromatin binding, protein binding -> DNA binding, protein binding	nucleus, nucleolus -> nucleus	HIR1, IXR1, RCS1
\|YNL175C\|	NOP13		RNA binding -> RNA binding	nucleolus, nucleoplasm -> nucleus	INO2, INO4
\|YPR183W\|	DPM1	N-linked glycosylation, O-linked glycosylation, GPI anchor biosynthesis -> lipid biosynthesis, biosynthesis, membrane lipid metabolism, protein metabolism, lipoprotein metabolism	transferase activity\, transferring glycosyl groups, dolichyl-phosphate beta-D-mannosyltransferase activity -> transferase activity\, transferring glycosyl groups	endoplasmic reticulum, nuclear envelope-endoplasmic reticulum network -> cytoplasm, endomembrane system	SWI5
\|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
\|YKL056C\|	NO SYMBOL
YOR078W	BUD21	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, MSS11, SIG1, SKO1
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
YGR245C	SDA1	actin cytoskeleton organization and biogenesis, start control point of mitotic cell cycle -> cell growth and/or maintenance		nucleus -> nucleus
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
YFR001W	LOC1	ribosomal large subunit biogenesis -> cell growth and/or maintenance	mRNA binding -> RNA binding	nucleus -> nucleus	ARG80, GAL4, GTS1, HAP4, HIR1, LEU3, MSN2, MSN4, RCS1, RLM1, SWI4
YJL109C	UTP10	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
\|YJL069C\|	UTP18				ABF1
YKL014C	NO SYMBOL				ABF1
YDR161W	NO SYMBOL
\|YER110C\|	KAP123	protein-nucleus import -> protein metabolism, cell growth and/or maintenance	protein carrier activity -> protein binding	cytoplasm, nuclear pore, nucleus -> cytoplasm, nucleus, integral to membrane, endomembrane system
YCL059C	KRR1	ribosome biogenesis, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
YNL075W	IMP4	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	rRNA primary transcript binding -> RNA binding	small nucleolar ribonucleoprotein complex, small nuclear ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	USV1
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
\|YCR072C\|	NO SYMBOL				YFL044C
YGL099W	LSG1	conjugation with cellular fusion, sporulation (sensu Saccharomyces), ribosome nucleus export -> conjugation, protein metabolism, cell growth and/or maintenance, sexual reproduction	GTPase activity -> purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	cytoplasm -> cytoplasm	PHO4
YCR016W	NO SYMBOL
\|YLR249W\|	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
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
\|YPR010C\|	RPA135	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	ROX1, SIG1
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
YDR449C	UTP6	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	FHL1, GAT3, HIR2, RAP1, RGM1, YAP5
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
YMR049C	ERB1	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			RTG3
YPL266W	DIM1	rRNA modification, 35S primary transcript processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	rRNA (adenine-N6\,N6-)-dimethyltransferase activity -> transferase activity\, transferring one-carbon groups	nucleolus -> nucleus	ARG81, STP2
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus
YDR083W	RRP8	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	methyltransferase activity -> transferase activity\, transferring one-carbon groups	nucleolus -> nucleus	MOT3
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
YGR187C	HGH1				ABF1, HAP3, HIR1, RCS1, RTG1
YPR144C	NOC4	ribosome biogenesis -> cell growth and/or maintenance		nucleus -> nucleus	HIR1
YML093W	UTP14	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
YHR196W	UTP9	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex, nucleolus, nucleus -> nucleus, ribonucleoprotein complex
\|YGL016W\|	KAP122	protein-nucleus import, response to drug -> response to abiotic stimulus, protein metabolism, cell growth and/or maintenance	protein carrier activity -> protein binding	cytoplasm, nuclear pore -> cytoplasm, nucleus, integral to membrane, endomembrane system	MSN2
\|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
YMR259C	NO SYMBOL				ARG80, GCR2, GTS1, HIR1, SRD1
YHR052W	CIC1	protein catabolism -> catabolism, protein metabolism	protein binding\, bridging -> protein binding	nucleolus, proteasome complex (sensu Eukarya) -> nucleus, cytoplasm	HAP4, MATa1
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
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
YLR276C	DBP9	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	MATa1, RCS1, RTG3, SWI5
\|YNL112W\|	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
YGR272C	NO SYMBOL				REB1, STP2
\|YMR310C\|	NO SYMBOL
\|YGR162W\|	TIF4631	translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	HSF1
\|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
YLR129W	DIP2	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ZMS1
YER006W	NUG1	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus, nucleus -> nucleus
YHR169W	DBP8	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
\|YNR046W\|	NO SYMBOL				ABF1
YNL110C	NOP15	ribosomal large subunit biogenesis -> cell growth and/or maintenance		nucleus, nucleolus -> nucleus
\|YIL122W\|	POG1	re-entry into mitotic cell cycle after pheromone arrest -> cell growth and/or maintenance, conjugation, perception of external stimulus, sexual reproduction, response to abiotic stimulus	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> nucleus	ASH1, CIN5, NRG1, RLM1, SMP1, YAP6
\|YHR128W\|	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups		CIN5
\|YCR090C\|	NO SYMBOL
YNL132W	KRE33
\|YEL026W\|	SNU13	mRNA splicing, processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	pre-mRNA splicing factor activity -> RNA binding	small nucleolar ribonucleoprotein complex, nucleolus, small nuclear ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
YBR104W	YMC2	transport -> cell growth and/or maintenance	transporter activity -> transporter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	FKH1, FKH2
YER082C	UTP7	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	CHA4
YNR024W	NO SYMBOL
YMR131C	RRB1	ribosome biogenesis -> cell growth and/or maintenance		nucleolus -> nucleus	FZF1, MATa1, RGT1
YMR290C	HAS1			nucleolus, nuclear membrane -> nucleus, endomembrane system	RAP1
YAL059W	ECM1	cell wall organization and biogenesis -> cell growth and/or maintenance			MOT3
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
YDL063C	NO SYMBOL				HAL9, HAP2, MOT3
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
YGR145W	ENP2
YDR365C	NO SYMBOL				ABF1, MSS11, YJL206C
YLR222C	UTP13	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1
Main:		cell growth and/or maintenance (0.80)	RNA binding (0.57)	nucleus (0.85)	ABF1 (0.20)
Score:		0.74	0.36	0.79	0.098
P-value:		9.716E-37 (ribosome biogenesis)	9.459E-10 (snoRNA binding)	5.497E-40 (nucleolus)	1.000E+00

