Discovering regulatory binding-site modules using rule-based learning

mRRPE(1) AND PAC(1) => SimExpr(YGR280C) OR SimExpr(other) : 63 13

EXPR: (0.157) mRRPE (P < 0.000) PAC (P < 0.000)

ORF	SYMBOL	P	F	C	TF
\|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
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
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
YGR245C	SDA1	actin cytoskeleton organization and biogenesis, start control point of mitotic cell cycle -> cell growth and/or maintenance		nucleus -> nucleus
YNL110C	NOP15	ribosomal large subunit biogenesis -> cell growth and/or maintenance		nucleus, nucleolus -> nucleus
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
YDR399W	HPT1	purine nucleotide biosynthesis -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	hypoxanthine phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups
YMR131C	RRB1	ribosome biogenesis -> cell growth and/or maintenance		nucleolus -> nucleus	FZF1, MATa1, RGT1
YAL059W	ECM1	cell wall organization and biogenesis -> cell growth and/or maintenance			MOT3
YLR197W	SIK1	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex, nucleus, nucleolus -> nucleus, ribonucleoprotein complex	DAL81, HAL9
\|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 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
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
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
YOR272W	YTM1	chromosome organization and biogenesis (sensu Eukarya), ribosomal large subunit biogenesis -> cell growth and/or maintenance		nucleus, nucleolus -> nucleus	LEU3, PUT3, REB1
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
\|YKL014C\|	NO SYMBOL				ABF1
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
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
YGR187C	HGH1				ABF1, HAP3, HIR1, RCS1, RTG1
YMR014W	BUD22	bud site selection -> cell growth and/or maintenance		nucleus -> nucleus	CUP9, HAL9, HIR2, LEU3, NDD1, RLM1, ROX1, SMP1, YAP6
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
YPR144C	NOC4	ribosome biogenesis -> cell growth and/or maintenance		nucleus -> nucleus	HIR1
YGR272C	NO SYMBOL				REB1, STP2
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
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
YDR101C	ARX1	ribosomal large subunit biogenesis -> cell growth and/or maintenance		nucleoplasm, cytoplasm -> nucleus, cytoplasm	IXR1, RFX1
\|YML125C\|	NO SYMBOL				MAL13, MSN4, NDD1, RME1, SWI5
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
\|YJL069C\|	UTP18				ABF1
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
YHR052W	CIC1	protein catabolism -> catabolism, protein metabolism	protein binding\, bridging -> protein binding\, bridging	nucleolus, proteasome complex (sensu Eukarya) -> nucleus, cytoplasm	HAP4, MATa1
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
YMR310C	NO SYMBOL
YNR046W	NO SYMBOL				ABF1
\|YNL292W\|	PUS4	tRNA modification -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pseudouridylate synthase activity -> carbon-oxygen lyase activity	mitochondrion, nucleus -> cytoplasm, nucleus	RCS1
YNR024W	NO SYMBOL
\|YMR259C\|	NO SYMBOL				ARG80, GCR2, GTS1, HIR1, SRD1
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
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
YGR145W	ENP2
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
\|YGL016W\|	KAP122	protein-nucleus import, response to drug -> response to abiotic stimulus, protein metabolism, cell growth and/or maintenance	protein carrier activity -> protein carrier activity	cytoplasm, nuclear pore -> cytoplasm, nucleus, integral to membrane, endomembrane system	MSN2
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
YKL172W	EBP2	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus	ABF1, FZF1, RFX1
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
YPL043W	NOP4	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus
YKL056C	NO SYMBOL
YGR162W	TIF4631	translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	HSF1
YGL169W	SUA5	cell growth and/or maintenance -> cell growth and/or maintenance			ABF1
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
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
\|YOR381W\|	FRE3	iron-siderochrome transport, iron ion homeostasis -> cell growth and/or maintenance	ferric-chelate reductase activity -> oxidoreductase activity\, oxidizing metal ions	plasma membrane, integral to membrane -> plasma membrane, integral to membrane	CIN5, PDR1, YAP6
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
YDR161W	NO SYMBOL
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
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
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
\|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
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
YNL175C	NOP13		RNA binding -> RNA binding	nucleolus, nucleoplasm -> nucleus	INO2, INO4
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
\|YMR049C\|	ERB1	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			RTG3
YDR496C	PUF6				RFX1
YNL112W	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
YNL308C	KRI1	ribosome biogenesis -> cell growth and/or maintenance		nucleolus -> nucleus
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
YDR365C	NO SYMBOL				ABF1, MSS11, YJL206C
YJR070C	NO SYMBOL				GAT3, 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
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
\|YOR359W\|	VTS1	protein-vacuolar targeting -> protein metabolism, cell growth and/or maintenance	intracellular transporter activity -> intracellular transporter activity	cytosol -> cytoplasm	RAP1
YNL132W	KRE33
YMR290C	HAS1			nucleolus, nuclear membrane -> nucleus, endomembrane system	RAP1
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
YDR184C	ATC1	response to stress, polar budding -> response to stress, asexual reproduction		nucleus -> nucleus	ARO80, GLN3, SIP4, SKO1
Main:		cell growth and/or maintenance (0.76)	RNA binding (0.57)	nucleus (0.83)	ABF1 (0.23)
Score:		0.70	0.36	0.75	0.114
P-value:		5.177E-29 (ribosome biogenesis)	2.275E-08 (snoRNA binding)	2.137E-32 (nucleolus)	3.563E-01 (ABF1)

mRRPE(1) AND PAC(1) AND SCB(1) => SimExpr(YGR280C) OR SimExpr(other) : 16 4

EXPR: (0.148) mRRPE (P < 0.000) PAC (P < 0.000) SCB (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
YDR399W	HPT1	purine nucleotide biosynthesis -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	hypoxanthine phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups
YMR131C	RRB1	ribosome biogenesis -> cell organization and biogenesis		nucleolus -> nucleus	FZF1, MATa1, RGT1
YLR197W	SIK1	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex, nucleus, nucleolus -> nucleus, ribonucleoprotein complex	DAL81, HAL9
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
YGR159C	NSR1	ribosomal small subunit assembly and maintenance, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	single-stranded DNA binding, RNA binding -> DNA binding, RNA binding	nucleolus, nucleus -> nucleus
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
YPR144C	NOC4	ribosome biogenesis -> cell organization and biogenesis		nucleus -> nucleus	HIR1
\|YJL069C\|	UTP18				ABF1
YHR052W	CIC1	protein catabolism -> catabolism, protein metabolism	protein binding\, bridging -> protein binding\, bridging	nucleolus, proteasome complex (sensu Eukarya) -> nucleus, cytoplasm	HAP4, MATa1
\|YNL292W\|	PUS4	tRNA modification -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pseudouridylate synthase activity -> carbon-oxygen lyase activity	mitochondrion, nucleus -> cytoplasm, nucleus	RCS1
\|YMR259C\|	NO SYMBOL				ARG80, GCR2, GTS1, HIR1, SRD1
YKL056C	NO SYMBOL
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
YMR239C	RNT1	35S primary transcript processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ribonuclease III activity -> hydrolase activity\, acting on ester bonds, RNA binding	nucleolus -> nucleus
\|YJL138C\|	TIF2	translational initiation, regulation of translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity, RNA helicase activity -> translation factor activity\, nucleic acid binding, RNA binding	ribosome, cytoplasm -> cytoplasm, ribonucleoprotein complex	PHD1
YNL112W	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
YJR070C	NO SYMBOL				GAT3, 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
YDR184C	ATC1	response to stress, polar budding -> response to stress, asexual reproduction		nucleus -> nucleus	ARO80, GLN3, SIP4, SKO1
Main:		cell organization and biogenesis (0.60)	RNA binding (0.64)	nucleus (0.80)	ABF1 (0.23)
Score:		0.53	0.40	0.75	0.077
P-value:		6.748E-07 (ribosome biogenesis)	5.928E-03 (RNA binding)	2.222E-07 (nucleolus)	4.089E-01 (SKO1)

mRRPE(1) AND PAC(1) AND MCM1'(1) => SimExpr(YGR280C) OR SimExpr(other) : 10 4

EXPR: (0.162) mRRPE (P < 0.000) PAC (P < 0.021) MCM1' (P < 0.000)

ORF	SYMBOL	P	F	C	TF
\|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
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
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
\|YML125C\|	NO SYMBOL				MAL13, MSN4, NDD1, RME1, SWI5
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
YPL043W	NOP4	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus
YGL169W	SUA5	cell growth and/or maintenance -> cell growth and/or maintenance			ABF1
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
\|YMR049C\|	ERB1	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			RTG3
YDR365C	NO SYMBOL				ABF1, MSS11, YJL206C
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
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
Main:		cell growth and/or maintenance (0.82)	RNA binding (0.57)	nucleus (1.00)	ABF1 (0.38)
Score:		0.78	0.29	1.00	0.179
P-value:		8.451E-07 (rRNA processing)	1.217E-01 (RNA binding)	6.765E-05 (nucleolus)	9.683E-01 (RLM1)

mRRPE(1) AND SWI5(1) AND PAC(1) => SimExpr(YGR280C) OR SimExpr(other) : 11 5

EXPR: (0.178) mRRPE (P < 0.006) SWI5 (P < 0.000) PAC (P < 0.095)

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 -> transferase activity\, transferring glycosyl groups
\|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
YMR229C	RRP5	rRNA processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding, snoRNA binding -> RNA binding	nucleolus, nucleolus organizer complex -> nucleus	FHL1, RAP1
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
YJR002W	MPP10	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nucleolar ribonucleoprotein complex, small nuclear ribonucleoprotein complex, nucleolus, nucleus -> nucleus, ribonucleoprotein complex
YFR001W	LOC1	ribosomal large subunit biogenesis -> cell organization and biogenesis	mRNA binding -> RNA binding	nucleus -> nucleus	ARG80, GAL4, GTS1, HAP4, HIR1, LEU3, MSN2, MSN4, RCS1, RLM1, SWI4
\|YML125C\|	NO SYMBOL				MAL13, MSN4, NDD1, RME1, SWI5
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
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
YNR024W	NO SYMBOL
\|YMR259C\|	NO SYMBOL				ARG80, GCR2, GTS1, HIR1, SRD1
\|YGL016W\|	KAP122	protein-nucleus import, response to drug -> response to abiotic stimulus, protein metabolism, transport	protein carrier activity -> protein carrier activity	cytoplasm, nuclear pore -> cytoplasm, nucleus, integral to membrane, endomembrane system	MSN2
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
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
Main:		cell organization and biogenesis (0.58)	RNA binding (0.44)	nucleus (0.82)	GCR2 ARG80 RLM1 MSN2 SWI5 MSN4 SWI6 HIR1 GTS1 (0.20)
Score:		0.56	0.19	0.76	0.156
P-value:		2.329E-04 (processing of 20S pre-rRNA)	4.169E-02 (snoRNA binding)	2.538E-04 (nucleolus)	8.743E-02 (MSN2)

REB1(1) AND PAC(1) => SimExpr(YGR280C) OR SimExpr(other) : 5 2

EXPR: (0.150) REB1 (P < 0.000) PAC (P < 0.026)

ORF	SYMBOL	P	F	C	TF
YOR272W	YTM1	chromosome organization and biogenesis (sensu Eukarya), ribosomal large subunit biogenesis -> chromosome organization and biogenesis (sensu Eukarya), ribosome biogenesis		nucleus, nucleolus -> nucleus, nucleolus	LEU3, PUT3, REB1
YOR021C	NO SYMBOL				ARG80, GCR2
YPL266W	DIM1	rRNA modification, 35S primary transcript processing -> RNA modification, ribosome biogenesis, rRNA metabolism, RNA processing, transcription from Pol I promoter	rRNA (adenine-N6\,N6-)-dimethyltransferase activity -> rRNA (adenine-N6\,N6-)-dimethyltransferase activity	nucleolus -> nucleolus	ARG81, STP2
\|YKL142W\|	MRP8	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	mitochondrial ribosome -> mitochondrial matrix, organellar ribosome	ACE2, CIN5, MBP1, PHO4, REB1, SKN7, STB1
YNL308C	KRI1	ribosome biogenesis -> ribosome biogenesis		nucleolus -> nucleolus
\|YML043C\|	RRN11	transcription from Pol I promoter -> transcription from Pol I promoter	RNA polymerase I transcription factor activity -> RNA polymerase I transcription factor activity	RNA polymerase I transcription factor complex -> nucleolus, transcription factor complex	MAL13
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> ribosome biogenesis, snRNA processing, RNA processing, transcription from Pol I promoter	RNA binding -> RNA binding	nucleolus -> nucleolus
Main:		ribosome biogenesis (0.67)	RNA binding (0.25)	nucleolus (0.83)	REB1 (0.40)
Score:		0.53	0.00	0.67	0.100
P-value:		1.591E-03 (ribosome biogenesis)	2.000E+00	1.148E-05 (nucleolus)	3.778E-01 (REB1)

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

EXPR: (0.135) LYS14 (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.002)

ORF	SYMBOL	P	F	C	TF
YNL110C	NOP15	ribosomal large subunit biogenesis -> cytoplasm organization and biogenesis		nucleus, nucleolus -> nucleus
YHR052W	CIC1	protein catabolism -> macromolecule catabolism, protein metabolism	protein binding\, bridging -> protein binding\, bridging	nucleolus, proteasome complex (sensu Eukarya) -> nucleus, cytoplasm	HAP4, MATa1
\|YMR259C\|	NO SYMBOL				ARG80, GCR2, GTS1, HIR1, SRD1
YML093W	UTP14	processing of 20S pre-rRNA -> cytoplasm organization and biogenesis, RNA metabolism, transcription	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
YGL099W	LSG1	conjugation with cellular fusion, sporulation (sensu Saccharomyces), ribosome nucleus export -> conjugation with cellular fusion, sporulation (sensu Fungi), cytoplasm organization and biogenesis, intracellular transport, protein metabolism, protein transport	GTPase activity -> purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	cytoplasm -> cytoplasm	PHO4
YJR070C	NO SYMBOL				GAT3, YAP5
YMR290C	HAS1			nucleolus, nuclear membrane -> nucleus, endomembrane system	RAP1
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> cytoplasm organization and biogenesis, RNA metabolism, transcription	RNA binding -> RNA binding	nucleolus -> nucleus
Main:		cytoplasm organization and biogenesis (0.80)	RNA binding (0.50)	nucleus (0.83)	GCR2 (0.20)
Score:		0.70	0.17	0.73	0.000
P-value:		3.082E-03 (ribosome biogenesis)	6.400E-01 (RNA binding)	3.460E-05 (nucleolus)	9.544E-01 (MATa1)

RAP1(1) AND MCM1'(1) => SimExpr(YOL120C) OR SimExpr(other) : 15 6

EXPR: (0.133) MCM1' (P < 0.000) RAP1 (P < 0.035)

ORF	SYMBOL	P	F	C	TF
YGL147C	RPL9A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, MBP1, RAP1, SWI4
\|YKL033W\|	NO SYMBOL				RPH1
YGL030W	RPL30	protein biosynthesis, rRNA processing, mRNA splicing, regulation of translation -> cell organization and biogenesis, biosynthesis, transcription, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya), cytoplasm -> cytosol, cytoplasm, ribosome	FHL1, GAT3, RAP1, SFP1
YGR214W	RPS0A	protein biosynthesis, ribosomal small subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosol, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, ribosome	FHL1, RAP1
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) -> cytosol, ribosome	FHL1, MIG1
YMR230W	RPS10B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosol, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, ribosome	FHL1, RAP1
YDL130W	RPP1B	protein biosynthesis, translational elongation -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, GAL4, RAP1, RFX1
YIL018W	RPL2B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, GAT3, PDR1, RAP1, RGM1, SWI5, YAP5
\|YGR254W\|	ENO1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphopyruvate hydratase activity -> phosphopyruvate hydratase activity	phosphopyruvate hydratase complex, cytoplasm -> cytosol, cytoplasm	FKH2, MSN4, PDR1, SWI5, YAP5
\|YKL152C\|	GPM1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphoglycerate mutase activity -> phosphoglycerate mutase activity	cytosol -> cytosol	GCR1, GCR2, HSF1, RAP1
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) -> cytosol, ribosome	FHL1, GAT3, GRF10(Pho2), GTS1, RAP1
YML073C	RPL6A	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) -> cytosol, ribosome	FHL1, GAT3, RAP1, YAP5
YNL069C	RPL16B	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, GAT3, PDR1, RAP1, RGM1, YAP5
YOL120C	RPL18A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, MAL13, RAP1, YAP5
\|YPL180W\|	BIT89	glycerol metabolism -> alcohol metabolism, glycerol ether metabolism, lipid metabolism			REB1, RGT1, SIG1
YDR450W	RPS18A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosol, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, ribosome	FHL1, GAT3, HIR2, RAP1, RGM1, YAP5
YLR344W	RPL26A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, RAP1
\|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 -> plasma membrane	DIG1, FHL1, RAP1, STE12
YPL090C	RPS6A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosol, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, ribosome	FHL1, GAT3, INO4, RAP1, YAP5
\|YJR139C\|	HOM6	homoserine biosynthesis, methionine metabolism, threonine metabolism -> amine metabolism, sulfur metabolism, biosynthesis, amino acid and derivative metabolism, organic acid metabolism	homoserine dehydrogenase activity -> homoserine dehydrogenase activity		HMS1, RAP1
YMR142C	RPL13B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, GAT3, RAP1, RGM1, YAP5
Main:		biosynthesis (0.90)	structural constituent of ribosome (0.79)	cytosol (0.94)	RAP1 (0.81)
Score:		0.82	0.61	0.89	0.752
P-value:		5.067E-09 (protein biosynthesis)	6.126E-14 (structural constituent of ribosome)	8.148E-16 (cytosolic ribosome (sensu Eukarya))	3.243E-20 (FHL1)