LYS14(1) AND mRRPE(1) AND PAC(1) => SimExpr(YNL110C) OR SimExpr(other) : 7 2

ALPHA1(1) AND SWI5(1) AND MCB(1) => SimExpr(YPR185W) OR SimExpr(other) : 7 3

RAP1(1) AND SWI5(1) AND SCB(1) => SimExpr(YMR194W) OR SimExpr(other) : 5 1

EXPR: (0.091) SWI5 (P < 0.000) SCB (P < 0.000) RAP1 (P < 0.020)

ORF	SYMBOL	P	F	C	TF
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
\|YPR080W\|	TEF1	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation elongation factor activity	ribosome -> ribosome	FHL1, PDR1, RAP1, YAP5
YLR249W	YEF3	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation elongation factor activity	ribosome -> ribosome	INO2, INO4
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
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
YMR194W	RPL36A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	ARG80, ARO80, BAS1, CUP9, FHL1, HAL9, HAP4, HAP5, HMS1, MET31, NRG1, RAP1, RCS1, RME1, STP2
Main:		protein biosynthesis (1.00)	structural constituent of ribosome (0.67)	ribosome (1.00)	FHL1 (0.83)
Score:		1.00	0.47	1.00	0.667
P-value:		2.007E-05 (protein biosynthesis)	2.134E-03 (structural constituent of ribosome)	3.416E-06 (ribosome)	6.123E-06 (FHL1)

RAP1(1) AND SFF'(1) AND SCB(1) => SimExpr(YMR194W) OR SimExpr(other) : 8 3

EXPR: (0.103) SFF' (P < 0.000) SCB (P < 0.000) RAP1 (P < 0.008)

ORF	SYMBOL	P	F	C	TF
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
\|YGR260W\|	TNA1	nicotinamide mononucleotide transport -> nicotinamide mononucleotide transport	nicotinamide mononucleotide permease activity -> nicotinamide mononucleotide permease activity	integral to plasma membrane -> integral to plasma membrane	HIR2, SUM1
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
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
YLR249W	YEF3	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation elongation factor activity	ribosome -> ribosome	INO2, INO4
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
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
YMR194W	RPL36A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	ARG80, ARO80, BAS1, CUP9, FHL1, HAL9, HAP4, HAP5, HMS1, MET31, NRG1, RAP1, RCS1, RME1, STP2
\|YNL024C\|	NO SYMBOL				GRF10(Pho2)
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 (0.90)	structural constituent of ribosome (0.70)	ribosome (0.90)	FHL1 (0.73)
Score:		0.80	0.49	0.80	0.509
P-value:		2.392E-06 (protein biosynthesis)	9.541E-06 (structural constituent of ribosome)	8.274E-08 (ribosome)	5.790E-09 (FHL1)

RAP1(1) AND SFF(1) AND SCB(1) => SimExpr(YMR194W) OR SimExpr(other) : 8 2

EXPR: (0.098) SFF (P < 0.000) SCB (P < 0.000) RAP1 (P < 0.007)

ORF	SYMBOL	P	F	C	TF
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
\|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
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
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
YLR249W	YEF3	translational elongation -> macromolecule biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
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
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
YMR194W	RPL36A	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	ARG80, ARO80, BAS1, CUP9, FHL1, HAL9, HAP4, HAP5, HMS1, MET31, NRG1, RAP1, RCS1, RME1, STP2
\|YNL024C\|	NO SYMBOL				GRF10(Pho2)
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
Main:		protein metabolism (1.00)	structural constituent of ribosome (0.88)	cytoplasm (1.00)	FHL1 (0.78)
Score:		1.00	0.75	1.00	0.583
P-value:		1.650E-05 (protein biosynthesis)	2.563E-06 (structural constituent of ribosome)	5.336E-07 (cytosolic large ribosomal subunit (sensu Eukarya))	1.258E-07 (FHL1)

RAP1(1) AND SFF(1) AND SWI5(1) AND SCB(1) => SimExpr(YMR194W) : 5

RAP1(1) AND SFF'(1) AND SWI5(1) AND SCB(1) => SimExpr(YMR194W) : 5

RAP1(1) AND SCB(1) => SimExpr(YHL033C) OR SimExpr(other) : 9 4

EXPR: (0.113) SCB (P < 0.000) RAP1 (P < 0.027)

ORF	SYMBOL	P	F	C	TF
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
YGR260W	TNA1	nicotinamide mononucleotide transport -> transport	nicotinamide mononucleotide permease activity -> nicotinamide mononucleotide permease activity	integral to plasma membrane -> integral to membrane, plasma membrane	HIR2, SUM1
\|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, extrinsic to membrane, cytoplasm, membrane coat, integral to membrane, endomembrane system, plasma membrane
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 elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	FHL1, RAP1
\|YPR080W\|	TEF1	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	FHL1, PDR1, RAP1, YAP5
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
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
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
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
YMR194W	RPL36A	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	ARG80, ARO80, BAS1, CUP9, FHL1, HAL9, HAP4, HAP5, HMS1, MET31, NRG1, RAP1, RCS1, RME1, STP2
\|YNL024C\|	NO SYMBOL				GRF10(Pho2)
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
Main:		protein metabolism (0.92)	structural constituent of ribosome (0.64)	cytoplasm (0.92)	FHL1 (0.75)
Score:		0.85	0.44	0.85	0.545
P-value:		1.318E-06 (protein biosynthesis)	4.455E-05 (structural constituent of ribosome)	4.008E-08 (ribosome)	7.806E-10 (FHL1)

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

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

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

RAP1(1) AND ALPHA1(1) AND mRRPE(1) => SimExpr(YMR116C) OR SimExpr(other) : 5 2

EXPR: (0.128) mRRPE (P < 0.000) RAP1 (P < 0.174) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
\|YKL072W\|	STB6				ARG81, ARO80, BAS1, CIN5, GCN4, GLN3, HAP3, MCM1, PHD1, REB1, RLM1, YJL206C, ZAP1
YDL130W	RPP1B	protein biosynthesis, translational elongation -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAL4, RAP1, RFX1
YMR116C	ASC1			cytoplasm -> cytoplasm	FHL1, RAP1
YMR013C	SEC59	protein-ER targeting, protein amino acid glycosylation -> organelle organization and biogenesis, protein biosynthesis, intracellular protein transport, secretory pathway, protein modification, glycoprotein metabolism, protein metabolism	dolichol kinase activity -> dolichol kinase activity	membrane -> membrane	FHL1, NDD1, RAP1, RLM1, RME1
\|YPR080W\|	TEF1	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	FHL1, PDR1, RAP1, YAP5
YLR249W	YEF3	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
YBR048W	RPS11B	protein biosynthesis, ribosomal small subunit assembly and maintenance, regulation of translational fidelity -> ribosome biogenesis and assembly, protein biosynthesis	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
Main:		protein biosynthesis (1.00)	translation elongation factor activity (0.40)	cytoplasm (0.83)	RAP1 FHL1 (0.57)
Score:		1.00	0.20	0.67	0.381
P-value:		9.360E-05 (translational elongation)	4.519E-03 (translation elongation factor activity)	1.212E-02 (ribosome)	1.050E-03 (FHL1)

RAP1(1) AND SCB(1) => SimExpr(YOR369C) OR SimExpr(other) : 9 4

RAP1(1) AND SWI5(1) AND SCB(1) => SimExpr(YOR369C) OR SimExpr(other) : 5 1

RAP1(1) AND SFF'(1) AND SCB(1) => SimExpr(YOR369C) OR SimExpr(other) : 9 2

RAP1(1) AND SFF(1) AND SCB(1) => SimExpr(YOR369C) OR SimExpr(other) : 8 2

RAP1(1) AND SFF(1) AND SWI5(1) AND SCB(1) => SimExpr(YOR369C) : 5

RAP1(1) AND SFF'(1) AND SWI5(1) AND SCB(1) => SimExpr(YOR369C) : 5

RAP1(1) AND SCB(1) => SimExpr(YPL131W) OR SimExpr(other) : 9 4

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

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

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

RAP1(1) AND SFF(1) AND SWI5(1) => SimExpr(YLR441C) OR SimExpr(other) : 13 6

EXPR: (0.129) SFF (P < 0.000) SWI5 (P < 0.000) RAP1 (P < 0.184)

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
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
YJL217W	NO SYMBOL				CIN5, MAC1, PHD1, SWI5, YAP6
YOR312C	RPL20B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, FKH2, GAT3, RAP1
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
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
\|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
\|YDL184C\|	RPL41A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, HAL9, HMS1, MAC1, MSS11, RAP1, RME1, SIG1
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
YGL115W	SNF4	regulation of transcription from Pol II promoter, peroxisome organization and biogenesis -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	protein kinase activator activity -> protein kinase activator activity	plasma membrane, nucleus, cytoplasm -> membrane, nucleus, cytoplasm	BAS1, CAD1, MAC1, NRG1, PDR1, RAP1, SMP1, YAP5
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
\|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
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
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
\|YKR092C\|	SRP40	nucleocytoplasmic transport -> transport	chaperone activity -> chaperone activity	nucleolus -> nucleus	CUP9, MET4, RAP1
YMR194W	RPL36A	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	ARG80, ARO80, BAS1, CUP9, FHL1, HAL9, HAP4, HAP5, HMS1, MET31, NRG1, RAP1, RCS1, RME1, STP2
\|YBR098W\|	MMS4	DNA repair, meiotic recombination -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	transcription co-activator activity, endonuclease activity -> transcription co-activator activity, endonuclease activity	nucleus -> nucleus
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
Main:		biosynthesis (0.67)	structural constituent of ribosome (0.61)	cytoplasm (0.72)	RAP1 (0.76)
Score:		0.44	0.37	0.57	0.728
P-value:		1.235E-06 (protein biosynthesis)	5.371E-08 (structural constituent of ribosome)	2.035E-09 (cytosolic ribosome (sensu Eukarya))	1.901E-12 (FHL1)

RAP1(1) AND SCB(1) => SimExpr(YLR249W) OR SimExpr(other) : 9 4

RAP1(1) AND SFF(1) AND SWI5(1) AND SCB(1) => SimExpr(YLR249W) : 5

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

RAP1(1) AND SFF'(1) AND SWI5(1) AND SCB(1) => SimExpr(YLR249W) : 5

RAP1(1) AND SFF(1) AND SWI5(1) AND SCB(1) => SimExpr(YBL087C) : 5

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

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

RAP1(1) AND SFF'(1) AND SWI5(1) AND SCB(1) => SimExpr(YBL087C) : 5

LYS14(1) AND mRRPE(1) AND PAC(1) => SimExpr(YMR290C) OR SimExpr(other) : 8 1

LYS14(1) AND SFF(1) AND mRRPE(1) AND PAC(1) => SimExpr(YMR290C) : 5

EXPR: (0.106) LYS14 (P < 0.000) SFF (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> rRNA processing, snRNA processing	RNA binding -> RNA binding	nucleolus -> nucleolus
YML093W	UTP14	processing of 20S pre-rRNA -> rRNA processing	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleolus, ribonucleoprotein complex
YMR259C	NO SYMBOL				ARG80, GCR2, GTS1, HIR1, SRD1
YHR052W	CIC1	protein catabolism -> protein catabolism	protein binding\, bridging -> protein binding\, bridging	nucleolus, proteasome complex (sensu Eukarya) -> nucleolus, cytosol, endoplasmic reticulum, nucleus	HAP4, MATa1
YMR290C	HAS1			nucleolus, nuclear membrane -> nucleolus, nuclear membrane	RAP1
Main:		rRNA processing (0.67)	RNA binding (0.67)	nucleolus (1.00)	GCR2 (0.33)
Score:		0.33	0.33	1.00	0.000
P-value:		1.630E-01 (rRNA processing)	2.709E-01 (RNA binding)	7.963E-05 (nucleolus)	3.566E-01 (MATa1)

mRRPE(1) AND PAC(1) => SimExpr(YMR229C) OR SimExpr(other) : 64 26

ALPHA1'(1) AND mRRPE(1) AND PAC(1) AND SCB(1) => SimExpr(YJL109C) OR SimExpr(other) : 7 3