RAP1(1) AND ALPHA1'(1) AND MCM1'(1) => SimExpr(YOL120C) OR SimExpr(other) : 6 2

EXPR: (0.133) ALPHA1' (P < 0.000) MCM1' (P < 0.000) RAP1 (P < 0.129)

ORF	SYMBOL	P	F	C	TF
\|YKL033W\|	NO SYMBOL				RPH1
YGR214W	RPS0A	protein biosynthesis, ribosomal small subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosol, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, ribosome	FHL1, RAP1
YDL130W	RPP1B	protein biosynthesis, translational elongation -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, GAL4, RAP1, RFX1
\|YGR254W\|	ENO1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphopyruvate hydratase activity -> phosphopyruvate hydratase activity	phosphopyruvate hydratase complex, cytoplasm -> cytosol, cytoplasm	FKH2, MSN4, PDR1, SWI5, YAP5
YOL120C	RPL18A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, MAL13, RAP1, YAP5
YLR344W	RPL26A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, RAP1
YPL090C	RPS6A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosol, eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, ribosome	FHL1, GAT3, INO4, RAP1, YAP5
YMR142C	RPL13B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosol, ribosome	FHL1, GAT3, RAP1, RGM1, YAP5
Main:		biosynthesis (1.00)	structural constituent of ribosome (0.86)	cytosol (1.00)	RAP1 FHL1 (0.75)
Score:		1.00	0.71	1.00	0.643
P-value:		3.960E-04 (protein biosynthesis)	4.603E-06 (structural constituent of ribosome)	2.692E-06 (cytosolic ribosome (sensu Eukarya))	2.046E-07 (FHL1)

MCM1(1) AND STRE(1) => SimExpr(YKL035W) OR SimExpr(other) : 5 1

EXPR: (0.148) STRE (P < 0.002) MCM1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
\|YJL079C\|	PRY1			nuclear membrane, endoplasmic reticulum -> nuclear membrane, endoplasmic reticulum	NDD1, PHD1, RAP1
YJL082W	IML2
YLR201C	NO SYMBOL				ABF1
YMR291W	NO SYMBOL				RAP1
YKL035W	UGP1	protein amino acid glycosylation, UDP-glucose metabolism -> protein amino acid glycosylation, UDP-glucose metabolism	UTP-glucose-1-phosphate uridylyltransferase activity -> UTP-glucose-1-phosphate uridylyltransferase activity
YOL087C	NO SYMBOL				DAL82
Main:		protein amino acid glycosylation (1.00)	UTP-glucose-1-phosphate uridylyltransferase activity (1.00)	endoplasmic reticulum (1.00)	RAP1 (0.50)
Score:		0.00	0.00	0.00	0.167
P-value:		0.000E+00	0.000E+00	0.000E+00	2.350E-01 (RAP1)

CSRE(1) AND PHO4(1) => SimExpr(YML117W) OR SimExpr(other) : 5 1

EXPR: (0.144) PHO4 (P < 0.007) CSRE (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YML117W	NAB6
YOR299W	BUD7	bud site selection -> cell proliferation, cell organization and biogenesis			HSF1, MTH1
YOR185C	GSP2	nuclear organization and biogenesis -> cell organization and biogenesis	RAN small monomeric GTPase activity -> RAN small monomeric GTPase activity	nucleus -> nucleus
YFL004W	VTC2	protein localization, vacuole fusion (non-autophagic) -> protein metabolism, cell organization and biogenesis		vacuolar membrane -> cytoplasm	CIN5, GCN4, STE12, YAP1, YAP6
YJL042W	MHP1	microtubule stabilization, cell wall organization and biogenesis -> cell organization and biogenesis	structural constituent of cytoskeleton -> structural constituent of cytoskeleton	microtubule -> cytoplasm	CRZ1, GAL4, GAT3, PDR1, RGM1, YAP5
\|YPL190C\|	NAB3	regulation of transcription from Pol II promoter -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	poly(A) binding -> poly(A) binding	nucleoplasm -> nucleus	RFX1
Main:		cell organization and biogenesis (0.80)	poly(A) binding (0.33)	cytoplasm (0.50)	MTH1 (0.25)
Score:		0.60	0.00	0.33	0.000
P-value:		3.488E-01 (organelle organization and biogenesis)	1.794E+00 (binding)	4.104E+00 (nucleus)	5.520E-01 (GAL4)

CSRE(1) AND mRRPE(1) AND SWI5(1) => SimExpr(YNL111C) OR SimExpr(other) : 8 3

EXPR: (0.168) mRRPE (P < 0.001) SWI5 (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 -> transferase activity\, transferring glycosyl groups
YOR342C	NO SYMBOL				RAP1
YNL111C	CYB5	sterol biosynthesis -> alcohol metabolism, biosynthesis, lipid metabolism	electron transporter activity -> electron transporter activity	microsome -> membrane fraction	ABF1, GCR2, GTS1, NRG1, REB1, ROX1
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
YOR063W	RPL3	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	GRF10(Pho2)
YKL181W	PRS1	histidine biosynthesis, tryptophan biosynthesis, purine salvage, 'de novo' IMP biosynthesis, 'de novo' pyrimidine base biosynthesis -> amine metabolism, nucleotide biosynthesis, purine ribonucleotide metabolism, aromatic compound metabolism, amino acid derivative biosynthesis, biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, amino acid and derivative metabolism, organic acid metabolism, heterocycle metabolism	ribose-phosphate pyrophosphokinase activity -> carbohydrate kinase activity, transferase activity\, transferring phosphorus-containing groups
\|YHR213W\|	NO SYMBOL				PHD1
\|YAR062W\|	NO SYMBOL
\|YKL093W\|	MBR1	aerobic respiration -> energy pathways
Main:		biosynthesis (0.50)	transferase activity\, transferring phosphorus-containing groups (0.40)	nucleus (0.60)	ABF1 ROX1 (0.33)
Score:		0.50	0.10	0.40	0.133
P-value:		1.633E-02 (purine nucleotide biosynthesis)	1.189E+00 (transferase activity\, transferring phosphorus-containing groups)	5.013E-01 (nucleolus)	3.026E-01 (ROX1)

CSRE(1) AND ALPHA1'(1) AND mRRPE(1) AND SWI5(1) => SimExpr(YNL111C) OR SimExpr(other) : 6 2

EXPR: (0.161) ALPHA1' (P < 0.000) mRRPE (P < 0.000) SWI5 (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
YNL111C	CYB5	sterol biosynthesis -> alcohol metabolism, biosynthesis, lipid metabolism	electron transporter activity -> electron transporter activity	microsome -> membrane fraction	ABF1, GCR2, GTS1, NRG1, REB1, ROX1
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
YOR063W	RPL3	protein biosynthesis, ribosomal large subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	GRF10(Pho2)
YKL181W	PRS1	histidine biosynthesis, tryptophan biosynthesis, purine salvage, 'de novo' IMP biosynthesis, 'de novo' pyrimidine base biosynthesis -> amine metabolism, nucleotide biosynthesis, purine ribonucleotide metabolism, aromatic compound metabolism, amino acid derivative biosynthesis, biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, amino acid and derivative metabolism, organic acid metabolism, heterocycle metabolism	ribose-phosphate pyrophosphokinase activity -> carbohydrate kinase activity, transferase activity\, transferring phosphorus-containing groups
\|YHR213W\|	NO SYMBOL				PHD1
\|YAR062W\|	NO SYMBOL
Main:		cell organization and biogenesis (0.50)	transferase activity\, transferring phosphorus-containing groups (0.50)	nucleus (0.60)	ABF1 ROX1 (0.40)
Score:		0.60	0.17	0.40	0.200
P-value:		4.354E-01 (transcription from Pol I promoter)	7.124E-01 (transferase activity\, transferring phosphorus-containing groups)	2.761E-01 (nucleolus)	1.467E-01 (ROX1)

REB1(1) AND PAC(1) => SimExpr(YNL308C) OR SimExpr(other) : 5 2

SFF'(1) AND STE12(1) AND PAC(1) => SimExpr(YNL308C) OR SimExpr(other) : 5 1

EXPR: (0.179) SFF' (P < 0.000) STE12 (P < 0.001) PAC (P < 0.183)

ORF	SYMBOL	P	F	C	TF
YGR158C	MTR3	35S primary transcript processing, mRNA catabolism -> ribosome biogenesis, mRNA catabolism, RNA processing, transcription from Pol I promoter	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
\|YKL142W\|	MRP8	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	mitochondrial ribosome -> cytoplasm, ribonucleoprotein complex	ACE2, CIN5, MBP1, PHO4, REB1, SKN7, STB1
YGR251W	NO SYMBOL				MSN4, PHD1, SKN7
YJL069C	UTP18				ABF1
YPR137W	RRP9	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> RNA modification, ribosome biogenesis, rRNA metabolism, RNA processing, transcription from Pol I promoter	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex, small nuclear ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, HIR1, RCS1
YNL308C	KRI1	ribosome biogenesis -> ribosome biogenesis		nucleolus -> nucleus
Main:		ribosome biogenesis (0.75)	RNA binding (0.67)	nucleus (0.75)	ABF1 SKN7 (0.40)
Score:		0.50	0.33	0.83	0.200
P-value:		2.288E-02 (ribosome biogenesis)	3.804E-01 (RNA binding)	1.782E-01 (nucleolus)	2.309E-01 (SKN7)

mRRPE(1) AND STE12(1) AND PAC(1) => SimExpr(YNL308C) : 5

EXPR: (0.142) mRRPE (P < 0.002) STE12 (P < 0.000) PAC (P < 0.012)

ORF	SYMBOL	P	F	C	TF
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
YJL069C	UTP18				ABF1
YNL308C	KRI1	ribosome biogenesis -> cell growth and/or maintenance		nucleolus -> nucleolus
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:		1.424E-01 (ribosome biogenesis)	0.000E+00	9.149E-02 (nucleolus)	1.419E-01 (MOT3)

REB1(1) AND PAC(1) => SimExpr(YPL266W) OR SimExpr(other) : 5 2

REB1(1) AND ALPHA1(1) AND MCM1'(1) => SimExpr(YGR012W) OR SimExpr(other) : 9 4

EXPR: (0.191) REB1 (P < 0.033) MCM1' (P < 0.001) ALPHA1 (P < 0.002)

ORF	SYMBOL	P	F	C	TF
YLR455W	NO SYMBOL
YMR121C	RPL15B	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	REB1
YOL148C	SPT20	chromatin modification, histone acetylation -> cell organization and biogenesis, protein metabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	protein binding -> protein binding	SAGA complex -> nucleus	GRF10(Pho2), MATa1, MIG1, PHO4
YKR048C	NAP1	nucleosome assembly, M phase of mitotic cell cycle -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, cell proliferation	protein binding -> protein binding	nucleus -> nucleus	SKN7
YDR073W	SNF11	chromatin modeling -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	general RNA polymerase II transcription factor activity -> general RNA polymerase II transcription factor activity	nucleosome remodeling complex, SWI/SNF complex -> nucleus	DAL81, RLM1
YOR152C	NO SYMBOL				HIR2
\|YGR147C\|	NAT2	N-terminal peptidyl-methionine acetylation -> protein metabolism, protein modification	peptide alpha-N-acetyltransferase activity -> peptide alpha-N-acetyltransferase activity	cytoplasm -> cytoplasm	HIR1, REB1
\|YGL097W\|	SRM1	rRNA-nucleus export, ribosome nucleus export -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism, transport	signal transducer activity -> signal transducer activity	nucleus -> nucleus
YIL112W	HOS4	negative regulation of meiosis, histone deacetylation -> cell proliferation, cell organization and biogenesis, protein metabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	NAD-dependent histone deacetylase activity, NAD-independent histone deacetylase activity -> NAD-dependent histone deacetylase activity, NAD-independent histone deacetylase activity	histone deacetylase complex -> nucleus	MAC1, REB1, YFL044C
\|YKR011C\|	NO SYMBOL				SWI4, SWI6
YGL237C	HAP2	transcription, regulation of carbohydrate metabolism -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, carbohydrate metabolism, energy pathways, regulation of metabolism	transcriptional activator activity -> transcriptional activator activity	nucleus, CCAAT-binding factor complex -> nucleus	REB1
\|YDL232W\|	OST4	N-linked glycosylation -> biosynthesis, protein metabolism	dolichyl-diphospho-oligosaccharide-protein glycosyltransferase activity, protein binding -> dolichyl-diphospho-oligosaccharide-protein glycosyltransferase activity, protein binding	endoplasmic reticulum membrane -> cytoplasm, endomembrane system	REB1
YGR012W	NO SYMBOL				MIG1, REB1
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.67)	protein binding (0.33)	nucleus (0.67)	REB1 (0.55)
Score:		0.75	0.08	0.50	0.291
P-value:		1.495E-02 (DNA packaging)	2.960E-01 (protein binding)	4.345E-02 (transcription factor complex)	5.257E-05 (REB1)

REB1(1) AND ALPHA1(1) AND ALPHA1'(1) AND MCM1'(1) => SimExpr(YGR012W) OR SimExpr(other) : 7 3

EXPR: (0.184) ALPHA1' (P < 0.002) REB1 (P < 0.026) MCM1' (P < 0.001) ALPHA1 (P < 0.001)

ORF	SYMBOL	P	F	C	TF
YLR455W	NO SYMBOL
YMR121C	RPL15B	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	REB1
YOL148C	SPT20	chromatin modification, histone acetylation -> cell organization and biogenesis, protein metabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	protein binding -> protein binding	SAGA complex -> nucleus	GRF10(Pho2), MATa1, MIG1, PHO4
YKR048C	NAP1	nucleosome assembly, M phase of mitotic cell cycle -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, cell proliferation	protein binding -> protein binding	nucleus -> nucleus	SKN7
YDR073W	SNF11	chromatin modeling -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	general RNA polymerase II transcription factor activity -> general RNA polymerase II transcription factor activity	nucleosome remodeling complex, SWI/SNF complex -> nucleus	DAL81, RLM1
\|YGR147C\|	NAT2	N-terminal peptidyl-methionine acetylation -> protein metabolism, protein modification	peptide alpha-N-acetyltransferase activity -> peptide alpha-N-acetyltransferase activity	cytoplasm -> cytoplasm	HIR1, REB1
YIL112W	HOS4	negative regulation of meiosis, histone deacetylation -> cell proliferation, cell organization and biogenesis, protein metabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	NAD-dependent histone deacetylase activity, NAD-independent histone deacetylase activity -> NAD-dependent histone deacetylase activity, NAD-independent histone deacetylase activity	histone deacetylase complex -> nucleus	MAC1, REB1, YFL044C
\|YKR011C\|	NO SYMBOL				SWI4, SWI6
\|YDL232W\|	OST4	N-linked glycosylation -> biosynthesis, protein metabolism	dolichyl-diphospho-oligosaccharide-protein glycosyltransferase activity, protein binding -> dolichyl-diphospho-oligosaccharide-protein glycosyltransferase activity, protein binding	endoplasmic reticulum membrane -> cytoplasm, endomembrane system	REB1
YGR012W	NO SYMBOL				MIG1, REB1
Main:		protein metabolism (0.71)	protein binding (0.43)	nucleus (0.57)	REB1 (0.56)
Score:		0.71	0.14	0.43	0.306
P-value:		4.728E-03 (DNA packaging)	1.219E-01 (protein binding)	2.066E-01 (nucleoplasm)	2.104E-04 (REB1)

REB1(1) AND PAC(1) => SimExpr(YOR021C) OR SimExpr(other) : 5 2

ALPHA1'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YOR272W) OR SimExpr(other) : 38 3

EXPR: (0.154) ALPHA1' (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.000)

ORF	SYMBOL	P	F	C	TF
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
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
YNL292W	PUS4	tRNA modification -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pseudouridylate synthase activity -> carbon-oxygen lyase activity	mitochondrion, nucleus -> cytoplasm, nucleus	RCS1
\|YOR381W\|	FRE3	iron-siderochrome transport, iron ion homeostasis -> cell growth and/or maintenance	ferric-chelate reductase activity -> oxidoreductase activity\, oxidizing metal ions	plasma membrane, integral to membrane -> plasma membrane, integral to membrane	CIN5, PDR1, YAP6
YNL112W	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
YDR184C	ATC1	response to stress, polar budding -> response to stress, asexual reproduction		nucleus -> nucleus	ARO80, GLN3, SIP4, SKO1
YGR245C	SDA1	actin cytoskeleton organization and biogenesis, start control point of mitotic cell cycle -> cell growth and/or maintenance		nucleus -> nucleus
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
YKL014C	NO SYMBOL				ABF1
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
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
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
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
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
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
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
YNL175C	NOP13		RNA binding -> RNA binding	nucleolus, nucleoplasm -> nucleus	INO2, INO4
YMR049C	ERB1	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			RTG3
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
YOR359W	VTS1	protein-vacuolar targeting -> protein metabolism, cell growth and/or maintenance	intracellular transporter activity -> intracellular transporter activity	cytosol -> cytoplasm	RAP1
YNL132W	KRE33
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
YOR272W	YTM1	chromosome organization and biogenesis (sensu Eukarya), ribosomal large subunit biogenesis -> cell growth and/or maintenance		nucleus, nucleolus -> nucleus	LEU3, PUT3, REB1
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
YNR024W	NO SYMBOL
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
YGR162W	TIF4631	translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	HSF1
YGL169W	SUA5	cell growth and/or maintenance -> cell growth and/or maintenance			ABF1
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
YDR496C	PUF6				RFX1
YJR070C	NO SYMBOL				GAT3, 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
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
YAL059W	ECM1	cell wall organization and biogenesis -> cell growth and/or maintenance			MOT3
\|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
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
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
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
YNL308C	KRI1	ribosome biogenesis -> cell growth and/or maintenance		nucleolus -> nucleus
Main:		cell growth and/or maintenance (0.78)	RNA binding (0.64)	nucleus (0.80)	ABF1 (0.20)
Score:		0.72	0.43	0.68	0.080
P-value:		6.573E-17 (ribosome biogenesis)	1.324E-08 (snoRNA binding)	8.040E-18 (nucleolus)	1.000E+00

REB1(1) AND PAC(1) => SimExpr(YOR272W) OR SimExpr(other) : 5 2

CSRE(1) AND SWI5(1) AND PAC(1) => SimExpr(YPR010C) OR SimExpr(other) : 5 1

EXPR: (0.128) SWI5 (P < 0.000) PAC (P < 0.004) CSRE (P < 0.000)

ORF	SYMBOL	P	F	C	TF
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
YGR245C	SDA1	actin cytoskeleton organization and biogenesis, start control point of mitotic cell cycle -> cell organization and biogenesis, cell proliferation		nucleus -> nucleus
\|YKL120W\|	OAC1	oxaloacetate transport, sulfate transport -> transport	oxaloacetate carrier activity, sulfate porter activity -> oxaloacetate carrier activity, sulfate porter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	LEU3, MTH1
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, SWI6
YDR399W	HPT1	purine nucleotide biosynthesis -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	hypoxanthine phosphoribosyltransferase activity -> hypoxanthine phosphoribosyltransferase activity
YPL143W	RPL33A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, MET4, NDD1, PDR1, RAP1, RME1
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.50)	oxaloacetate carrier activity (0.25)	nucleus (0.60)	ABF1 (0.25)
Score:		0.33	0.00	0.50	0.000
P-value:		2.269E-01 (transcription from Pol I promoter)	9.575E-01 (transferase activity)	1.782E-01 (nucleolus)	7.609E-01 (LEU3)

ABF1(1) AND PAC(1) => SimExpr(YPR010C) OR SimExpr(other) : 12 3

EXPR: (0.153) ABF1 (P < 0.000) PAC (P < 0.004)

ORF	SYMBOL	P	F	C	TF
YGR283C	NO SYMBOL				ACE2, RAP1, SMP1
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
YNL292W	PUS4	tRNA modification -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pseudouridylate synthase activity -> carbon-oxygen lyase activity	mitochondrion, nucleus -> cytoplasm, nucleus	RCS1
YNL112W	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
YKL014C	NO SYMBOL				ABF1
YKL172W	EBP2	rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus	ABF1, FZF1, RFX1
YLR197W	SIK1	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex, nucleus, nucleolus -> nucleus, ribonucleoprotein complex	DAL81, HAL9
YGR187C	HGH1				ABF1, HAP3, HIR1, RCS1, RTG1
YKL078W	DHR2	ribosome biogenesis -> cell organization and biogenesis	RNA helicase activity -> RNA binding	nucleolus -> nucleus	ABF1
YOL041C	NOP12	rRNA metabolism -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus	GTS1, MET31
\|YHR027C\|	RPN1	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity, receptor activity -> peptidase activity, receptor activity	proteasome regulatory particle (sensu Eukarya), endoplasmic reticulum, cytoplasm -> cytoplasm, nucleus
YJL050W	MTR4	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
\|YJL069C\|	UTP18				ABF1
YNR046W	NO SYMBOL				ABF1
\|YDR527W\|	NO SYMBOL				ABF1, SKN7
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.75)	RNA binding (0.57)	nucleus (0.89)	ABF1 (0.58)
Score:		0.64	0.29	0.78	0.333
P-value:		3.084E-02 (transcription from Pol I promoter)	4.360E-03 (RNA helicase activity)	9.555E-05 (nucleolus)	4.241E-04 (ABF1)

CSRE(1) AND mRRPE(1) AND SWI5(1) => SimExpr(YPR010C) OR SimExpr(other) : 8 3

ABF1(1) AND ALPHA1'(1) AND PAC(1) => SimExpr(YPR010C) : 5

EXPR: (0.123) ABF1 (P < 0.000) ALPHA1' (P < 0.000) PAC (P < 0.017)

ORF	SYMBOL	P	F	C	TF
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
YNL292W	PUS4	tRNA modification -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pseudouridylate synthase activity -> carbon-oxygen lyase activity	mitochondrion, nucleus -> cytoplasm, nucleus	RCS1
YNL112W	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
YKL014C	NO SYMBOL				ABF1
YOL041C	NOP12	rRNA metabolism -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus	GTS1, MET31
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (1.00)	RNA binding (0.50)	nucleus (0.75)	ABF1 (0.25)
Score:		1.00	0.17	0.50	0.000
P-value:		2.945E-01 (RNA metabolism)	3.207E-01 (RNA binding)	9.149E-02 (nucleolus)	3.426E-01 (SIG1)

CSRE(1) AND mRRPE(1) AND PAC(1) => SimExpr(YPR010C) : 5

EXPR: (0.093) mRRPE (P < 0.000) PAC (P < 0.001) CSRE (P < 0.000)

ORF	SYMBOL	P	F	C	TF
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
YGR245C	SDA1	actin cytoskeleton organization and biogenesis, start control point of mitotic cell cycle -> cell organization and biogenesis, cell proliferation		nucleus -> nucleus
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
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, SWI6
YDR399W	HPT1	purine nucleotide biosynthesis -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	hypoxanthine phosphoribosyltransferase activity -> hypoxanthine phosphoribosyltransferase activity
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:		7.183E-03 (transcription from Pol I promoter)	7.087E-01 (transferase activity)	3.698E-03 (nucleolus)	2.284E-01 (SIG1)

mRRPE(1) AND PAC(1) => SimExpr(YOR310C) OR SimExpr(other) : 56 20

CSRE(1) AND mRRPE(1) AND SWI5(1) => SimExpr(YOR310C) OR SimExpr(other) : 8 3

mRRPE(1) AND SWI5(1) AND PAC(1) => SimExpr(YOR310C) OR SimExpr(other) : 11 5

mRRPE(1) AND PAC(1) AND SCB(1) => SimExpr(YOR310C) OR SimExpr(other) : 16 4

ALPHA1'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YOR310C) OR SimExpr(other) : 30 11

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

SFF'(1) AND mRRPE(1) AND PAC(1) AND SCB(1) => SimExpr(YOR310C) OR SimExpr(other) : 9 2

EXPR: (0.131) SFF' (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.001) SCB (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YHR052W	CIC1	protein catabolism -> macromolecule catabolism, protein metabolism	protein binding\, bridging -> protein binding\, bridging	nucleolus, proteasome complex (sensu Eukarya) -> nucleus, cytoplasm	HAP4, MATa1
\|YNL292W\|	PUS4	tRNA modification -> RNA metabolism	pseudouridylate synthase activity -> carbon-oxygen lyase activity	mitochondrion, nucleus -> cytoplasm, nucleus	RCS1
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
YNL112W	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
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
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
YLR249W	YEF3	translational elongation -> macromolecule biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
YKL056C	NO SYMBOL
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> cytoplasm organization and biogenesis, RNA metabolism, transcription	RNA binding -> RNA binding	nucleolus -> nucleus
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cytoplasm organization and biogenesis, RNA metabolism, transcription\, DNA-dependent		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, SWI6
\|YJL069C\|	UTP18				ABF1
Main:		RNA metabolism (0.62)	RNA binding (0.62)	nucleus (0.67)	ABF1 (0.43)
Score:		0.46	0.39	0.72	0.143
P-value:		2.618E-03 (processing of 20S pre-rRNA)	1.000E-02 (RNA binding)	3.708E-04 (nucleolus)	3.796E-01 (ABF1)

ALPHA1'(1) AND mRRPE(1) AND PAC(1) AND SCB(1) => SimExpr(YOR310C) OR SimExpr(other) : 7 1

EXPR: (0.131) ALPHA1' (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.001) SCB (P < 0.000)

ORF	SYMBOL	P	F	C	TF
\|YNL292W\|	PUS4	tRNA modification -> RNA processing, tRNA metabolism	pseudouridylate synthase activity -> carbon-oxygen lyase activity	mitochondrion, nucleus -> cytoplasm, nucleus	RCS1
YNL112W	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
YDR184C	ATC1	response to stress, polar budding -> response to stress, polar budding		nucleus -> nucleus	ARO80, GLN3, SIP4, SKO1
YOR078W	BUD21	processing of 20S pre-rRNA -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, MSS11, SIG1, SKO1
YJL109C	UTP10	processing of 20S pre-rRNA -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
YJR070C	NO SYMBOL				GAT3, YAP5
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent	RNA binding -> RNA binding	nucleolus -> nucleus
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> RNA processing, ribosome biogenesis and assembly, rRNA metabolism, transcription\, DNA-dependent		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, SWI6
Main:		RNA processing (0.83)	RNA binding (0.80)	nucleus (0.86)	ABF1 SKO1 (0.40)
Score:		0.67	0.60	0.71	0.200
P-value:		7.533E-04 (processing of 20S pre-rRNA)	7.782E-03 (snoRNA binding)	2.268E-04 (small nucleolar ribonucleoprotein complex)	2.853E-02 (SKO1)

ALPHA1'(1) AND mRRPE(1) AND SWI5(1) AND PAC(1) => SimExpr(YOR310C) OR SimExpr(other) : 8 2

EXPR: (0.154) ALPHA1' (P < 0.000) mRRPE (P < 0.002) SWI5 (P < 0.000) PAC (P < 0.013)

ORF	SYMBOL	P	F	C	TF
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
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
YGR245C	SDA1	actin cytoskeleton organization and biogenesis, start control point of mitotic cell cycle -> cell organization and biogenesis, cell proliferation		nucleus -> nucleus
YMR229C	RRP5	rRNA processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding, snoRNA binding -> RNA binding	nucleolus, nucleolus organizer complex -> nucleus	FHL1, RAP1
YFR001W	LOC1	ribosomal large subunit biogenesis -> cell organization and biogenesis	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 organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
YNR024W	NO SYMBOL
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
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
\|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
Main:		cell organization and biogenesis (0.75)	RNA binding (0.67)	nucleus (0.88)	RLM1 SWI6 (0.33)
Score:		0.68	0.40	0.75	0.133
P-value:		2.132E-04 (transcription from Pol I promoter)	1.419E-02 (snoRNA binding)	1.670E-04 (nucleolus)	4.867E-01 (RLM1)

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

EXPR: (0.117) mRRPE (P < 0.000) SWI5 (P < 0.000) PAC (P < 0.001) SCB (P < 0.000)

ORF	SYMBOL	P	F	C	TF
\|YMR259C\|	NO SYMBOL				ARG80, GCR2, GTS1, HIR1, SRD1
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
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
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
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, SWI6
YDR399W	HPT1	purine nucleotide biosynthesis -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	hypoxanthine phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.80)	RNA binding (0.50)	nucleus (0.75)	ABF1 (0.33)
Score:		0.70	0.17	0.83	0.000
P-value:		9.864E-03 (rRNA processing)	3.308E-01 (nucleic acid binding)	8.330E-03 (small nucleolar ribonucleoprotein complex)	7.610E-01 (SRD1)

CSRE(1) AND mRRPE(1) AND PAC(1) => SimExpr(YOR310C) : 5

CSRE(1) AND ALPHA1'(1) AND mRRPE(1) AND SWI5(1) => SimExpr(YOR063W) OR SimExpr(other) : 6 2

ABF1(1) AND RPN4(1) => SimExpr(YGR253C) OR SimExpr(other) : 6 1

EXPR: (0.152) ABF1 (P < 0.000) RPN4 (P < 0.047)

ORF	SYMBOL	P	F	C	TF
YFR020W	NO SYMBOL				MIG1
\|YNL251C\|	NRD1	nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleus -> nucleus	ABF1, MAC1
YJR006W	HYS2	leading strand elongation, lagging strand elongation, mutagenesis, base-excision repair, nucleotide-excision repair, postreplication repair, mismatch repair -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, DNA repair, cell proliferation	delta DNA polymerase activity -> delta DNA polymerase activity	delta DNA polymerase complex -> cytoplasm, nucleus	ABF1
YHR027C	RPN1	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity, receptor activity -> endopeptidase activity, receptor activity	proteasome regulatory particle (sensu Eukarya), endoplasmic reticulum, cytoplasm -> cytoplasm, nucleus
YGR253C	PUP2	ubiquitin-dependent protein catabolism, response to stress, sporulation (sensu Saccharomyces) -> catabolism, response to stress, sporulation, protein metabolism	endopeptidase activity -> endopeptidase activity	proteasome core complex (sensu Eukarya) -> cytoplasm, nucleus	ABF1, HIR2, PHO4
YHL024W	RIM4	sporulation, meiosis, premeiotic DNA synthesis, meiotic recombination -> sporulation, M phase, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, cell proliferation	RNA binding -> RNA binding	cytoplasm -> cytoplasm	FKH2, PHD1
YOR362C	PRE10	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity -> endopeptidase activity	proteasome core complex (sensu Eukarya) -> cytoplasm, nucleus
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.50)	endopeptidase activity (0.50)	cytoplasm (0.83)	ABF1 (0.60)
Score:		0.47	0.27	0.93	0.300
P-value:		1.746E-02 (ubiquitin-dependent protein catabolism)	7.474E-04 (endopeptidase activity)	6.518E-04 (proteasome complex (sensu Eukarya))	6.278E-02 (ABF1)

CSRE(1) AND SWI5(1) AND PAC(1) => SimExpr(YDR399W) OR SimExpr(other) : 5 1

CSRE(1) AND mRRPE(1) AND PAC(1) => SimExpr(YDR399W) : 5

ALPHA2(1) AND ABF1(1) => SimExpr(YGL207W) OR SimExpr(other) : 9 4

EXPR: (0.190) ALPHA2 (P < 0.006) ABF1 (P < 0.075)