EXPR: (0.130) ALPHA1' (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.005) SCB (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> rRNA modification, rRNA processing		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, SWI6
YDR184C	ATC1	response to stress, polar budding -> response to stress, polar budding		nucleus -> nucleus	ARO80, GLN3, SIP4, SKO1
YJR070C	NO SYMBOL				GAT3, YAP5
\|YOR078W\|	BUD21	processing of 20S pre-rRNA -> rRNA processing	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, MSS11, SIG1, SKO1
YJL109C	UTP10	processing of 20S pre-rRNA -> rRNA processing	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
YCL059C	KRR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis, rRNA processing		nucleolus -> nucleus
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> rRNA processing, snRNA processing	RNA binding -> RNA binding	nucleolus -> nucleus
\|YNL112W\|	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
YBR104W	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	FKH1, FKH2
\|YER082C\|	UTP7	processing of 20S pre-rRNA -> rRNA processing	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	CHA4
Main:		rRNA processing (0.75)	RNA binding (0.83)	nucleus (0.78)	ABF1 SKO1 (0.33)
Score:		0.54	0.67	0.58	0.133
P-value:		3.188E-06 (rRNA processing)	2.343E-04 (snoRNA binding)	6.139E-06 (nucleolus)	6.211E-02 (SKO1)

ALPHA1'(1) AND SFF'(1) AND mRRPE(1) AND PAC(1) AND SCB(1) => SimExpr(YJL109C) OR SimExpr(other) : 5 2

EXPR: (0.122) ALPHA1' (P < 0.000) SFF' (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.001) SCB (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> rRNA modification, rRNA processing		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> small nuclear ribonucleoprotein complex, nucleolus, ribonucleoprotein complex	ABF1, SWI6
\|YOR078W\|	BUD21	processing of 20S pre-rRNA -> rRNA processing	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleolus, ribonucleoprotein complex	ABF1, MSS11, SIG1, SKO1
YJL109C	UTP10	processing of 20S pre-rRNA -> rRNA processing	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleolus, ribonucleoprotein complex
YCL059C	KRR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis, rRNA processing		nucleolus -> nucleolus
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> rRNA processing, snRNA processing	RNA binding -> RNA binding	nucleolus -> nucleolus
\|YNL112W\|	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Saccharomyces)
YBR104W	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> mitochondrion, inner membrane	FKH1, FKH2
Main:		rRNA processing (0.83)	RNA binding (0.80)	nucleolus (0.71)	ABF1 (0.67)
Score:		0.67	0.60	0.48	0.333
P-value:		1.127E-05 (rRNA processing)	6.477E-03 (snoRNA binding)	1.695E-05 (nucleolus)	5.107E-01 (SKO1)

ALPHA1(1) AND ALPHA2(1) AND MCB(1) => SimExpr(YOR144C) OR SimExpr(other) : 6 3

EXPR: (0.132) ALPHA2 (P < 0.000) MCB (P < 0.048) ALPHA1 (P < 0.001)

ORF	SYMBOL	P	F	C	TF
YNL082W	PMS1	mismatch repair, meiosis -> DNA metabolism, cell proliferation	ATPase activity, ATP binding, DNA binding -> ATP binding, DNA binding, hydrolase activity\, acting on acid anhydrides\, in phosphorus-containing anhydrides	nuclear chromosome -> intracellular	MTH1
\|YOR284W\|	HUA2				RFX1, YAP6
YJL095W	BCK1	protein amino acid phosphorylation, protein kinase cascade, response to nutrients, establishment of cell polarity (sensu Saccharomyces) -> phosphorus metabolism, signal transduction, response to extracellular stimulus, cell organization and biogenesis, protein metabolism, response to abiotic stimulus	MAP kinase kinase kinase activity -> protein kinase activity	intracellular -> intracellular	YAP1
YPR185W	APG13	protein-vacuolar targeting, autophagy -> cell organization and biogenesis, autophagy, protein metabolism, transport	protein binding -> protein binding	extrinsic to membrane -> extrinsic to membrane	MET4, SWI6
YOR144C	ELG1	negative regulation of DNA transposition, negative regulation of DNA recombination -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			YJL206C
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 -> intracellular	ASH1, HSF1, MBP1, NDD1, PHD1, ROX1, STB1, SWI4
YFR027W	ECO1	sister chromatid cohesion, DNA replication, DNA repair -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, cell proliferation	acetyltransferase activity -> acyltransferase activity	nuclear chromatin -> intracellular
\|YER047C\|	SAP1				MSS11
\|YPL140C\|	MKK2	protein amino acid phosphorylation, signal transduction -> phosphorus metabolism, signal transduction, protein metabolism	MAP kinase kinase activity -> protein kinase activity	intracellular -> intracellular	FKH1, FKH2
Main:		cell organization and biogenesis (0.43)	protein kinase activity (0.33)	intracellular (0.83)	SWI4 (0.12)
Score:		0.48	0.07	0.67	0.000
P-value:		6.497E-01 (DNA replication)	5.827E-01 (protein kinase activity)	2.383E-01 (nuclear chromosome)	1.000E+00

ALPHA1(1) AND ALPHA1'(1) AND SFF(1) AND mRRPE(1) AND PAC(1) => SimExpr(YJL033W) OR SimExpr(other) : 5 2

EXPR: (0.130) ALPHA1' (P < 0.000) SFF (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.011) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
\|YPR183W\|	DPM1	N-linked glycosylation, O-linked glycosylation, GPI anchor biosynthesis -> protein amino acid glycosylation, phosphoinositide biosynthesis, protein lipidation, phosphoinositide metabolism	transferase activity\, transferring glycosyl groups, dolichyl-phosphate beta-D-mannosyltransferase activity -> transferase activity\, transferring glycosyl groups	endoplasmic reticulum, nuclear envelope-endoplasmic reticulum network -> endoplasmic reticulum, nuclear envelope-endoplasmic reticulum network	SWI5
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
YJL109C	UTP10	processing of 20S pre-rRNA -> rRNA processing	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleolus, ribonucleoprotein complex
\|YCR072C\|	NO SYMBOL				YFL044C
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis, rRNA processing		nucleolus -> nucleolus
YHR169W	DBP8	35S primary transcript processing -> rRNA processing	ATP dependent RNA helicase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleolus
YJL033W	HCA4	35S primary transcript processing -> rRNA processing	ATP dependent RNA helicase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleolus	HIR2, USV1
Main:		rRNA processing (0.80)	RNA binding (0.75)	nucleolus (0.80)	RTS2 (0.25)
Score:		0.60	0.50	0.60	0.000
P-value:		5.741E-04 (rRNA processing)	1.253E-02 (ATP dependent RNA helicase activity)	5.230E-04 (nucleolus)	4.642E-01 (RTS2)

ALPHA2(1) AND SFF'(1) AND MCB(1) => SimExpr(YFR027W) OR SimExpr(other) : 5 1

EXPR: (0.129) ALPHA2 (P < 0.000) SFF' (P < 0.000) MCB (P < 0.019)