ORF	SYMBOL	P	F	C	TF
YDL195W	SEC31	ER to Golgi transport -> transport, vesicle-mediated transport	structural molecule activity -> structural molecule activity	COPII vesicle coat -> cytoplasm	ABF1, GAT1, MTH1, SFL1, SIG1
YLR429W	CRN1	actin filament organization, microtubule-based process -> cell organization and biogenesis	actin cross-linking activity, microtubule binding -> actin cross-linking activity, microtubule binding	actin cortical patch (sensu Saccharomyces) -> cell cortex, cytoplasm
\|YJL097W\|	NO SYMBOL				ARG80, HAP3
\|YNL111C\|	CYB5	sterol biosynthesis -> alcohol metabolism, biosynthesis, lipid metabolism	electron transporter activity -> electron transporter activity	microsome -> membrane fraction	ABF1, GCR2, GTS1, NRG1, REB1, ROX1
YKR046C	PET10			lipid particle -> cytoplasm	ABF1
YGL207W	SPT16	chromatin modeling, regulation of global transcription from Pol II promoter, RNA elongation from Pol II promoter -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, DNA metabolism	transcriptional elongation regulator activity -> transcriptional elongation regulator activity	alpha DNA polymerase\:primase complex, nuclear chromatin, transcription elongation factor complex -> nucleus, chromosome	RTG1
\|YKL172W\|	EBP2	rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus	ABF1, FZF1, RFX1
YAL016W	TPD3	protein biosynthesis, actin filament organization, mitotic spindle checkpoint, bud growth, protein amino acid dephosphorylation -> biosynthesis, cell organization and biogenesis, asexual reproduction, phosphorus metabolism, cell proliferation, cell cycle, protein metabolism	protein phosphatase type 2A activity -> protein phosphatase type 2A activity	protein phosphatase type 2A complex, bud neck, nucleus, cytoplasm, shmoo tip, bud tip, spindle pole body -> protein phosphatase type 2A complex, nucleus, site of polarized growth (sensu Fungi), site of polarized growth (sensu Saccharomyces), cytoplasm, microtubule organizing center	ABF1
YJL091C	GWT1	GPI anchor biosynthesis -> biosynthesis, membrane lipid metabolism, protein metabolism, lipid metabolism		membrane -> membrane
YHR027C	RPN1	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity, receptor activity -> endopeptidase activity, receptor activity	proteasome regulatory particle (sensu Eukarya), endoplasmic reticulum, cytoplasm -> cytoplasm, nucleus
YKR084C	HBS1	protein biosynthesis -> biosynthesis, protein metabolism			PHO4
\|YNR046W\|	NO SYMBOL				ABF1
YNL059C	ARP5	protein-vacuolar targeting -> cell organization and biogenesis, protein metabolism, transport		nucleus -> nucleus	ABF1, GRF10(Pho2)
Main:		cell organization and biogenesis (0.50)	electron transporter activity (0.17)	cytoplasm (0.50)	ABF1 (0.70)
Score:		0.51	0.00	0.42	0.467
P-value:		3.890E-01 (actin filament organization)	2.991E+00 (hydrolase activity)	1.171E+00 (cytoskeleton)	1.272E-04 (ABF1)

SFF(1) AND MCB(1) AND ATRepeat(1) => SimExpr(YJR006W) OR SimExpr(other) : 6 2

EXPR: (0.171) SFF (P < 0.000) MCB (P < 0.030) ATRepeat (P < 0.005)

ORF	SYMBOL	P	F	C	TF
YDL003W	MCD1	mitotic sister chromatid cohesion, mitotic chromosome condensation -> cell proliferation, cell cycle		nuclear cohesin complex -> chromosome, nucleus	CIN5, MBP1, SWI6
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
YLR212C	TUB4	microtubule nucleation, mitotic spindle assembly (sensu Saccharomyces) -> cell organization and biogenesis, cell proliferation, cell cycle	structural constituent of cytoskeleton -> structural constituent of cytoskeleton	inner plaque of spindle pole body, outer plaque of spindle pole body -> cytoplasm
YPL123C	RNY1	cellular morphogenesis -> cell organization and biogenesis	endoribonuclease activity -> hydrolase activity\, acting on ester bonds, RNA binding	extracellular -> extracellular	ARG80, CUP9, DAL81, FZF1, NRG1, STB1
YJR006W	HYS2	leading strand elongation, lagging strand elongation, mutagenesis, base-excision repair, nucleotide-excision repair, postreplication repair, mismatch repair -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, DNA repair, cell proliferation	delta DNA polymerase activity -> transferase activity\, transferring phosphorus-containing groups	delta DNA polymerase complex -> cytoplasm, nucleus	ABF1
\|YNL102W\|	POL1	DNA replication\, priming, DNA replication initiation, lagging strand elongation, DNA repair synthesis -> DNA metabolism, cell proliferation	alpha DNA polymerase activity -> transferase activity\, transferring phosphorus-containing groups	alpha DNA polymerase\:primase complex -> nucleus	LEU3, MBP1
YLR430W	SEN1	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	ARG80, GTS1, HAP5, RTG3, SIP4
\|YMR102C\|	NO SYMBOL
Main:		cell organization and biogenesis (0.57)	RNA binding (0.33)	nucleus (0.57)	ARG80 MBP1 SWI6 (0.33)
Score:		0.62	0.13	0.33	0.200
P-value:		3.346E-03 (lagging strand elongation)	1.223E-02 (DNA-directed DNA polymerase activity)	1.056E-02 (replication fork)	1.376E-01 (ARG80)

CSRE(1) AND PHO4(1) => SimExpr(YOR299W) OR SimExpr(other) : 5 1

mRRPE(1) AND PAC(1) => SimExpr(YGR159C) OR SimExpr(other) : 52 24

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

CSRE(1) AND mRRPE(1) AND PAC(1) => SimExpr(YGR245C) : 5

CSRE(1) AND OAF1(1) => SimExpr(YJR019C) OR SimExpr(other) : 5 1

EXPR: (0.153) OAF1 (P < 0.010) CSRE (P < 0.001)

ORF	SYMBOL	P	F	C	TF
YJR019C	TES1	fatty acid oxidation -> lipid metabolism, carboxylic acid metabolism	acyl-CoA thioesterase activity -> acyl-CoA thioesterase activity	peroxisome -> cytoplasm	DAL82, MTH1
YLR174W	IDP2	isocitrate metabolism, glutamate biosynthesis -> carbohydrate metabolism, amine biosynthesis, amine metabolism, carboxylic acid metabolism, energy derivation by oxidation of organic compounds, amino acid and derivative metabolism	isocitrate dehydrogenase (NADP+) activity -> isocitrate dehydrogenase (NADP+) activity	cytosol -> cytoplasm	ABF1, CBF1, RAP1
YMR135C	GID8	negative regulation of gluconeogenesis -> alcohol biosynthesis, regulation of biosynthesis, monosaccharide metabolism, carbohydrate metabolism, negative regulation of metabolism, carbohydrate biosynthesis, energy derivation by oxidation of organic compounds, regulation of metabolism			ASH1, CUP9, DAL81, INO4, NDD1, NRG1, PHD1, ROX1, SKN7, SWI4, YAP6
\|YDR134C\|	NO SYMBOL				ASH1, NRG1, SOK2, SWI4
YNL329C	PEX6	peroxisome organization and biogenesis -> cytoplasm organization and biogenesis	ATPase activity -> ATPase activity	peroxisome -> cytoplasm	RAP1
YML042W	CAT2	carnitine metabolism -> amine metabolism, carboxylic acid metabolism, water-soluble vitamin metabolism, amino acid derivative metabolism	carnitine O-acetyltransferase activity -> carnitine O-acetyltransferase activity	peroxisomal matrix, mitochondrion, peroxisome -> cytoplasm	MAL13
Main:		carboxylic acid metabolism (0.60)	ATPase activity (0.25)	cytoplasm (1.00)	SWI4 RAP1 ASH1 NRG1 (0.33)
Score:		0.40	0.00	1.00	0.133
P-value:		4.936E-02 (organic acid metabolism)	1.308E+00 (hydrolase activity)	2.629E-04 (peroxisome)	2.324E-02 (ASH1)

RAP1(1) AND SCB(1) => SimExpr(YLR344W) OR SimExpr(other) : 10 2

EXPR: (0.145) SCB (P < 0.000) RAP1 (P < 0.093)

ORF	SYMBOL	P	F	C	TF
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
\|YOL160W\|	NO SYMBOL				ARO80, NRG1, PHO4, RLM1, SIP4, SWI6
YNL024C	NO SYMBOL				GRF10(Pho2)
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
\|YPL189W\|	GUP2			membrane -> membrane	RFX1
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
YLR344W	RPL26A	protein biosynthesis -> biosynthesis, protein metabolism	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
YGR260W	TNA1	nicotinamide mononucleotide transport -> transport	nicotinamide mononucleotide permease activity -> nicotinamide mononucleotide permease activity	integral to plasma membrane -> membrane	HIR2, SUM1
YPR080W	TEF1	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	FHL1, PDR1, RAP1, YAP5
YOR369C	RPS12	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ARG80, FHL1, FKH2, LEU3, NDD1, PDR1, RME1, SMP1, YAP6
YLR208W	SEC13	nonselective vesicle assembly, ER to Golgi transport, ER-associated protein catabolism -> macromolecule catabolism, transport, protein metabolism		cytoplasm, COPII vesicle coat, nuclear pore, extrinsic to plasma membrane -> nucleus, cytoplasm, membrane coat, membrane
Main:		protein metabolism (0.89)	structural constituent of ribosome (0.62)	cytoplasm (0.80)	FHL1 (0.55)
Score:		0.81	0.39	0.69	0.291
P-value:		2.067E-03 (protein biosynthesis)	4.393E-03 (structural constituent of ribosome)	1.274E-04 (ribosome)	1.492E-05 (FHL1)

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

RAP1(1) AND SWI5(1) => SimExpr(YLR344W) OR SimExpr(other) : 16 7

EXPR: (0.164) SWI5 (P < 0.000) RAP1 (P < 0.395)

ORF	SYMBOL	P	F	C	TF
\|YOR213C\|	SAS5	chromatin silencing at telomere -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	acetyltransferase activity -> transferase activity\, transferring groups other than amino-acyl groups	nuclear chromosome\, telomeric region, nuclear chromatin -> chromosome, nuclear chromosome	GRF10(Pho2), SUM1
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
\|YMR013C\|	SEC59	protein-ER targeting, protein amino acid glycosylation -> cell organization and biogenesis, biosynthesis, protein modification, protein metabolism, transport	dolichol kinase activity -> phosphotransferase activity\, alcohol group as acceptor	membrane -> membrane	FHL1, NDD1, RAP1, RLM1, RME1
YKR092C	SRP40	nucleocytoplasmic transport -> transport	chaperone activity -> chaperone activity	nucleolus -> nucleus	CUP9, MET4, RAP1
YLR441C	RPS1A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1, YAP5
YMR224C	MRE11	DNA repair, double-strand break repair via nonhomologous end-joining, meiotic DNA double-strand break formation, meiotic DNA double-strand break processing, double-strand break repair via break-induced replication -> DNA metabolism, cell proliferation, catabolism	endonuclease activity, 3'-5' exonuclease activity, protein binding -> nuclease activity, protein binding	nucleus -> nucleus	RAP1
YDR450W	RPS18A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, HIR2, RAP1, RGM1, YAP5
\|YGL196W\|	NO SYMBOL
YGL030W	RPL30	protein biosynthesis, rRNA processing, mRNA splicing, regulation of translation -> cell organization and biogenesis, biosynthesis, transcription, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya), cytoplasm -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1, SFP1
\|YNL311C\|	NO SYMBOL				GCN4, RAP1
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
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
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
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
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
\|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
\|YJL217W\|	NO SYMBOL				CIN5, MAC1, PHD1, SWI5, YAP6
YOL120C	RPL18A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, MAL13, RAP1, YAP5
YPR080W	TEF1	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	FHL1, PDR1, RAP1, YAP5
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
\|YPR161C\|	SGV1	transcription, protein amino acid phosphorylation -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, phosphorus metabolism, protein metabolism	cyclin-dependent protein kinase activity -> phosphotransferase activity\, alcohol group as acceptor	nucleus -> nucleus	RAP1
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
Main:		protein metabolism (0.75)	structural constituent of ribosome (0.55)	cytoplasm (0.70)	RAP1 (0.82)
Score:		0.59	0.30	0.53	0.745
P-value:		3.312E-07 (protein biosynthesis)	3.091E-07 (structural constituent of ribosome)	1.091E-08 (cytosolic ribosome (sensu Eukarya))	5.425E-17 (RAP1)

RAP1(1) AND SWI5(1) AND MCM1'(1) => SimExpr(YLR344W) : 7

EXPR: (0.110) SWI5 (P < 0.000) MCM1' (P < 0.000) RAP1 (P < 0.005)

ORF	SYMBOL	P	F	C	TF
YDR450W	RPS18A	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, small ribosomal subunit	FHL1, GAT3, HIR2, RAP1, RGM1, YAP5
YGL030W	RPL30	protein biosynthesis, rRNA processing, mRNA splicing, regulation of translation -> protein biosynthesis, rRNA processing, mRNA splicing, regulation of translation	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya), cytoplasm -> cytosolic ribosome (sensu Eukarya), cytoplasm, large ribosomal subunit	FHL1, GAT3, RAP1, SFP1
YNL069C	RPL16B	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), large ribosomal subunit	FHL1, GAT3, PDR1, RAP1, RGM1, YAP5
YLR344W	RPL26A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), large ribosomal subunit	FHL1, RAP1
YOL120C	RPL18A	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), large ribosomal subunit	FHL1, MAL13, RAP1, YAP5
YLR452C	SST2	signal transduction, adaptation to pheromone during conjugation with cellular fusion -> signal transduction, adaptation to pheromone during conjugation with cellular fusion	GTPase activator activity -> GTPase activator activity	plasma membrane -> plasma membrane	DIG1, FHL1, RAP1, STE12
YKL006W	RPL14A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), large ribosomal subunit	FHL1, GAT3, GRF10(Pho2), GTS1, RAP1
Main:		protein biosynthesis (0.86)	structural constituent of ribosome (0.86)	cytosolic ribosome (sensu Eukarya) (0.86)	RAP1 FHL1 (1.00)
Score:		0.71	0.71	0.71	1.000
P-value:		1.231E-04 (protein biosynthesis)	2.118E-06 (structural constituent of ribosome)	5.117E-07 (cytosolic ribosome (sensu Eukarya))	1.933E-10 (FHL1)

RAP1(1) AND ALPHA1'(1) AND SCB(1) => SimExpr(YLR344W) : 6

EXPR: (0.117) ALPHA1' (P < 0.000) SCB (P < 0.000) RAP1 (P < 0.027)

ORF	SYMBOL	P	F	C	TF
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)
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
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
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
Main:		protein biosynthesis (1.00)	structural constituent of ribosome (0.80)	ribosome (1.00)	FHL1 (0.83)
Score:		1.00	0.60	1.00	0.667
P-value:		8.374E-04 (protein biosynthesis)	1.274E-03 (structural constituent of ribosome)	1.752E-04 (ribosome)	2.789E-06 (FHL1)

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

EXPR: (0.111) SWI5 (P < 0.000) SCB (P < 0.000) RAP1 (P < 0.015)

ORF	SYMBOL	P	F	C	TF
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
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
YLR249W	YEF3	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation elongation factor activity	ribosome -> ribosome	INO2, INO4
YPR080W	TEF1	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation elongation factor activity	ribosome -> ribosome	FHL1, PDR1, RAP1, YAP5
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
Main:		protein biosynthesis (1.00)	structural constituent of ribosome (0.60)	ribosome (1.00)	FHL1 (0.80)
Score:		1.00	0.40	1.00	0.600
P-value:		1.732E-04 (protein biosynthesis)	1.679E-03 (translation elongation factor activity)	3.116E-05 (ribosome)	8.308E-05 (FHL1)

RPN4(1) => SimExpr(YGL201C) OR SimExpr(other) : 35 17

EXPR: (0.190) RPN4 (P < 0.547)

ORF	SYMBOL	P	F	C	TF
YFR020W	NO SYMBOL				MIG1
YGR135W	PRE9	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya) -> cytoplasm, nucleus	REB1, SKO1
\|YNL251C\|	NRD1	nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleus -> nucleus	ABF1, MAC1
\|YGR184C\|	UBR1	protein polyubiquitination, protein monoubiquitination -> catabolism, protein metabolism	ubiquitin-protein ligase activity -> ligase activity\, forming carbon-nitrogen bonds	proteasome complex (sensu Eukarya) -> cytoplasm, nucleus	HMS1, REB1, RIM101
\|YGR286C\|	BIO2	biotin biosynthesis -> biosynthesis, coenzymes and prosthetic group metabolism, vitamin metabolism, heterocycle metabolism, organic acid metabolism, sulfur metabolism	biotin synthase activity -> transferase activity\, transferring sulfur-containing groups
YDR427W	RPN9	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity -> peptidase activity	proteasome regulatory particle (sensu Eukarya), proteasome regulatory particle\, lid subcomplex (sensu Eukarya) -> cytoplasm, nucleus	ARG81, IXR1
\|YJR159W\|	SOR1	fructose metabolism, mannose metabolism -> alcohol metabolism, carbohydrate metabolism	L-iditol 2-dehydrogenase activity -> oxidoreductase activity\, acting on CH-OH group of donors		ASH1, CUP9, MOT3, MTH1, NRG1, PHD1, RLM1, ROX1, SOK2, YAP6
YGR142W	BTN2	regulation of pH, intracellular protein transport -> cell homeostasis, transport		cytosol -> cytoplasm	HSF1, MSN4
YFR050C	PRE4	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya) -> cytoplasm, nucleus	MTH1, REB1
\|YGR235C\|	NO SYMBOL				REB1
YFR010W	UBP6	protein deubiquitination -> catabolism, protein metabolism	ubiquitin-specific protease activity -> peptidase activity	proteasome regulatory particle (sensu Eukarya) -> cytoplasm, nucleus	ABF1
\|YPL190C\|	NAB3	regulation of transcription from Pol II promoter -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	poly(A) binding -> RNA binding	nucleoplasm -> nucleus	RFX1
\|YJL058C\|	BIT61
YGL201C	MCM6	DNA unwinding, DNA replication initiation -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	chromatin binding, ATP dependent DNA helicase activity -> DNA binding, adenyl nucleotide binding, hydrolase activity\, acting on acid anhydrides	cytoplasm, nucleus, pre-replicative complex -> cytoplasm, nucleus	MCM1
YOR097C	NO SYMBOL
YJR006W	HYS2	leading strand elongation, lagging strand elongation, mutagenesis, base-excision repair, nucleotide-excision repair, postreplication repair, mismatch repair -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, DNA repair, cell proliferation	delta DNA polymerase activity -> transferase activity\, transferring phosphorus-containing groups	delta DNA polymerase complex -> cytoplasm, nucleus	ABF1
\|YNL012W\|	SPO1	meiosis -> cell proliferation	phospholipase activity -> hydrolase activity\, acting on ester bonds	nucleus -> nucleus	ARO80, SRD1
\|YJL045W\|	NO SYMBOL				MBP1, ROX1
YFL044C	NO SYMBOL
YIL075C	RPN2	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	receptor activity, endopeptidase activity -> receptor activity, peptidase activity	proteasome regulatory particle (sensu Eukarya) -> cytoplasm, nucleus	MSS11, REB1, SFL1
YMR100W	MUB1	regulation of budding -> asexual reproduction
YFL056C	AAD6	aldehyde metabolism -> aldehyde metabolism	benzyl alcohol dehydrogenase activity -> oxidoreductase activity\, acting on CH-OH group of donors		ACE2, YAP1
YOR007C	SGT2
\|YJR015W\|	NO SYMBOL
YML092C	PRE8	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya) -> cytoplasm, nucleus
YNL097C	PHO23	chromatin modification -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleus -> nucleus	MAC1
YGR124W	ASN2	asparagine biosynthesis -> amine metabolism, amino acid and derivative metabolism, organic acid metabolism, biosynthesis	asparagine synthase (glutamine-hydrolyzing) activity -> ligase activity\, forming carbon-nitrogen bonds		ASH1, ROX1
YKL135C	APL2	vesicle-mediated transport -> transport	clathrin binding -> protein binding	AP-1 adaptor complex -> cytoplasmic vesicle, cytoplasm	ABF1, DOT6
YGL238W	CSE1	protein-nucleus export -> protein metabolism, transport	importin-alpha export receptor activity -> protein binding	nuclear membrane -> nucleus, endomembrane system	REB1
\|YGL096W\|	TOS8		transcription factor activity -> DNA binding		IXR1, SOK2, SWI4
YGL062W	PYC1	NADPH regeneration, gluconeogenesis -> coenzymes and prosthetic group metabolism, alcohol metabolism, carbohydrate metabolism, vitamin metabolism, biosynthesis, energy pathways	pyruvate carboxylase activity -> ligase activity\, forming carbon-carbon bonds	cytosol -> cytoplasm	DIG1, GCR1, STE12
\|YKL203C\|	TOR2	cytoskeleton organization and biogenesis, ribosome biogenesis, signal transduction, Rho protein signal transduction, regulation of cell cycle, G1 phase of mitotic cell cycle, cell cycle dependent actin filament reorganization -> cell organization and biogenesis, signal transduction, cell cycle, cytoplasm organization and biogenesis	phosphatidylinositol 3-kinase activity, protein binding -> transferase activity\, transferring phosphorus-containing groups, protein binding, lipid kinase activity	vacuolar membrane, plasma membrane -> cytoplasm, plasma membrane	BAS1, HIR1, REB1, RTG1
YOL131W	NO SYMBOL
YGL122C	NAB2	poly(A)+ mRNA-nucleus export, mRNA polyadenylation -> transport, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	poly(A) binding -> RNA binding	nucleus, cytoplasm -> nucleus, cytoplasm	ABF1
YOL038W	PRE6	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya) -> cytoplasm, nucleus
\|YNL241C\|	ZWF1	pentose-phosphate shunt -> coenzymes and prosthetic group metabolism, alcohol metabolism, water-soluble vitamin metabolism, carbohydrate metabolism, energy derivation by oxidation of organic compounds, catabolism	glucose-6-phosphate 1-dehydrogenase activity -> oxidoreductase activity\, acting on CH-OH group of donors	cytoplasm -> cytoplasm	ACE2, ADR1, FKH2, HIR1, IME4, MBP1, NDD1, PHO4, RCS1, SFP1, SKN7, SWI5
\|YGR060W\|	ERG25	ergosterol biosynthesis -> alcohol metabolism, biosynthesis, lipid metabolism	C-4 methyl sterol oxidase activity -> C-4 methyl sterol oxidase activity	endoplasmic reticulum membrane, plasma membrane -> cytoplasm, plasma membrane, endomembrane system	HSF1, MAL13, MET4, NDD1, SWI5
YJL116C	NCA3	mitochondrion organization and biogenesis -> cell organization and biogenesis			CBF1, MBP1, SKN7, SWI6
YKL145W	RPT1	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	ATPase activity, endopeptidase activity -> purine nucleotide binding, peptidase activity, hydrolase activity\, acting on acid anhydrides	proteasome regulatory particle (sensu Eukarya) -> cytoplasm, nucleus	REB1
YHR027C	RPN1	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity, receptor activity -> peptidase activity, receptor activity	proteasome regulatory particle (sensu Eukarya), endoplasmic reticulum, cytoplasm -> cytoplasm, nucleus
YGR253C	PUP2	ubiquitin-dependent protein catabolism, response to stress, sporulation (sensu Saccharomyces) -> catabolism, response to stress, sporulation, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya) -> cytoplasm, nucleus	ABF1, HIR2, PHO4
YOR052C	NO SYMBOL
\|YHL024W\|	RIM4	sporulation, meiosis, premeiotic DNA synthesis, meiotic recombination -> sporulation, M phase, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, cell proliferation	RNA binding -> RNA binding	cytoplasm -> cytoplasm	FKH2, PHD1
YKL210W	UBA1	ubiquitin cycle -> catabolism, protein metabolism	ubiquitin activating enzyme activity -> ubiquitin activating enzyme activity	nucleus, cytoplasm -> nucleus, cytoplasm	SKO1
YDL126C	CDC48	ubiquitin-dependent protein catabolism, nonselective vesicle fusion, cell cycle, apoptosis, protein transport, ER-associated protein catabolism -> cell proliferation, cell death, macromolecule catabolism, transport, protein metabolism	ATPase activity -> purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleus, microsome, endoplasmic reticulum, cytosol -> nucleus, membrane fraction, cytoplasm	DAL82, MAL33, SWI4
YKL054C	DEF1	response to DNA damage, ubiquitin-dependent protein catabolism -> response to biotic stimulus, catabolism, protein metabolism		nucleus -> nucleus
YER021W	RPN3	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity -> peptidase activity	proteasome regulatory particle (sensu Eukarya) -> cytoplasm, nucleus
YJR090C	GRR1	ubiquitin-dependent protein catabolism, G1/S transition of mitotic cell cycle -> catabolism, cell proliferation, protein metabolism	ubiquitin-protein ligase activity, protein binding -> ligase activity\, forming carbon-nitrogen bonds, protein binding	nuclear ubiquitin ligase complex, nucleus, cytoplasm, contractile ring (sensu Saccharomyces) -> nucleus, site of polarized growth (sensu Fungi), cell cortex, cytoplasm, ubiquitin ligase complex	REB1
YDL007W	RPT2	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	ATPase activity, endopeptidase activity -> purine nucleotide binding, peptidase activity, hydrolase activity\, acting on acid anhydrides	proteasome regulatory particle (sensu Eukarya) -> cytoplasm, nucleus	REB1
YOR362C	PRE10	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya) -> cytoplasm, nucleus
\|YKL160W\|	ELF1	cell growth -> cell growth
\|YOR339C\|	UBC11	protein polyubiquitination, protein monoubiquitination -> catabolism, protein metabolism	ubiquitin conjugating enzyme activity -> ubiquitin conjugating enzyme activity	cytoplasm -> cytoplasm	HAP2, IXR1
Main:		protein metabolism (0.49)	peptidase activity (0.36)	cytoplasm (0.82)	REB1 (0.28)
Score:		0.32	0.16	0.92	0.129
P-value:		4.128E-16 (ubiquitin-dependent protein catabolism)	4.363E-12 (endopeptidase activity)	8.639E-17 (proteasome complex (sensu Eukarya))	9.749E-04 (REB1)

ALPHA1(1) AND RPN4(1) => SimExpr(YGL201C) OR SimExpr(other) : 13 6

EXPR: (0.188) RPN4 (P < 0.477) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YGR135W	PRE9	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya) -> cytoplasm, nucleus	REB1, SKO1
\|YNL251C\|	NRD1	nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleus -> nucleus	ABF1, MAC1
\|YGR184C\|	UBR1	protein polyubiquitination, protein monoubiquitination -> catabolism, protein metabolism	ubiquitin-protein ligase activity -> ligase activity\, forming carbon-nitrogen bonds	proteasome complex (sensu Eukarya) -> cytoplasm, nucleus	HMS1, REB1, RIM101
YFR050C	PRE4	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya) -> cytoplasm, nucleus	MTH1, REB1
YGL201C	MCM6	DNA unwinding, DNA replication initiation -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	chromatin binding, ATP dependent DNA helicase activity -> DNA binding, adenyl nucleotide binding, hydrolase activity\, acting on acid anhydrides	cytoplasm, nucleus, pre-replicative complex -> cytoplasm, nucleus	MCM1
\|YJR015W\|	NO SYMBOL
YNL097C	PHO23	chromatin modification -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleus -> nucleus	MAC1
YGR124W	ASN2	asparagine biosynthesis -> amine metabolism, amino acid and derivative metabolism, organic acid metabolism, biosynthesis	asparagine synthase (glutamine-hydrolyzing) activity -> ligase activity\, forming carbon-nitrogen bonds		ASH1, ROX1
\|YGL096W\|	TOS8		transcription factor activity -> DNA binding		IXR1, SOK2, SWI4
YGL062W	PYC1	NADPH regeneration, gluconeogenesis -> coenzymes and prosthetic group metabolism, alcohol metabolism, carbohydrate metabolism, vitamin metabolism, biosynthesis, energy pathways	pyruvate carboxylase activity -> ligase activity\, forming carbon-carbon bonds	cytosol -> cytoplasm	DIG1, GCR1, STE12
\|YKL203C\|	TOR2	cytoskeleton organization and biogenesis, ribosome biogenesis, signal transduction, Rho protein signal transduction, regulation of cell cycle, G1 phase of mitotic cell cycle, cell cycle dependent actin filament reorganization -> cell organization and biogenesis, signal transduction, cell cycle, cytoplasm organization and biogenesis	phosphatidylinositol 3-kinase activity, protein binding -> transferase activity\, transferring phosphorus-containing groups, protein binding, lipid kinase activity	vacuolar membrane, plasma membrane -> cytoplasm, plasma membrane	BAS1, HIR1, REB1, RTG1
\|YGR060W\|	ERG25	ergosterol biosynthesis -> alcohol metabolism, biosynthesis, lipid metabolism	C-4 methyl sterol oxidase activity -> C-4 methyl sterol oxidase activity	endoplasmic reticulum membrane, plasma membrane -> cytoplasm, plasma membrane, endomembrane system	HSF1, MAL13, MET4, NDD1, SWI5
YKL145W	RPT1	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	ATPase activity, endopeptidase activity -> purine nucleotide binding, peptidase activity, hydrolase activity\, acting on acid anhydrides	proteasome regulatory particle (sensu Eukarya) -> cytoplasm, nucleus	REB1
YGR253C	PUP2	ubiquitin-dependent protein catabolism, response to stress, sporulation (sensu Saccharomyces) -> catabolism, response to stress, sporulation, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya) -> cytoplasm, nucleus	ABF1, HIR2, PHO4
YOR052C	NO SYMBOL
YDL126C	CDC48	ubiquitin-dependent protein catabolism, nonselective vesicle fusion, cell cycle, apoptosis, protein transport, ER-associated protein catabolism -> cell proliferation, cell death, macromolecule catabolism, transport, protein metabolism	ATPase activity -> purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleus, microsome, endoplasmic reticulum, cytosol -> nucleus, membrane fraction, cytoplasm	DAL82, MAL33, SWI4
YKL054C	DEF1	response to DNA damage, ubiquitin-dependent protein catabolism -> response to biotic stimulus, catabolism, protein metabolism		nucleus -> nucleus
YJR090C	GRR1	ubiquitin-dependent protein catabolism, G1/S transition of mitotic cell cycle -> catabolism, cell proliferation, protein metabolism	ubiquitin-protein ligase activity, protein binding -> ligase activity\, forming carbon-nitrogen bonds, protein binding	nuclear ubiquitin ligase complex, nucleus, cytoplasm, contractile ring (sensu Saccharomyces) -> nucleus, site of polarized growth (sensu Fungi), cell cortex, cytoplasm, ubiquitin ligase complex	REB1
YOR362C	PRE10	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya) -> cytoplasm, nucleus
Main:		protein metabolism (0.56)	peptidase activity (0.33)	cytoplasm (0.80)	REB1 (0.40)
Score:		0.38	0.17	0.91	0.171
P-value:		1.337E-08 (ubiquitin-dependent protein catabolism)	7.207E-05 (endopeptidase activity)	6.134E-07 (proteasome complex (sensu Eukarya))	1.378E-03 (REB1)