ORF	SYMBOL	P	F	C	TF
YJL095W	BCK1	protein amino acid phosphorylation, protein kinase cascade, response to nutrients, establishment of cell polarity (sensu Saccharomyces) -> phosphorus metabolism, signal transduction, response to extracellular stimulus, cell organization and biogenesis, protein metabolism, response to abiotic stimulus	MAP kinase kinase kinase activity -> protein kinase activity	intracellular -> intracellular	YAP1
YPR185W	APG13	protein-vacuolar targeting, autophagy -> cell organization and biogenesis, autophagy, protein metabolism, transport	protein binding -> protein binding	extrinsic to membrane -> extrinsic to membrane	MET4, SWI6
YFR027W	ECO1	sister chromatid cohesion, DNA replication, DNA repair -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, cell proliferation	acetyltransferase activity -> acyltransferase activity	intracellular -> intracellular
YPL140C	MKK2	protein amino acid phosphorylation, signal transduction -> phosphorus metabolism, signal transduction, protein metabolism	MAP kinase kinase activity -> protein kinase activity	intracellular -> intracellular	FKH1, FKH2
YDR297W	SUR2	sphingolipid metabolism, sphingolipid biosynthesis -> lipid metabolism, biosynthesis	sphingosine hydroxylase activity -> sphingosine hydroxylase activity	intracellular -> intracellular	CBF1, MTH1
\|YPL241C\|	CIN2	microtubule-based process -> cell organization and biogenesis			HIR2
Main:		cell organization and biogenesis (0.50)	protein kinase activity (0.40)	intracellular (0.80)	MTH1 (0.20)
Score:		0.33	0.10	0.60	0.000
P-value:		1.834E-01 (protein amino acid phosphorylation)	2.368E-01 (protein kinase activity)	3.838E+00 (intracellular)	6.695E-01 (MET4)

ALPHA1'(1) AND STE12(1) AND PAC(1) => SimExpr(YPR137W) OR SimExpr(other) : 5 1

EXPR: (0.129) ALPHA1' (P < 0.000) STE12 (P < 0.000) PAC (P < 0.020)

ORF	SYMBOL	P	F	C	TF
YGR158C	MTR3	35S primary transcript processing, mRNA catabolism -> cell organization and biogenesis, catabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	3'-5' exoribonuclease activity -> hydrolase activity\, acting on ester bonds, RNA binding	nuclear exosome (RNase complex), cytoplasmic exosome (RNase complex) -> exosome (RNase complex), cytoplasm, nucleus	ZMS1
YPR137W	RRP9	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex, small nuclear ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, HIR1, RCS1
YNL308C	KRI1	ribosome biogenesis -> cell organization and biogenesis		nucleolus -> nucleus
\|YMR302C\|	PRP12	mitochondrial genome maintenance, rRNA processing -> cell organization and biogenesis, RNA metabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	exonuclease activity -> hydrolase activity\, acting on ester bonds	mitochondrial inner membrane -> cytoplasm, inner membrane
YGR251W	NO SYMBOL				MSN4, PHD1, SKN7
YAL059W	ECM1	cell wall organization and biogenesis -> cell organization and biogenesis			MOT3
Main:		cell organization and biogenesis (1.00)	RNA binding (0.67)	nucleus (0.75)	ABF1 (0.25)
Score:		1.00	0.67	0.67	0.000
P-value:		7.075E-04 (ribosome biogenesis)	1.507E-02 (exonuclease activity)	1.602E-01 (nucleolus)	3.331E-01 (ZMS1)

ALPHA2(1) AND ALPHA1'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YJR070C) OR SimExpr(other) : 5 2

EXPR: (0.126) ALPHA2 (P < 0.000) ALPHA1' (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.002)

ORF	SYMBOL	P	F	C	TF
YJR070C	NO SYMBOL				GAT3, YAP5
YPR183W	DPM1	N-linked glycosylation, O-linked glycosylation, GPI anchor biosynthesis -> lipid biosynthesis, biosynthesis, membrane lipid metabolism, protein metabolism, lipoprotein metabolism	transferase activity\, transferring glycosyl groups, dolichyl-phosphate beta-D-mannosyltransferase activity -> transferase activity\, transferring glycosyl groups	endoplasmic reticulum, nuclear envelope-endoplasmic reticulum network -> endoplasmic reticulum, nuclear envelope-endoplasmic reticulum network	SWI5
YMR049C	ERB1	rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			RTG3
\|YGL029W\|	CGR1	ribosome biogenesis, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleolus
YHR128W	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups		CIN5
\|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 -> nucleolus	HIR2, USV1
YLR222C	UTP13	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleolus, ribonucleoprotein complex	ABF1
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.83)	RNA binding (0.50)	nucleolus (0.75)	ABF1 (0.17)
Score:		0.73	0.33	0.50	0.000
P-value:		5.741E-04 (rRNA processing)	1.075E-01 (transferase activity\, transferring glycosyl groups)	1.279E-02 (nucleolus)	6.889E-01 (USV1)

ABF1(1) AND SFF(1) AND PAC(1) => SimExpr(YDL063C) OR SimExpr(other) : 6 3

EXPR: (0.124) ABF1 (P < 0.000) SFF (P < 0.000) PAC (P < 0.037)

ORF	SYMBOL	P	F	C	TF
YOL041C	NOP12	rRNA metabolism -> rRNA metabolism	RNA binding -> RNA binding	nucleolus -> nucleus	GTS1, MET31
\|YGR283C\|	NO SYMBOL				ACE2, RAP1, SMP1
\|YDR312W\|	SSF2	ribosomal large subunit assembly and maintenance, conjugation with cellular fusion -> ribosome biogenesis and assembly, conjugation with cellular fusion	rRNA binding -> RNA binding	nucleolus -> nucleus	ABF1, FKH2, INO4, RAP1
YJL069C	UTP18				ABF1
YKL014C	NO SYMBOL				ABF1
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
YGR187C	HGH1				ABF1, HAP3, HIR1, RCS1, RTG1
YDL063C	NO SYMBOL				HAL9, HAP2, MOT3
\|YKL078W\|	DHR2	ribosome biogenesis -> ribosome biogenesis and assembly	RNA helicase activity -> RNA binding	nucleolus -> nucleus	ABF1
Main:		ribosome biogenesis and assembly (0.50)	RNA binding (0.75)	nucleus (1.00)	ABF1 (0.62)
Score:		0.17	0.50	1.00	0.393
P-value:		6.381E-01 (ribosome biogenesis and assembly)	1.473E-01 (RNA binding)	2.890E-02 (nucleolus)	2.023E-03 (ABF1)