ALPHA1(1) AND LYS14(1) AND RPN4(1) => SimExpr(YGL201C) OR SimExpr(other) : 5 1

EXPR: (0.174) LYS14 (P < 0.001) RPN4 (P < 0.258) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YGL201C	MCM6	DNA unwinding, DNA replication initiation -> cell cycle, DNA metabolism	chromatin binding, ATP dependent DNA helicase activity -> chromatin binding, ATP dependent DNA helicase activity	cytoplasm, nucleus, pre-replicative complex -> cytoplasm, nucleus	MCM1
YNL097C	PHO23	chromatin modification -> nuclear organization and biogenesis, DNA metabolism		nucleus -> nucleus	MAC1
\|YGR060W\|	ERG25	ergosterol biosynthesis -> alcohol metabolism, lipid biosynthesis, steroid metabolism	C-4 methyl sterol oxidase activity -> C-4 methyl sterol oxidase activity	endoplasmic reticulum membrane, plasma membrane -> cytoplasm, plasma membrane, endomembrane system	HSF1, MAL13, MET4, NDD1, SWI5
YGR253C	PUP2	ubiquitin-dependent protein catabolism, response to stress, sporulation (sensu Saccharomyces) -> macromolecule catabolism, response to stress, sporulation (sensu Fungi), protein metabolism	endopeptidase activity -> endopeptidase activity	proteasome core complex (sensu Eukarya) -> cytoplasm, nucleus	ABF1, HIR2, PHO4
YOR052C	NO SYMBOL
YKL054C	DEF1	response to DNA damage, ubiquitin-dependent protein catabolism -> response to stress, macromolecule catabolism, protein metabolism		nucleus -> nucleus
Main:		DNA metabolism (0.40)	chromatin binding (0.33)	nucleus (0.80)	ABF1 (0.25)
Score:		0.20	0.00	0.80	0.000
P-value:		1.924E-01 (ubiquitin-dependent protein catabolism)	1.308E+00 (hydrolase activity)	4.424E-01 (endoplasmic reticulum)	6.578E-01 (MAL13)

ALPHA1'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YGL029W) OR SimExpr(other) : 35 6

ALPHA1(1) AND mRRPE(1) AND PAC(1) => SimExpr(YGL029W) OR SimExpr(other) : 19 3

EXPR: (0.162) mRRPE (P < 0.000) PAC (P < 0.015) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YPL266W	DIM1	rRNA modification, 35S primary transcript processing -> RNA processing, ribosome biogenesis and assembly, rRNA metabolism, transcription\, DNA-dependent	rRNA (adenine-N6\,N6-)-dimethyltransferase activity -> transferase activity\, transferring one-carbon groups	nucleolus -> nucleus	ARG81, STP2
\|YOR381W\|	FRE3	iron-siderochrome transport, iron ion homeostasis -> iron-siderochrome transport, cation homeostasis	ferric-chelate reductase activity -> oxidoreductase activity\, oxidizing metal ions	plasma membrane, integral to membrane -> plasma membrane, integral to membrane	CIN5, PDR1, YAP6
YMR229C	RRP5	rRNA processing, processing of 20S pre-rRNA -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent	RNA binding, snoRNA binding -> RNA binding	nucleolus, nucleolus organizer complex -> nucleus	FHL1, RAP1
YJR002W	MPP10	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> RNA processing, ribosome biogenesis and assembly, rRNA metabolism, transcription\, DNA-dependent		small nucleolar ribonucleoprotein complex, small nuclear ribonucleoprotein complex, nucleolus, nucleus -> nucleus, ribonucleoprotein complex
YFR001W	LOC1	ribosomal large subunit biogenesis -> ribosome biogenesis and assembly	mRNA binding -> RNA binding	nucleus -> nucleus	ARG80, GAL4, GTS1, HAP4, HIR1, LEU3, MSN2, MSN4, RCS1, RLM1, SWI4
\|YMR259C\|	NO SYMBOL				ARG80, GCR2, GTS1, HIR1, SRD1
YHR196W	UTP9	processing of 20S pre-rRNA -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex, nucleolus, nucleus -> nucleus, ribonucleoprotein complex
YJL109C	UTP10	processing of 20S pre-rRNA -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
YJL033W	HCA4	35S primary transcript processing -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent	ATP dependent RNA helicase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleus	HIR2, USV1
YNL075W	IMP4	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> RNA processing, ribosome biogenesis and assembly, rRNA metabolism, transcription\, DNA-dependent	rRNA primary transcript binding -> RNA binding	small nucleolar ribonucleoprotein complex, small nuclear ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	USV1
YOR095C	RKI1	pentose-phosphate shunt -> monosaccharide catabolism, main pathways of carbohydrate metabolism, oxidoreduction coenzyme metabolism, hexose metabolism, water-soluble vitamin metabolism	ribose-5-phosphate isomerase activity -> intramolecular isomerase activity		FHL1, FKH2, RAP1
YMR290C	HAS1			nucleolus, nuclear membrane -> nucleus, endomembrane system	RAP1
YHR169W	DBP8	35S primary transcript processing -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent	ATP dependent RNA helicase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleus
YLR249W	YEF3	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent		nucleolus -> nucleus
YKL056C	NO SYMBOL
YJR070C	NO SYMBOL				GAT3, YAP5
YMR131C	RRB1	ribosome biogenesis -> ribosome biogenesis and assembly		nucleolus -> nucleus	FZF1, MATa1, RGT1
\|YPR183W\|	DPM1	N-linked glycosylation, O-linked glycosylation, GPI anchor biosynthesis -> phospholipid biosynthesis, protein biosynthesis, glycerophospholipid metabolism, protein modification, glycoprotein 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
YJL069C	UTP18				ABF1
YMR239C	RNT1	35S primary transcript processing -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent	ribonuclease III activity -> hydrolase activity\, acting on ester bonds, RNA binding	nucleolus -> nucleus
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
Main:		ribosome biogenesis and assembly (0.75)	RNA binding (0.62)	nucleus (0.81)	RAP1 (0.20)
Score:		0.56	0.36	0.70	0.048
P-value:		1.227E-10 (ribosome biogenesis)	3.388E-03 (RNA binding)	3.803E-11 (nucleolus)	7.433E-01 (USV1)

MCM1(1) AND STRE(1) => SimExpr(YOL087C) OR SimExpr(other) : 5 1

ALPHA1(1) AND ALPHA1'(1) AND STRE(1) => SimExpr(YOL087C) OR SimExpr(other) : 5 2

EXPR: (0.177) ALPHA1' (P < 0.002) STRE (P < 0.035) ALPHA1 (P < 0.003)

ORF	SYMBOL	P	F	C	TF
YPR184W	GDB1	glycogen catabolism -> carbohydrate metabolism, energy derivation by oxidation of organic compounds, catabolism	4-alpha-glucanotransferase activity, amylo-1\,6-glucosidase activity -> transferase activity\, transferring hexosyl groups, hydrolase activity\, hydrolyzing O-glycosyl compounds		CIN5
YOL087C	NO SYMBOL				DAL82
\|YNL098C\|	RAS2	pseudohyphal growth, sporulation (sensu Saccharomyces), adenylate cyclase activation, RAS protein signal transduction -> cell organization and biogenesis, sporulation, signal transduction	RAS small monomeric GTPase activity -> guanyl nucleotide binding, hydrolase activity\, acting on acid anhydrides\, in phosphorus-containing anhydrides	plasma membrane -> plasma membrane	ACE2, SKN7
\|YIL052C\|	RPL34B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	RME1
YGL062W	PYC1	NADPH regeneration, gluconeogenesis -> coenzymes and prosthetic group metabolism, alcohol metabolism, carbohydrate metabolism, vitamin metabolism, biosynthesis, energy pathways	pyruvate carboxylase activity -> pyruvate carboxylase activity	cytosol -> cytoplasm	DIG1, GCR1, STE12
YKL035W	UGP1	protein amino acid glycosylation, UDP-glucose metabolism -> biosynthesis, alcohol metabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism, carbohydrate metabolism	UTP-glucose-1-phosphate uridylyltransferase activity -> nucleotidyltransferase activity
YFL036W	RPO41	mitochondrial genome maintenance, transcription from mitochondrial promoter -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	DNA-directed RNA polymerase activity -> nucleotidyltransferase activity	mitochondrial matrix -> cytoplasm
Main:		biosynthesis (0.50)	nucleotidyltransferase activity (0.33)	cytoplasm (0.75)	ACE2 (0.20)
Score:		0.47	0.07	0.50	0.000
P-value:		9.418E-02 (carbohydrate metabolism)	4.324E-02 (nucleotidyltransferase activity)	1.068E+00 (cytosol)	5.887E-01 (DAL82)

RAP1(1) AND MCM1'(1) => SimExpr(YGR085C) OR SimExpr(other) : 15 6

MIG1(1) AND ABF1(1) => SimExpr(YKR046C) OR SimExpr(other) : 7 2

EXPR: (0.171) ABF1 (P < 0.000) MIG1 (P < 0.005)

ORF	SYMBOL	P	F	C	TF
YNL138W	SRV2	cytoskeleton organization and biogenesis, RAS protein signal transduction -> cell organization and biogenesis, signal transduction	cytoskeletal protein binding, adenylate cyclase binding -> cytoskeletal protein binding, adenylate cyclase binding	actin cortical patch (sensu Saccharomyces) -> intracellular	ABF1
\|YMR280C\|	CAT8	gluconeogenesis, positive regulation of transcription from Pol II promoter -> alcohol metabolism, monosaccharide metabolism, carbohydrate metabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, biosynthesis, energy pathways	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> intracellular	ABF1, REB1
YOR317W	FAA1	N-terminal protein myristoylation, lipid metabolism, lipid transport -> biosynthesis, lipid metabolism, transport, protein metabolism	ligase activity -> ligase activity	lipid particle -> intracellular	ASH1, CIN5, HSF1, INO4, RAP1
YKR046C	PET10			lipid particle -> intracellular	ABF1
YAL016W	TPD3	protein biosynthesis, actin filament organization, mitotic spindle checkpoint, bud growth, protein amino acid dephosphorylation -> biosynthesis, cell organization and biogenesis, asexual reproduction, phosphorus metabolism, cell proliferation, cell cycle, protein metabolism	protein phosphatase type 2A activity -> protein phosphatase type 2A activity	protein phosphatase type 2A complex, bud neck, nucleus, cytoplasm, shmoo tip, bud tip, spindle pole body -> protein phosphatase type 2A complex, site of polarized growth (sensu Fungi), site of polarized growth (sensu Saccharomyces), intracellular	ABF1
YKL034W	TUL1	protein transport -> transport	ligase activity -> ligase activity	intracellular -> intracellular
YPL111W	CAR1	arginine catabolism to ornithine -> amine metabolism, nitrogen metabolism, amino acid and derivative metabolism, organic acid metabolism, catabolism	arginase activity -> arginase activity	cytosol -> intracellular	GCN4
YOR322C	NO SYMBOL				ABF1
\|YDL020C\|	RPN4	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity -> endopeptidase activity	proteasome regulatory particle (sensu Eukarya) -> intracellular	ABF1, CBF1, HSF1, PUT3, YAP1
Main:		biosynthesis (0.43)	ligase activity (0.29)	intracellular (1.00)	ABF1 (0.75)
Score:		0.38	0.05	1.00	0.571
P-value:		1.690E+00 (cytoskeleton organization and biogenesis)	1.516E-01 (ligase activity)	2.216E-02 (lipid particle)	7.301E-05 (ABF1)

ALPHA1(1) AND ALPHA1'(1) AND STRE(1) => SimExpr(YPR184W) OR SimExpr(other) : 5 2

MIG1(1) AND ABF1(1) => SimExpr(YAL016W) OR SimExpr(other) : 7 2

mRRPE(1) AND PAC(1) => SimExpr(YOR095C) OR SimExpr(other) : 57 19

mRRPE(1) AND PAC(1) AND MCM1'(1) => SimExpr(YOR095C) OR SimExpr(other) : 10 4

ALPHA1(1) AND mRRPE(1) AND PAC(1) => SimExpr(YOR095C) OR SimExpr(other) : 16 6

SFF(1) AND MCB(1) AND ATRepeat(1) => SimExpr(YPR185W) OR SimExpr(other) : 6 2

RAP1(1) AND SFF(1) AND SWI5(1) => SimExpr(YMR194W) OR SimExpr(other) : 10 4

EXPR: (0.169) SFF (P < 0.000) SWI5 (P < 0.000) RAP1 (P < 0.059)

ORF	SYMBOL	P	F	C	TF
YMR194W	RPL36A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	ARG80, ARO80, BAS1, CUP9, FHL1, HAL9, HAP4, HAP5, HMS1, MET31, NRG1, RAP1, RCS1, RME1, STP2
YKR092C	SRP40	nucleocytoplasmic transport -> nucleocytoplasmic transport	chaperone activity -> chaperone activity	nucleolus -> nucleus	CUP9, MET4, RAP1
YLR441C	RPS1A	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, RAP1, YAP5
\|YMR224C\|	MRE11	DNA repair, double-strand break repair via nonhomologous end-joining, meiotic DNA double-strand break formation, meiotic DNA double-strand break processing, double-strand break repair via break-induced replication -> mitotic recombination, M phase, DNA catabolism, DNA recombination, DNA repair	endonuclease activity, 3'-5' exonuclease activity, protein binding -> endonuclease activity, 3'-5' exonuclease activity, protein binding	nucleus -> nucleus	RAP1
YNL069C	RPL16B	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, YAP5
YLR344W	RPL26A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YOR312C	RPL20B	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, FKH2, GAT3, RAP1
YJR145C	RPS4A	protein biosynthesis -> protein biosynthesis	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
YLR249W	YEF3	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
\|YGL115W\|	SNF4	regulation of transcription from Pol II promoter, peroxisome organization and biogenesis -> regulation of transcription, organelle organization and biogenesis, transcription\, DNA-dependent	protein kinase activator activity -> protein kinase activator activity	plasma membrane, nucleus, cytoplasm -> plasma membrane, nucleus, cytoplasm	BAS1, CAD1, MAC1, NRG1, PDR1, RAP1, SMP1, YAP5
\|YJL217W\|	NO SYMBOL				CIN5, MAC1, PHD1, SWI5, YAP6
\|YLR452C\|	SST2	signal transduction, adaptation to pheromone during conjugation with cellular fusion -> signal transduction, conjugation with cellular fusion, perception of chemical substance, sensory perception	GTPase activator activity -> GTPase activator activity	plasma membrane -> plasma membrane	DIG1, FHL1, RAP1, STE12
YOR369C	RPS12	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	ARG80, FHL1, FKH2, LEU3, NDD1, PDR1, RME1, SMP1, YAP6
YKL006W	RPL14A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, GRF10(Pho2), GTS1, RAP1
Main:		protein biosynthesis (0.69)	structural constituent of ribosome (0.62)	cytoplasm (0.77)	RAP1 (0.79)
Score:		0.46	0.36	0.63	0.747
P-value:		3.886E-05 (protein biosynthesis)	2.931E-06 (structural constituent of ribosome)	4.999E-07 (cytosolic ribosome (sensu Eukarya))	3.510E-10 (RAP1)

RAP1(1) AND ALPHA1'(1) AND SCB(1) => SimExpr(YMR194W) : 6

RAP1(1) AND PAC(1) => SimExpr(YGR283C) : 5

EXPR: (0.145) PAC (P < 0.008) RAP1 (P < 0.004)

ORF	SYMBOL	P	F	C	TF
YMR014W	BUD22	bud site selection -> cytokinesis, cytoplasm organization and biogenesis		nucleus -> nucleus	CUP9, HAL9, HIR2, LEU3, NDD1, RLM1, ROX1, SMP1, YAP6
YGR283C	NO SYMBOL				ACE2, RAP1, SMP1
YKR092C	SRP40	nucleocytoplasmic transport -> intracellular transport	chaperone activity -> chaperone activity	nucleolus -> nucleus	CUP9, MET4, RAP1
YLR249W	YEF3	translational elongation -> macromolecule biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
YDR449C	UTP6	processing of 20S pre-rRNA -> cytoplasm organization and biogenesis, RNA metabolism, transcription	snoRNA binding -> snoRNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	FHL1, GAT3, HIR2, RAP1, RGM1, YAP5
Main:		cytoplasm organization and biogenesis (0.50)	translation elongation factor activity (0.33)	nucleus (0.75)	RAP1 (0.60)
Score:		0.17	0.00	0.67	0.600
P-value:		1.792E+00 (cytoplasm organization and biogenesis)	8.180E-01 (nucleic acid binding)	1.067E-01 (nucleolus)	3.225E-02 (HIR2)

RAP1(1) AND SFF(1) AND SWI5(1) => SimExpr(YOR369C) OR SimExpr(other) : 10 4

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

RAP1(1) AND ALPHA1'(1) AND SCB(1) => SimExpr(YOR369C) : 6

RAP1(1) AND MCM1'(1) => SimExpr(YDL130W) OR SimExpr(other) : 15 6

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

RAP1(1) AND SFF'(1) AND SCB(1) => SimExpr(YPL131W) OR SimExpr(other) : 7 3

EXPR: (0.160) SFF' (P < 0.000) SCB (P < 0.000) RAP1 (P < 0.170)

ORF	SYMBOL	P	F	C	TF
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
\|YOL160W\|	NO SYMBOL				ARO80, NRG1, PHO4, RLM1, SIP4, SWI6
YNL024C	NO SYMBOL				GRF10(Pho2)
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
\|YPL189W\|	GUP2			membrane -> membrane	RFX1
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
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
YLR249W	YEF3	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation elongation factor activity	ribosome -> ribosome	INO2, INO4
\|YGR260W\|	TNA1	nicotinamide mononucleotide transport -> nicotinamide mononucleotide transport	nicotinamide mononucleotide permease activity -> nicotinamide mononucleotide permease activity	integral to plasma membrane -> membrane	HIR2, SUM1
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
Main:		protein biosynthesis (0.86)	structural constituent of ribosome (0.71)	ribosome (0.75)	FHL1 (0.50)
Score:		0.71	0.48	0.57	0.244
P-value:		4.861E-03 (protein biosynthesis)	1.080E-03 (structural constituent of ribosome)	4.143E-04 (ribosome)	1.468E-04 (FHL1)

RAP1(1) AND SFF(1) AND SCB(1) => SimExpr(YPL131W) OR SimExpr(other) : 7 2

EXPR: (0.152) SFF (P < 0.000) SCB (P < 0.000) RAP1 (P < 0.136)

ORF	SYMBOL	P	F	C	TF
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
\|YOL160W\|	NO SYMBOL				ARO80, NRG1, PHO4, RLM1, SIP4, SWI6
YNL024C	NO SYMBOL				GRF10(Pho2)
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
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
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
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
\|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
Main:		protein metabolism (1.00)	structural constituent of ribosome (0.83)	cytoplasm (1.00)	FHL1 (0.62)
Score:		1.00	0.67	1.00	0.393
P-value:		2.149E-03 (protein biosynthesis)	5.672E-04 (structural constituent of ribosome)	1.623E-04 (ribosome)	6.829E-05 (FHL1)

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

EXPR: (0.116) ALPHA1' (P < 0.000) SFF (P < 0.000) SCB (P < 0.000) RAP1 (P < 0.042)

ORF	SYMBOL	P	F	C	TF
YMR194W	RPL36A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), large ribosomal subunit	ARG80, ARO80, BAS1, CUP9, FHL1, HAL9, HAP4, HAP5, HMS1, MET31, NRG1, RAP1, RCS1, RME1, STP2
YNL024C	NO SYMBOL				GRF10(Pho2)
YPL131W	RPL5	protein biosynthesis, ribosomal large subunit assembly and maintenance -> protein biosynthesis, ribosomal large subunit assembly and maintenance	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), large ribosomal subunit	FHL1, GAT3, RAP1
YLR344W	RPL26A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), large ribosomal subunit	FHL1, RAP1
YOR369C	RPS12	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, small ribosomal subunit	ARG80, FHL1, FKH2, LEU3, NDD1, PDR1, RME1, SMP1, YAP6
Main:		protein biosynthesis (1.00)	structural constituent of ribosome (1.00)	cytosolic ribosome (sensu Eukarya) (1.00)	FHL1 (0.80)
Score:		1.00	1.00	1.00	0.600
P-value:		6.205E-03 (protein biosynthesis)	4.455E-04 (structural constituent of ribosome)	2.052E-04 (cytosolic ribosome (sensu Eukarya))	7.961E-05 (FHL1)

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

EXPR: (0.116) ALPHA1' (P < 0.000) SFF' (P < 0.000) SCB (P < 0.000) RAP1 (P < 0.043)

ORF	SYMBOL	P	F	C	TF
YMR194W	RPL36A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), large ribosomal subunit	ARG80, ARO80, BAS1, CUP9, FHL1, HAL9, HAP4, HAP5, HMS1, MET31, NRG1, RAP1, RCS1, RME1, STP2
YNL024C	NO SYMBOL				GRF10(Pho2)
YPL131W	RPL5	protein biosynthesis, ribosomal large subunit assembly and maintenance -> protein biosynthesis, ribosomal large subunit assembly and maintenance	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), large ribosomal subunit	FHL1, GAT3, RAP1
YLR344W	RPL26A	protein biosynthesis -> protein biosynthesis	RNA binding, structural constituent of ribosome -> RNA binding, structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), large ribosomal subunit	FHL1, RAP1
YOR369C	RPS12	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> cytosolic ribosome (sensu Eukarya), eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, small ribosomal subunit	ARG80, FHL1, FKH2, LEU3, NDD1, PDR1, RME1, SMP1, YAP6
Main:		protein biosynthesis (1.00)	structural constituent of ribosome (1.00)	cytosolic ribosome (sensu Eukarya) (1.00)	FHL1 (0.80)
Score:		1.00	1.00	1.00	0.600
P-value:		6.205E-03 (protein biosynthesis)	4.455E-04 (structural constituent of ribosome)	2.052E-04 (cytosolic ribosome (sensu Eukarya))	7.961E-05 (FHL1)

RAP1(1) AND ALPHA1'(1) AND SCB(1) => SimExpr(YNL024C) : 6

RAP1(1) AND MCM1'(1) => SimExpr(YKL006W) OR SimExpr(other) : 15 6

ALPHA2(1) AND mRRPE(1) AND PAC(1) => SimExpr(YLR249W) OR SimExpr(other) : 7 2

EXPR: (0.135) ALPHA2 (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.009)

ORF	SYMBOL	P	F	C	TF
YKL172W	EBP2	rRNA processing -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent		nucleolus -> nucleus	ABF1, FZF1, RFX1
\|YJL033W\|	HCA4	35S primary transcript processing -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent	ATP dependent RNA helicase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleus	HIR2, USV1
YMR049C	ERB1	rRNA processing -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent			RTG3
YLR249W	YEF3	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent		nucleolus -> nucleus
YJR070C	NO SYMBOL				GAT3, YAP5
YLR222C	UTP13	processing of 20S pre-rRNA -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1
\|YPR183W\|	DPM1	N-linked glycosylation, O-linked glycosylation, GPI anchor biosynthesis -> phospholipid biosynthesis, protein biosynthesis, glycerophospholipid metabolism, protein modification, glycoprotein 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
YNR046W	NO SYMBOL				ABF1
Main:		RNA processing (0.71)	RNA binding (0.50)	nucleus (0.67)	ABF1 (0.38)
Score:		0.52	0.17	0.53	0.107
P-value:		5.052E-05 (rRNA processing)	9.380E-01 (RNA binding)	2.195E-03 (nucleolus)	2.138E-01 (ABF1)

RAP1(1) AND SFF(1) AND SWI5(1) => SimExpr(YLR249W) OR SimExpr(other) : 10 4

RAP1(1) AND ALPHA1'(1) AND SCB(1) => SimExpr(YPR080W) OR SimExpr(other) : 5 1

RPN4(1) => SimExpr(YDL126C) OR SimExpr(other) : 35 17

LYS14(1) AND mRRPE(1) AND PAC(1) => SimExpr(YMR290C) OR SimExpr(other) : 7 1

SFF'(1) AND STE12(1) AND PAC(1) => SimExpr(YJL069C) OR SimExpr(other) : 5 1

ALPHA1(1) AND RPN4(1) => SimExpr(YOR052C) OR SimExpr(other) : 13 6

mRRPE(1) AND SWI5(1) AND PAC(1) AND SCB(1) => SimExpr(YJL109C) OR SimExpr(other) : 5 1

ALPHA1(1) AND ALPHA1'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YJL109C) OR SimExpr(other) : 9 4

EXPR: (0.192) ALPHA1' (P < 0.000) mRRPE (P < 0.002) PAC (P < 0.024) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
\|YOR381W\|	FRE3	iron-siderochrome transport, iron ion homeostasis -> iron-siderochrome transport, di-\, tri-valent inorganic cation homeostasis, metal ion homeostasis	ferric-chelate reductase activity -> oxidoreductase activity\, oxidizing metal ions	plasma membrane, integral to membrane -> plasma membrane, integral to membrane	CIN5, PDR1, YAP6
YMR229C	RRP5	rRNA processing, processing of 20S pre-rRNA -> ribosome biogenesis, RNA processing, transcription from Pol I promoter	RNA binding, snoRNA binding -> RNA binding	nucleolus, nucleolus organizer complex -> nucleus	FHL1, RAP1
\|YFR001W\|	LOC1	ribosomal large subunit biogenesis -> ribosome biogenesis	mRNA binding -> RNA binding	nucleus -> nucleus	ARG80, GAL4, GTS1, HAP4, HIR1, LEU3, MSN2, MSN4, RCS1, RLM1, SWI4
\|YHR196W\|	UTP9	processing of 20S pre-rRNA -> ribosome biogenesis, RNA processing, transcription from Pol I promoter	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex, nucleolus, nucleus -> nucleus, ribonucleoprotein complex
YJL109C	UTP10	processing of 20S pre-rRNA -> ribosome biogenesis, RNA processing, transcription from Pol I promoter	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex
YJL033W	HCA4	35S primary transcript processing -> ribosome biogenesis, RNA processing, transcription from Pol I promoter	ATP dependent RNA helicase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleus	HIR2, USV1
YNL075W	IMP4	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> RNA modification, ribosome biogenesis, rRNA metabolism, RNA processing, transcription from Pol I promoter	rRNA primary transcript binding -> RNA binding	small nucleolar ribonucleoprotein complex, small nuclear ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	USV1
YOR095C	RKI1	pentose-phosphate shunt -> hexose catabolism, main pathways of carbohydrate metabolism, pyridine nucleotide metabolism, glucose metabolism	ribose-5-phosphate isomerase activity -> intramolecular isomerase activity		FHL1, FKH2, RAP1
YHR169W	DBP8	35S primary transcript processing -> ribosome biogenesis, RNA processing, transcription from Pol I promoter	ATP dependent RNA helicase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleus
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis, RNA processing, transcription from Pol I promoter		nucleolus -> nucleus
YJR070C	NO SYMBOL				GAT3, YAP5
\|YPR183W\|	DPM1	N-linked glycosylation, O-linked glycosylation, GPI anchor biosynthesis -> glycoprotein biosynthesis, glycerophospholipid biosynthesis, lipoprotein biosynthesis, glycerophospholipid metabolism, protein modification	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
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
Main:		ribosome biogenesis (0.73)	RNA binding (0.70)	nucleus (0.80)	USV1 RAP1 FHL1 (0.22)
Score:		0.51	0.47	0.62	0.056
P-value:		1.250E-07 (ribosome biogenesis)	4.011E-04 (RNA binding)	1.704E-06 (nucleolus)	1.899E-01 (USV1)

ALPHA1(1) AND RPN4(1) => SimExpr(YKL145W) OR SimExpr(other) : 13 6

ALPHA1'(1) AND GCN4(1) AND SCB(1) => SimExpr(YDR473C) OR SimExpr(other) : 5 2

EXPR: (0.175) ALPHA1' (P < 0.000) GCN4 (P < 0.028) SCB (P < 0.002)

ORF	SYMBOL	P	F	C	TF
YFL028C	CAF16	regulation of transcription\, DNA-dependent -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ATP-binding cassette (ABC) transporter activity -> ATP-binding cassette (ABC) transporter activity	CCR4-NOT complex, cytoplasm -> nucleus, cytoplasm
YFR028C	CDC14	DNA dependent DNA replication, protein amino acid dephosphorylation, regulation of exit from mitosis -> phosphorus metabolism, cell cycle, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	protein phosphatase activity -> protein phosphatase activity	nucleus, spindle pole body, nucleolus -> cytoplasm, nucleus, microtubule organizing center
\|YMR300C\|	ADE4	purine base metabolism -> aromatic compound metabolism, heterocycle metabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	amidophosphoribosyltransferase activity -> amidophosphoribosyltransferase activity		BAS1
YDR473C	PRP3	mRNA splicing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pre-mRNA splicing factor activity -> pre-mRNA splicing factor activity	small nuclear ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ARG80, ARG81, DOT6, FZF1, GCR2, HAP4, HAP5, NRG1, RIM101, RLM1, RTG1, RTG3, SFP1, SRD1, STP1, THI2
YLR271W	NO SYMBOL
YKL211C	TRP3	tryptophan biosynthesis -> amine metabolism, aromatic compound biosynthesis, aromatic compound metabolism, amino acid and derivative metabolism, biosynthesis, organic acid metabolism, heterocycle metabolism	anthranilate synthase activity, indole-3-glycerol-phosphate synthase activity -> anthranilate synthase activity, indole-3-glycerol-phosphate synthase activity		CRZ1
\|YPR145W\|	ASN1	asparagine biosynthesis -> amine metabolism, amino acid and derivative metabolism, organic acid metabolism, biosynthesis	asparagine synthase (glutamine-hydrolyzing) activity -> asparagine synthase (glutamine-hydrolyzing) activity		DAL81, GCN4, GLN3, MET4, RAP1, SUM1
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.67)	pre-mRNA splicing factor activity (0.17)	nucleus (1.00)	GCR2 (0.25)
Score:		0.53	0.00	1.00	0.000
P-value:		4.613E-02 (aromatic compound metabolism)	1.306E+00 (enzyme activity)	2.826E+00 (nucleus)	1.000E+00

ALPHA1(1) AND RPN4(1) => SimExpr(YNL097C) OR SimExpr(other) : 14 5

LYS14(1) AND ALPHA1'(1) AND PAC(1) => SimExpr(YJR070C) OR SimExpr(other) : 6 2

EXPR: (0.181) LYS14 (P < 0.000) ALPHA1' (P < 0.000) PAC (P < 0.139)

ORF	SYMBOL	P	F	C	TF
YGR191W	HIP1	manganese ion transport, histidine transport -> transport, organic acid transport	histidine transporter activity -> carboxylic acid transporter activity	plasma membrane -> plasma membrane	GLN3, HAP3, HIR2, MBP1, MCM1, REB1, YAP1
\|YGR178C\|	PBP1	mRNA polyadenylation -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		cytoplasm, nucleus -> cytoplasm, nucleus	CIN5, DOT6, MSS11
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
YDR361C	BCP1				ABF1, ARO80, GLN3, HAP5, IXR1, YAP1
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
\|YOL075C\|	NO SYMBOL				CRZ1, DAL82, SIP4
YJR070C	NO SYMBOL				GAT3, 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
Main:		cell organization and biogenesis (0.60)	RNA binding (0.50)	nucleus (0.60)	YAP1 GLN3 (0.33)
Score:		0.60	0.17	0.40	0.067
P-value:		6.030E-02 (ribosome biogenesis)	6.400E-01 (RNA binding)	2.761E-01 (nucleolus)	9.199E-02 (GLN3)

ALPHA2(1) AND ALPHA1'(1) AND PAC(1) => SimExpr(YLR222C) OR SimExpr(other) : 5 2

EXPR: (0.165) ALPHA2 (P < 0.000) ALPHA1' (P < 0.000) PAC (P < 0.120)

ORF	SYMBOL	P	F	C	TF
YJL033W	HCA4	35S primary transcript processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ATP dependent RNA helicase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleus	HIR2, USV1
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 -> nucleus
YJR070C	NO SYMBOL				GAT3, YAP5
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
\|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
\|YPL106C\|	SSE1	protein folding -> protein metabolism	co-chaperone activity -> co-chaperone activity	cytoplasm -> cytoplasm	HSF1, MSN4
Main:		cell organization and biogenesis (0.67)	RNA binding (0.50)	nucleus (0.60)	ABF1 (0.17)
Score:		0.47	0.17	0.40	0.000
P-value:		4.417E-04 (rRNA processing)	6.066E-01 (RNA binding)	1.424E-02 (nucleolus)	6.376E-01 (USV1)

ALPHA2(1) AND ALPHA1'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YLR222C) OR SimExpr(other) : 5 1

EXPR: (0.146) ALPHA2 (P < 0.000) ALPHA1' (P < 0.000) mRRPE (P < 0.004) PAC (P < 0.028)

ORF	SYMBOL	P	F	C	TF
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
YMR049C	ERB1	rRNA processing -> rRNA processing			RTG3
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis, rRNA processing		nucleolus -> nucleolus
YJR070C	NO SYMBOL				GAT3, YAP5
YLR222C	UTP13	processing of 20S pre-rRNA -> rRNA processing	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleolus, ribonucleoprotein complex	ABF1
\|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
Main:		rRNA processing (0.80)	RNA binding (0.67)	nucleolus (0.75)	ABF1 (0.20)
Score:		0.60	0.33	0.50	0.000
P-value:		1.829E-04 (rRNA processing)	4.564E-01 (RNA binding)	7.182E-03 (nucleolus)	4.272E-01 (USV1)