ABF1(1) AND mRRPE(1) AND PAC(1) => SimExpr(YDL063C) OR SimExpr(other) : 8 2

EXPR: (0.122) ABF1 (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.023)

ORF	SYMBOL	P	F	C	TF
YKL172W	EBP2	rRNA processing -> ribosome biogenesis, RNA processing, transcription from Pol I promoter		nucleolus -> nucleus	ABF1, FZF1, RFX1
YJL069C	UTP18				ABF1
YKL014C	NO SYMBOL				ABF1
YER110C	KAP123	protein-nucleus import -> protein targeting, nucleocytoplasmic transport	protein carrier activity -> protein carrier activity	cytoplasm, nuclear pore, nucleus -> cytoplasm, nucleus, integral to membrane, endomembrane system
\|YPR010C\|	RPA135	transcription from Pol I promoter -> transcription from Pol I promoter	DNA-directed RNA polymerase activity -> DNA-directed RNA polymerase activity	DNA-directed RNA polymerase I complex -> nucleus	ROX1, SIG1
YGR187C	HGH1				ABF1, HAP3, HIR1, RCS1, RTG1
YJL050W	MTR4	35S primary transcript processing -> ribosome biogenesis, RNA processing, transcription from Pol I promoter	ATP dependent RNA helicase activity -> RNA helicase activity, ATP dependent helicase activity, RNA dependent ATPase activity	nucleolus -> nucleus
YNL112W	DBP2		RNA helicase activity -> RNA helicase activity	bud neck -> site of polarized growth (sensu Fungi)
\|YNR046W\|	NO SYMBOL				ABF1
YDL063C	NO SYMBOL				HAL9, HAP2, MOT3
Main:		transcription from Pol I promoter (0.75)	RNA helicase activity (0.50)	nucleus (0.80)	ABF1 (0.71)
Score:		0.50	0.17	0.60	0.476
P-value:		8.012E-02 (transcription from Pol I promoter)	3.529E-02 (RNA helicase activity)	4.007E-02 (nucleolus)	3.060E-03 (ABF1)

ABF1(1) AND SFF(1) AND mRRPE(1) AND PAC(1) => SimExpr(YDL063C) : 5

EXPR: (0.095) ABF1 (P < 0.000) SFF (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YJL069C	UTP18				ABF1
YKL014C	NO SYMBOL				ABF1
YER110C	KAP123	protein-nucleus import -> protein-nucleus import	protein carrier activity -> protein carrier activity	cytoplasm, nuclear pore, nucleus -> cytoplasm, nuclear pore, nucleus
YGR187C	HGH1				ABF1, HAP3, HIR1, RCS1, RTG1
YDL063C	NO SYMBOL				HAL9, HAP2, MOT3
Main:		protein-nucleus import (1.00)	protein carrier activity (1.00)	nuclear pore (1.00)	ABF1 (0.75)
Score:		0.00	0.00	0.00	0.500
P-value:		0.000E+00	0.000E+00	0.000E+00	2.194E-02 (ABF1)

mRRPE(1) AND PAC(1) => SimExpr(YKL172W) OR SimExpr(other) : 63 27

SFF(1) AND mRRPE(1) AND PAC(1) => SimExpr(YML093W) OR SimExpr(other) : 30 7

SFF(1) AND mRRPE(1) AND PAC(1) AND MCM1'(1) => SimExpr(YML093W) : 6

LYS14(1) AND mRRPE(1) AND PAC(1) => SimExpr(YHR052W) OR SimExpr(other) : 8 1

LYS14(1) AND SFF(1) AND mRRPE(1) AND PAC(1) => SimExpr(YHR052W) : 5

SFF'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YLR276C) OR SimExpr(other) : 36 11

SFF(1) AND BAS1(1) AND PAC(1) => SimExpr(YLR276C) OR SimExpr(other) : 5 2

EXPR: (0.124) SFF (P < 0.000) BAS1 (P < 0.000) PAC (P < 0.018)

ORF	SYMBOL	P	F	C	TF
\|YER115C\|	SPR6	sporulation (sensu Fungi) -> sporulation (sensu Fungi)			ARG80, RTG3
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
YCL059C	KRR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis, rRNA processing		nucleolus -> nucleolus
YLR276C	DBP9	ribosomal large subunit assembly and maintenance, 35S primary transcript processing -> ribosomal subunit assembly, rRNA processing	ATP dependent RNA helicase activity -> ATP dependent RNA helicase activity	nucleolus -> nucleolus	MATa1, RCS1, RTG3, SWI5
\|YCR090C\|	NO SYMBOL
YBR104W	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> mitochondrial inner membrane	FKH1, FKH2
YNR024W	NO SYMBOL
Main:		rRNA processing (0.50)	ATP dependent RNA helicase activity (0.50)	nucleolus (0.67)	RTG3 (0.50)
Score:		0.17	0.00	0.33	0.167
P-value:		3.283E-01 (rRNA processing)	2.000E+00	1.871E-01 (nucleolus)	4.091E-02 (RTG3)

SFF(1) AND SFF'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YLR276C) OR SimExpr(other) : 27 7

EXPR: (0.130) SFF (P < 0.000) SFF' (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YNR053C	NOG2	mRNA splicing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	GTPase activity -> purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleus, nucleolus, nucleoplasm -> nucleus, nucleoplasm	ABF1, AZF1
YML125C	NO SYMBOL				MAL13, MSN4, NDD1, RME1, SWI5
YDR101C	ARX1	ribosomal large subunit biogenesis -> cell organization and biogenesis		nucleoplasm, cytoplasm -> nucleus, cytoplasm	IXR1, RFX1
YDR279W	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
\|YOR359W\|	VTS1	protein-vacuolar targeting -> cell organization and biogenesis, protein metabolism, transport	intracellular transporter activity -> transporter activity	cytosol -> cytoplasm	RAP1
\|YPR183W\|	DPM1	N-linked glycosylation, O-linked glycosylation, GPI anchor biosynthesis -> lipid biosynthesis, biosynthesis, membrane lipid metabolism, protein metabolism, lipoprotein metabolism	transferase activity\, transferring glycosyl groups, dolichyl-phosphate beta-D-mannosyltransferase activity -> transferase activity\, transferring glycosyl groups	endoplasmic reticulum, nuclear envelope-endoplasmic reticulum network -> cytoplasm, endomembrane system	SWI5
YOR078W	BUD21	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, MSS11, SIG1, SKO1
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
YJL109C	UTP10	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
YJL069C	UTP18				ABF1
YKL014C	NO SYMBOL				ABF1
\|YER110C\|	KAP123	protein-nucleus import -> protein metabolism, transport	protein carrier activity -> transporter activity	cytoplasm, nuclear pore, nucleus -> cytoplasm, nucleus, integral to membrane, endomembrane system
YCL059C	KRR1	ribosome biogenesis, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
\|YCR072C\|	NO SYMBOL				YFL044C
YCR016W	NO SYMBOL
\|YLR249W\|	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
YDR449C	UTP6	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	FHL1, GAT3, HIR2, RAP1, RGM1, YAP5
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus
YGR187C	HGH1				ABF1, HAP3, HIR1, RCS1, RTG1
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
\|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
YHR052W	CIC1	protein catabolism -> catabolism, protein metabolism	protein binding\, bridging -> protein binding\, bridging	nucleolus, proteasome complex (sensu Eukarya) -> nucleus, cytoplasm	HAP4, MATa1
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
YLR276C	DBP9	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	MATa1, RCS1, RTG3, SWI5
YHR169W	DBP8	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
\|YCR090C\|	NO SYMBOL
YBR104W	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	FKH1, FKH2
YNR024W	NO SYMBOL
YMR290C	HAS1			nucleolus, nuclear membrane -> nucleus, endomembrane system	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
YDL063C	NO SYMBOL				HAL9, HAP2, MOT3
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
YGR145W	ENP2
YLR222C	UTP13	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1
Main:		cell organization and biogenesis (0.62)	RNA binding (0.56)	nucleus (0.77)	ABF1 (0.26)
Score:		0.54	0.37	0.76	0.099
P-value:		8.576E-08 (rRNA processing)	4.244E-04 (RNA helicase activity)	1.720E-10 (nucleolus)	1.000E+00

SFF(1) AND mRRPE(1) AND BAS1(1) AND PAC(1) => SimExpr(YLR276C) OR SimExpr(other) : 5 1

EXPR: (0.108) SFF (P < 0.000) mRRPE (P < 0.000) BAS1 (P < 0.000) PAC (P < 0.001)

ORF	SYMBOL	P	F	C	TF
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
YCL059C	KRR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis, rRNA processing		nucleolus -> nucleolus
YLR276C	DBP9	ribosomal large subunit assembly and maintenance, 35S primary transcript processing -> ribosomal subunit assembly, rRNA processing	ATP dependent RNA helicase activity -> ATP dependent RNA helicase activity	nucleolus -> nucleolus	MATa1, RCS1, RTG3, SWI5
\|YCR090C\|	NO SYMBOL
YBR104W	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> mitochondrial inner membrane	FKH1, FKH2
YNR024W	NO SYMBOL
Main:		rRNA processing (0.67)	ATP dependent RNA helicase activity (0.50)	nucleolus (0.67)	RTS2 (0.33)
Score:		0.33	0.00	0.33	0.000
P-value:		2.394E-01 (rRNA processing)	2.000E+00	1.373E-01 (nucleolus)	4.793E-01 (MATa1)

SFF'(1) AND mRRPE(1) AND BAS1(1) AND PAC(1) => SimExpr(YLR276C) OR SimExpr(other) : 5 1

EXPR: (0.108) SFF' (P < 0.000) mRRPE (P < 0.001) BAS1 (P < 0.000) PAC (P < 0.002)

ORF	SYMBOL	P	F	C	TF
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
YCL059C	KRR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis, rRNA processing		nucleolus -> nucleolus
YLR276C	DBP9	ribosomal large subunit assembly and maintenance, 35S primary transcript processing -> ribosomal subunit assembly, rRNA processing	ATP dependent RNA helicase activity -> ATP dependent RNA helicase activity	nucleolus -> nucleolus	MATa1, RCS1, RTG3, SWI5
\|YCR090C\|	NO SYMBOL
YBR104W	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> mitochondrial inner membrane	FKH1, FKH2
YNR024W	NO SYMBOL
Main:		rRNA processing (0.67)	ATP dependent RNA helicase activity (0.50)	nucleolus (0.67)	RTS2 (0.33)
Score:		0.33	0.00	0.33	0.000
P-value:		2.394E-01 (rRNA processing)	2.000E+00	1.373E-01 (nucleolus)	4.793E-01 (MATa1)

ALPHA1'(1) AND SFF(1) AND mRRPE(1) AND PAC(1) AND SCB(1) => SimExpr(YBR104W) : 5

EXPR: (0.113) ALPHA1' (P < 0.000) SFF (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.004) SCB (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YOR078W	BUD21	processing of 20S pre-rRNA -> rRNA processing	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleolus, ribonucleoprotein complex	ABF1, MSS11, SIG1, SKO1
YJL109C	UTP10	processing of 20S pre-rRNA -> rRNA processing	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleolus, ribonucleoprotein complex
YCL059C	KRR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis, rRNA processing		nucleolus -> nucleolus
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> rRNA processing, snRNA processing	RNA binding -> RNA binding	nucleolus -> nucleolus
YBR104W	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> mitochondrion, inner membrane	FKH1, FKH2
Main:		rRNA processing (0.80)	RNA binding (0.75)	nucleolus (0.80)	ABF1 (0.50)
Score:		0.60	0.50	0.60	0.000
P-value:		8.613E-05 (rRNA processing)	3.111E-03 (snoRNA binding)	1.062E-04 (nucleolus)	3.159E-01 (SKO1)

SFF(1) AND BAS1(1) AND PAC(1) => SimExpr(YCL059C) OR SimExpr(other) : 5 2

mRRPE(1) AND BAS1(1) AND PAC(1) => SimExpr(YCL059C) OR SimExpr(other) : 6 1

EXPR: (0.111) mRRPE (P < 0.000) BAS1 (P < 0.000) PAC (P < 0.003)