ABF1(1) AND PAC(1) => SimExpr(YNR046W) OR SimExpr(other) : 12 3

ABF1(1) AND mRRPE(1) AND PAC(1) => SimExpr(YNR046W) OR SimExpr(other) : 9 1

EXPR: (0.132) ABF1 (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.002)

ORF	SYMBOL	P	F	C	TF
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
YNL292W	PUS4	tRNA modification -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pseudouridylate synthase activity -> pseudouridylate synthase activity	mitochondrion, nucleus -> cytoplasm, nucleus	RCS1
YNL112W	DBP2		RNA helicase activity -> RNA helicase activity	bud neck -> site of polarized growth (sensu Fungi)
YKL014C	NO SYMBOL				ABF1
YKL172W	EBP2	rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus	ABF1, FZF1, RFX1
YLR197W	SIK1	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex, nucleus, nucleolus -> nucleus, ribonucleoprotein complex	DAL81, HAL9
YGR187C	HGH1				ABF1, HAP3, HIR1, RCS1, RTG1
YJL050W	MTR4	35S primary transcript processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ATP dependent RNA helicase activity -> RNA helicase activity, ATP dependent helicase activity, RNA dependent ATPase activity	nucleolus -> nucleus
\|YJL069C\|	UTP18				ABF1
YNR046W	NO SYMBOL				ABF1
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (1.00)	RNA helicase activity (0.50)	nucleus (0.83)	ABF1 (0.62)
Score:		1.00	0.17	0.67	0.393
P-value:		5.162E-03 (transcription from Pol I promoter)	4.041E-02 (RNA helicase activity)	2.661E-03 (nucleolus)	2.954E-03 (ABF1)

ALPHA2(1) AND RPN4(1) => SimExpr(YOL038W) OR SimExpr(other) : 7 2

EXPR: (0.179) ALPHA2 (P < 0.002) RPN4 (P < 0.490)

ORF	SYMBOL	P	F	C	TF
YGR184C	UBR1	protein polyubiquitination, protein monoubiquitination -> ubiquitin-dependent protein catabolism, protein modification	ubiquitin-protein ligase activity -> ubiquitin-protein ligase activity	proteasome complex (sensu Eukarya) -> cytosol, endoplasmic reticulum, nucleus	HMS1, REB1, RIM101
YOR097C	NO SYMBOL
\|YJL045W\|	NO SYMBOL				MBP1, ROX1
YGL096W	TOS8		transcription factor activity -> transcription factor activity		IXR1, SOK2, SWI4
YOL038W	PRE6	ubiquitin-dependent protein catabolism -> ubiquitin-dependent protein catabolism	endopeptidase activity -> endopeptidase activity	proteasome core complex (sensu Eukarya) -> cytosol, endoplasmic reticulum, nucleus
\|YGR060W\|	ERG25	ergosterol biosynthesis -> ergosterol biosynthesis	C-4 methyl sterol oxidase activity -> C-4 methyl sterol oxidase activity	endoplasmic reticulum membrane, plasma membrane -> endoplasmic reticulum, plasma membrane, nuclear envelope-endoplasmic reticulum network	HSF1, MAL13, MET4, NDD1, SWI5
YHR027C	RPN1	ubiquitin-dependent protein catabolism -> ubiquitin-dependent protein catabolism	endopeptidase activity, receptor activity -> endopeptidase activity, receptor activity	proteasome regulatory particle (sensu Eukarya), endoplasmic reticulum, cytoplasm -> cytosol, endoplasmic reticulum, cytoplasm, nucleus
YDL126C	CDC48	ubiquitin-dependent protein catabolism, nonselective vesicle fusion, cell cycle, apoptosis, protein transport, ER-associated protein catabolism -> ubiquitin-dependent protein catabolism, nonselective vesicle fusion, cell cycle, apoptosis, protein transport, misfolded or incompletely synthesized protein catabolism	ATPase activity -> ATPase activity	nucleus, microsome, endoplasmic reticulum, cytosol -> nucleus, vesicular fraction, endoplasmic reticulum, cytosol	DAL82, MAL33, SWI4
YKL054C	DEF1	response to DNA damage, ubiquitin-dependent protein catabolism -> response to DNA damage, ubiquitin-dependent protein catabolism		nucleus -> nucleus
Main:		ubiquitin-dependent protein catabolism (0.83)	endopeptidase activity (0.33)	endoplasmic reticulum (0.83)	SWI4 (0.40)
Score:		0.67	0.07	0.93	0.100
P-value:		2.376E-05 (ubiquitin-dependent protein catabolism)	4.572E-02 (endopeptidase activity)	1.385E-03 (proteasome complex (sensu Eukarya))	7.177E-01 (MAL33)

ALPHA2(1) AND SFF(1) AND RPN4(1) => SimExpr(YOL038W) : 6

EXPR: (0.151) ALPHA2 (P < 0.000) SFF (P < 0.000) RPN4 (P < 0.112)

ORF	SYMBOL	P	F	C	TF
YGR184C	UBR1	protein polyubiquitination, protein monoubiquitination -> ubiquitin-dependent protein catabolism, protein modification	ubiquitin-protein ligase activity -> ubiquitin-protein ligase activity	proteasome complex (sensu Eukarya) -> cytosol, endoplasmic reticulum, nucleus	HMS1, REB1, RIM101
YOR097C	NO SYMBOL
YGL096W	TOS8		transcription factor activity -> transcription factor activity		IXR1, SOK2, SWI4
YOL038W	PRE6	ubiquitin-dependent protein catabolism -> ubiquitin-dependent protein catabolism	endopeptidase activity -> endopeptidase activity	proteasome core complex (sensu Eukarya) -> cytosol, endoplasmic reticulum, nucleus
YDL126C	CDC48	ubiquitin-dependent protein catabolism, nonselective vesicle fusion, cell cycle, apoptosis, protein transport, ER-associated protein catabolism -> ubiquitin-dependent protein catabolism, nonselective vesicle fusion, cell cycle, apoptosis, protein transport, misfolded or incompletely synthesized protein catabolism	ATPase activity -> ATPase activity	nucleus, microsome, endoplasmic reticulum, cytosol -> nucleus, vesicular fraction, endoplasmic reticulum, cytosol	DAL82, MAL33, SWI4
YKL054C	DEF1	response to DNA damage, ubiquitin-dependent protein catabolism -> response to DNA damage, ubiquitin-dependent protein catabolism		nucleus -> nucleus
Main:		ubiquitin-dependent protein catabolism (1.00)	transcription factor activity (0.25)	nucleus (1.00)	SWI4 (0.67)
Score:		1.00	0.00	1.00	0.333
P-value:		1.086E-04 (ubiquitin-dependent protein catabolism)	1.635E+00 (hydrolase activity)	2.147E-02 (proteasome complex (sensu Eukarya))	1.888E-01 (SWI4)

RPN4(1) => SimExpr(YHR027C) OR SimExpr(other) : 35 17

ABF1(1) AND RPN4(1) => SimExpr(YHR027C) OR SimExpr(other) : 5 2

ABF1(1) AND PAC(1) => SimExpr(YKL172W) OR SimExpr(other) : 13 2

ABF1(1) AND mRRPE(1) AND PAC(1) => SimExpr(YKL172W) : 10

ABF1(1) AND ALPHA1'(1) AND PAC(1) => SimExpr(YKL014C) : 5

ABF1(1) AND STE12(1) => SimExpr(YFL008W) OR SimExpr(other) : 5 1

EXPR: (0.153) ABF1 (P < 0.001) STE12 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YLR429W	CRN1	actin filament organization, microtubule-based process -> cytoplasm organization and biogenesis	actin cross-linking activity, microtubule binding -> protein binding	actin cortical patch (sensu Saccharomyces) -> cell cortex, cytoplasm
YDR303C	RSC3	regulation of transcription\, DNA-dependent, regulation of cell cycle -> cell cycle, transcription	DNA binding -> DNA binding	RSC complex, nucleus -> nucleus
YNL258C	DSL1	retrograde (Golgi to ER) transport -> secretory pathway, vesicle-mediated transport		endoplasmic reticulum -> cytoplasm	ABF1, ARG80, HAP5, YJL206C
\|YJL069C\|	UTP18				ABF1
YFL008W	SMC1	mitotic chromosome segregation -> cell cycle, mitotic cell cycle	DNA secondary structure binding, AT DNA binding, double-stranded DNA binding, ATPase activity -> DNA binding, double-stranded DNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nuclear cohesin complex -> chromosome, nucleus	MBP1
YKL022C	CDC16	mitotic spindle elongation, ubiquitin-dependent protein catabolism, mitotic metaphase/anaphase transition, mitotic chromosome segregation, cyclin catabolism -> cytoplasm organization and biogenesis, macromolecule catabolism, cell cycle, M phase, mitotic cell cycle, protein metabolism	ubiquitin-protein ligase activity, protein binding -> ligase activity\, forming carbon-nitrogen bonds, protein binding	anaphase-promoting complex -> nucleus, ubiquitin ligase complex	AZF1
Main:		cell cycle (0.60)	protein binding (0.50)	nucleus (0.60)	ABF1 (0.50)
Score:		0.40	0.33	0.40	0.167
P-value:		1.792E-02 (mitotic chromosome segregation)	3.414E-01 (protein binding)	2.133E+00 (nucleus)	3.489E-01 (ABF1)

mRRPE(1) AND PAC(1) => SimExpr(YLR197W) OR SimExpr(other) : 60 16

LYS14(1) AND mRRPE(1) AND PAC(1) => SimExpr(YML093W) OR SimExpr(other) : 7 1

LYS14(1) AND mRRPE(1) AND PAC(1) => SimExpr(YHR052W) OR SimExpr(other) : 7 1

SFF'(1) AND SWI5(1) AND Yap1(1) => SimExpr(YOR173W) OR SimExpr(other) : 5 2

EXPR: (0.151) SFF' (P < 0.000) SWI5 (P < 0.000) Yap1 (P < 0.008)

ORF	SYMBOL	P	F	C	TF
YPL091W	GLR1	response to oxidative stress -> response to oxidative stress	glutathione reductase (NADPH) activity -> glutathione reductase (NADPH) activity
YOR173W	DCS2				CAD1
\|YFL056C\|	AAD6	aldehyde metabolism -> aldehyde metabolism	benzyl alcohol dehydrogenase activity -> benzyl alcohol dehydrogenase activity		ACE2, YAP1
YFR014C	CMK1	protein amino acid phosphorylation, signal transduction -> protein amino acid phosphorylation, signal transduction	calmodulin-dependent protein kinase I activity -> calmodulin-dependent protein kinase I activity	cytoplasm -> cytoplasm	USV1
YOL048C	NO SYMBOL				SKN7
YDR453C	TSA2	regulation of redox homeostasis -> regulation of redox homeostasis	thioredoxin peroxidase activity -> thioredoxin peroxidase activity	nucleus -> nucleus	SWI4
\|YPR005C\|	HAL1	salinity response, transcription initiation from Pol II promoter -> salinity response, transcription initiation from Pol II promoter		cytoplasm -> cytoplasm	CIN5
Main:		signal transduction (0.20)	calmodulin-dependent protein kinase I activity (0.25)	cytoplasm (0.67)	SWI4 (0.17)
Score:		0.00	0.00	0.33	0.000
P-value:		3.521E-01 (response to stress)	4.856E-02 (oxidoreductase activity)	4.860E+00 (cytoplasm)	4.959E-01 (USV1)

SFF(1) AND SWI5(1) AND Yap1(1) => SimExpr(YOR173W) OR SimExpr(other) : 5 2

EXPR: (0.151) SFF (P < 0.000) SWI5 (P < 0.000) Yap1 (P < 0.010)

ORF	SYMBOL	P	F	C	TF
YPL091W	GLR1	response to oxidative stress -> response to oxidative stress	glutathione reductase (NADPH) activity -> glutathione reductase (NADPH) activity
YOR173W	DCS2				CAD1
\|YFL056C\|	AAD6	aldehyde metabolism -> aldehyde metabolism	benzyl alcohol dehydrogenase activity -> benzyl alcohol dehydrogenase activity		ACE2, YAP1
YFR014C	CMK1	protein amino acid phosphorylation, signal transduction -> protein amino acid phosphorylation, signal transduction	calmodulin-dependent protein kinase I activity -> calmodulin-dependent protein kinase I activity	cytoplasm -> cytoplasm	USV1
YOL048C	NO SYMBOL				SKN7
YDR453C	TSA2	regulation of redox homeostasis -> regulation of redox homeostasis	thioredoxin peroxidase activity -> thioredoxin peroxidase activity	nucleus -> nucleus	SWI4
\|YPR005C\|	HAL1	salinity response, transcription initiation from Pol II promoter -> salinity response, transcription initiation from Pol II promoter		cytoplasm -> cytoplasm	CIN5
Main:		signal transduction (0.20)	calmodulin-dependent protein kinase I activity (0.25)	cytoplasm (0.67)	SWI4 (0.17)
Score:		0.00	0.00	0.33	0.000
P-value:		3.521E-01 (response to stress)	4.856E-02 (oxidoreductase activity)	4.860E+00 (cytoplasm)	4.959E-01 (USV1)

ALPHA1'(1) AND BAS1(1) AND STE12(1) => SimExpr(YJL005W) OR SimExpr(other) : 5 2

EXPR: (0.186) ALPHA1' (P < 0.004) BAS1 (P < 0.024) STE12 (P < 0.005)

ORF	SYMBOL	P	F	C	TF
YJL005W	CYR1	meiosis, G-protein signaling\, coupled to cAMP nucleotide second messenger, RAS protein signal transduction, regulation of cell cycle -> nuclear division, G-protein coupled receptor protein signaling pathway, RAS protein signal transduction, regulation of cell cycle, cyclic-nucleotide-mediated signaling	adenylate cyclase activity -> adenylate cyclase activity	plasma membrane -> plasma membrane
YMR019W	STB4		DNA binding -> DNA binding	nucleus -> nucleus	PHD1, SKN7, SWI4
\|YPR015C\|	NO SYMBOL
YLR328W	NMA1	nicotinamide adenine dinucleotide metabolism -> pyridine nucleotide metabolism	nicotinamide-nucleotide adenylyltransferase activity -> nicotinamide-nucleotide adenylyltransferase activity		CIN5, MSN1, ROX1
YDR462W	MRPL28	protein biosynthesis -> protein biosynthesis	structural constituent of ribosome -> structural constituent of ribosome	mitochondrial large ribosomal subunit -> mitochondrial large ribosomal subunit	ABF1
YMR148W	NO SYMBOL
\|YOR212W\|	STE4	signal transduction during conjugation with cellular fusion -> G-protein coupled receptor protein signaling pathway, conjugation with cellular fusion, chemosensory perception	heterotrimeric G-protein GTPase activity -> heterotrimeric G-protein GTPase activity	heterotrimeric G-protein complex, plasma membrane, shmoo tip -> heterotrimeric G-protein complex, plasma membrane, shmoo tip
Main:		G-protein coupled receptor protein signaling pathway (0.50)	nicotinamide-nucleotide adenylyltransferase activity (0.20)	plasma membrane (0.50)	ABF1 (0.33)
Score:		0.17	0.00	0.17	0.000
P-value:		9.778E-03 (G-protein coupled receptor protein signaling pathway)	2.754E+00 (binding)	4.795E-01 (plasma membrane)	2.021E-01 (MSN1)

RPN4(1) => SimExpr(YFL056C) OR SimExpr(other) : 37 15

mRRPE(1) AND STE12(1) AND PAC(1) => SimExpr(YMR310C) : 5

AVERAGE SCORES:

P
  SCORE: 0.612 (Part of genes covered by "Main": 0.711) (No. rules=58/59)
  P-VALUE: 0.638
F
  SCORE: 0.263 (Part of genes covered by "Main": 0.508) (No. rules=57/59)
  P-VALUE: 0.386
C
  SCORE: 0.694 (Part of genes covered by "Main": 0.789) (No. rules=57/59)
  P-VALUE: 0.614
TF
  SCORE: 0.244 (Part of genes covered by "Main": 0.448) (No. rules=57/59)
  P-VALUE: 0.351
EXPRESSION: 0.729 (59)

Discovering regulatory binding-site modules using rule-based learning

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