ORF	SYMBOL	P	F	C	TF
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
YCL059C	KRR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis, rRNA processing		nucleolus -> nucleolus
YMR049C	ERB1	rRNA processing -> rRNA processing			RTG3
YLR276C	DBP9	ribosomal large subunit assembly and maintenance, 35S primary transcript processing -> ribosomal subunit assembly, rRNA processing	ATP dependent RNA helicase activity -> ATP dependent RNA helicase activity	nucleolus -> nucleolus	MATa1, RCS1, RTG3, SWI5
\|YCR090C\|	NO SYMBOL
YBR104W	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> mitochondrial inner membrane	FKH1, FKH2
YNR024W	NO SYMBOL
Main:		rRNA processing (0.75)	ATP dependent RNA helicase activity (0.50)	nucleolus (0.67)	RTG3 (0.50)
Score:		0.50	0.00	0.33	0.167
P-value:		1.729E-02 (rRNA processing)	2.000E+00	1.871E-01 (nucleolus)	3.682E-02 (RTG3)

ALPHA1'(1) AND SFF'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YCL059C) OR SimExpr(other) : 24 5

ALPHA1'(1) AND SFF(1) AND mRRPE(1) AND PAC(1) => SimExpr(YCL059C) OR SimExpr(other) : 19 5

EXPR: (0.128) ALPHA1' (P < 0.000) SFF (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YNR053C	NOG2	mRNA splicing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	GTPase activity -> purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleus, nucleolus, nucleoplasm -> nucleus, nucleoplasm	ABF1, AZF1
YDR279W	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
YDR496C	PUF6				RFX1
\|YOR359W\|	VTS1	protein-vacuolar targeting -> cell organization and biogenesis, protein metabolism, transport	intracellular transporter activity -> transporter activity	cytosol -> cytoplasm	RAP1
\|YPR183W\|	DPM1	N-linked glycosylation, O-linked glycosylation, GPI anchor biosynthesis -> lipid biosynthesis, biosynthesis, membrane lipid metabolism, protein metabolism, lipoprotein metabolism	transferase activity\, transferring glycosyl groups, dolichyl-phosphate beta-D-mannosyltransferase activity -> transferase activity\, transferring glycosyl groups	endoplasmic reticulum, nuclear envelope-endoplasmic reticulum network -> cytoplasm, endomembrane system	SWI5
YOR078W	BUD21	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, MSS11, SIG1, SKO1
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
YJL109C	UTP10	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
YKL014C	NO SYMBOL				ABF1
\|YER110C\|	KAP123	protein-nucleus import -> protein metabolism, transport	protein carrier activity -> transporter activity	cytoplasm, nuclear pore, nucleus -> cytoplasm, nucleus, integral to membrane, endomembrane system
YCL059C	KRR1	ribosome biogenesis, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
\|YCR072C\|	NO SYMBOL				YFL044C
YCR016W	NO SYMBOL
YDR449C	UTP6	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	FHL1, GAT3, HIR2, RAP1, RGM1, YAP5
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus
YML093W	UTP14	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
YLR276C	DBP9	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	MATa1, RCS1, RTG3, SWI5
YHR169W	DBP8	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
\|YCR090C\|	NO SYMBOL
YBR104W	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	FKH1, FKH2
YNR024W	NO SYMBOL
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
YLR222C	UTP13	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1
Main:		cell organization and biogenesis (0.75)	RNA binding (0.64)	nucleus (0.81)	ABF1 (0.29)
Score:		0.68	0.46	0.70	0.099
P-value:		7.285E-10 (rRNA processing)	8.857E-06 (snoRNA binding)	2.077E-10 (nucleolus)	1.000E+00

ALPHA1'(1) AND SFF(1) AND mRRPE(1) AND PAC(1) AND SCB(1) => SimExpr(YCL059C) : 5

ALPHA1'(1) AND SFF'(1) AND mRRPE(1) AND PAC(1) AND SCB(1) => SimExpr(YCL059C) : 7

ndt80(MSE)(1) AND PDR(1) => SimExpr(YCR045C) OR SimExpr(other) : 5 1

EXPR: (0.128) ndt80(MSE) (P < 0.000) PDR (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YBR159W	NO SYMBOL				ACE2, ARG81, GCR2, HIR2, LEU3, MOT3, PDR1, PHD1, SKN7, USV1
YDR317W	NO SYMBOL				HAL9, RLM1
YCR045C	NO SYMBOL
\|YKL096W\|	CWP1	cell wall organization and biogenesis -> cell wall organization and biogenesis	structural constituent of cell wall -> structural constituent of cell wall	cell wall (sensu Fungi) -> cell wall (sensu Fungi)	RLM1, SMP1, STE12, SWI4
YMR252C	NO SYMBOL				SKN7
YDR281C	PHM6				PHO4, SUM1
Main:		cell wall organization and biogenesis (1.00)	structural constituent of cell wall (1.00)	cell wall (sensu Fungi) (1.00)	RLM1 SKN7 (0.40)
Score:		0.00	0.00	0.00	0.200
P-value:		0.000E+00	0.000E+00	0.000E+00	1.236E-01 (RLM1)

MCB(1) AND PAC(1) => SimExpr(YPR144C) OR SimExpr(other) : 5 2

mRRPE(1) AND STE12(1) AND PAC(1) => SimExpr(YBR247C) : 5

EXPR: (0.108) mRRPE (P < 0.000) STE12 (P < 0.000) PAC (P < 0.003)

ORF	SYMBOL	P	F	C	TF
YNL308C	KRI1	ribosome biogenesis -> cell growth and/or maintenance		nucleolus -> nucleolus
YJL069C	UTP18				ABF1
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 -> snoRNA binding	nucleolus, nucleus -> nucleolus, nucleus
YMR310C	NO SYMBOL
YAL059W	ECM1	cell wall organization and biogenesis -> cell growth and/or maintenance			MOT3
Main:		cell growth and/or maintenance (1.00)	snoRNA binding (1.00)	nucleolus (1.00)	ABF1 (0.50)
Score:		1.00	0.00	1.00	0.000
P-value:		1.419E-01 (ribosome biogenesis)	0.000E+00	9.406E-02 (nucleolus)	1.688E-01 (MOT3)

AVERAGE SCORES:

P
  SCORE: 0.661 (Part of genes covered by "Main": 0.771) (No. rules=51/53)
  P-VALUE: 0.667
F
  SCORE: 0.337 (Part of genes covered by "Main": 0.567) (No. rules=43/53)
  P-VALUE: 0.512
C
  SCORE: 0.697 (Part of genes covered by "Main": 0.817) (No. rules=50/53)
  P-VALUE: 0.600
TF
  SCORE: 0.285 (Part of genes covered by "Main": 0.481) (No. rules=49/53)
  P-VALUE: 0.388
EXPRESSION: 0.962 (53)

Discovering regulatory binding-site modules using rule-based learning

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