Discovering regulatory binding-site modules using rule-based learning

ndt80(MSE)(1) AND SWI5(1) => SimExpr(YGL116W) OR SimExpr(other) : 16 7

EXPR: (0.210) ndt80(MSE) (P < 0.161) SWI5 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YDR042C	NO SYMBOL				ARG80, ARG81, AZF1, CIN5, CUP9, DIG1, FZF1, GCR2, HAL9, HAP2, HAP4, HAP5, HIR2, HMS1, IXR1, LEU3, MBP1, MCM1, MET31, NRG1, PDR1, RLM1, RME1, ROX1, RTG1, RTG3, SRD1, STE12, SUM1, YAP6, ZAP1
\|YCR045C\|	NO SYMBOL
YJR007W	SUI2	translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity -> translation initiation factor activity	ribosome, cytoplasm -> cytoplasm, ribonucleoprotein complex	GLN3, HAP3, HIR1, RCS1
\|YBR159W\|	NO SYMBOL				ACE2, ARG81, GCR2, HIR2, LEU3, MOT3, PDR1, PHD1, SKN7, USV1
\|YNL196C\|	NO SYMBOL
YOR338W	NO SYMBOL				RAP1
YNL034W	NO SYMBOL				MAC1, MET4, NDD1, RME1
YMR001C	CDC5	DNA dependent DNA replication, protein amino acid phosphorylation -> phosphorus metabolism, cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	protein serine/threonine kinase activity -> protein serine/threonine kinase activity	nucleus, spindle pole, bud neck -> nucleus, cytoplasm, site of polarized growth (sensu Fungi)	NDD1, REB1, SWI6
\|YLR154C\|	RNH203				RLM1
YFR023W	PES4	DNA dependent DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			DIG1, FKH1, FKH2, GLN3, HAP3, MCM1, MSN2, RIM101, RLM1, RTG3, STE12, SUM1, THI2, YAP1
\|YMR280C\|	CAT8	gluconeogenesis, positive regulation of transcription from Pol II promoter -> alcohol metabolism, monosaccharide metabolism, carbohydrate metabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, biosynthesis, energy pathways	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> nucleus	ABF1, REB1
YFR012W	NO SYMBOL				DAL81
YOL132W	GAS4			cell wall (sensu Fungi) -> cell wall
YHR124W	NDT80	meiosis, transcription -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	transcription factor activity -> transcription factor activity	nuclear chromosome -> chromosome, nucleus	SUM1
YBR069C	TAT1	amino acid transport -> transport	amino acid transporter activity -> amino acid transporter activity	plasma membrane -> plasma membrane	CIN5, DAL81, PHD1, SWI4
YKL104C	GFA1	cell wall chitin biosynthesis -> cell organization and biogenesis, biosynthesis, polysaccharide metabolism, carbohydrate metabolism	glucosamine-fructose-6-phosphate aminotransferase (isomerizing) activity -> glucosamine-fructose-6-phosphate aminotransferase (isomerizing) activity		REB1
YFR032C	NO SYMBOL				PUT3, SUM1
YOR214C	NO SYMBOL				BAS1
YGL116W	CDC20	mitotic spindle elongation, ubiquitin-dependent protein catabolism, mitotic metaphase/anaphase transition, mitotic chromosome segregation, cyclin catabolism -> cell organization and biogenesis, catabolism, cell proliferation, cell cycle, protein metabolism	enzyme activator activity -> enzyme activator activity	anaphase-promoting complex -> nucleus, ubiquitin ligase complex	DIG1, FKH2, INO2, INO4, IXR1, MCM1, NDD1
YLR049C	NO SYMBOL				MBP1, SWI5
\|YHL043W\|	ECM34	cell wall organization and biogenesis -> cell organization and biogenesis
YPR122W	AXL1	axial budding, bud site selection, conjugation with cellular fusion, peptide pheromone maturation -> asexual reproduction, conjugation, protein metabolism, cell proliferation, cell organization and biogenesis, sexual reproduction	metalloendopeptidase activity -> metalloendopeptidase activity	integral to membrane, bud neck, shmoo tip -> integral to membrane, site of polarized growth (sensu Fungi)	CIN5
\|YKR005C\|	NO SYMBOL
Main:		cell proliferation (0.50)	metalloendopeptidase activity (0.12)	nucleus (0.50)	SUM1 (0.22)
Score:		0.53	0.00	0.29	0.163
P-value:		2.212E+00 (carbohydrate biosynthesis)	4.226E+00 (transcription regulator activity)	1.310E+00 (bud neck)	4.860E-02 (SUM1)

SFF(1) AND ndt80(MSE)(1) AND MCM1'(1) => SimExpr(YGL116W) OR SimExpr(other) : 9 2

EXPR: (0.176) SFF (P < 0.000) ndt80(MSE) (P < 0.086) MCM1' (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YNR034W	SOL1	tRNA processing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			YFL044C
YKL096W	CWP1	cell wall organization and biogenesis -> cell organization and biogenesis	structural constituent of cell wall -> structural constituent of cell wall	cell wall (sensu Fungi) -> cell wall	RLM1, SMP1, STE12, SWI4
YFR023W	PES4	DNA dependent DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			DIG1, FKH1, FKH2, GLN3, HAP3, MCM1, MSN2, RIM101, RLM1, RTG3, STE12, SUM1, THI2, YAP1
YGL116W	CDC20	mitotic spindle elongation, ubiquitin-dependent protein catabolism, mitotic metaphase/anaphase transition, mitotic chromosome segregation, cyclin catabolism -> cell organization and biogenesis, catabolism, cell proliferation, cell cycle, protein metabolism	enzyme activator activity -> enzyme activator activity	anaphase-promoting complex -> nucleus, ubiquitin ligase complex	DIG1, FKH2, INO2, INO4, IXR1, MCM1, NDD1
YJR007W	SUI2	translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity -> translation initiation factor activity	ribosome, cytoplasm -> cytoplasm, ribonucleoprotein complex	GLN3, HAP3, HIR1, RCS1
YGL230C	NO SYMBOL				HIR1, MATa1
YPL255W	BBP1	microtubule nucleation -> cell organization and biogenesis	structural constituent of cytoskeleton -> structural constituent of cytoskeleton	spindle pole body -> cytoplasm	STB1, SWI4
\|YOL028C\|	YAP7	positive regulation of transcription from Pol II promoter -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	RNA polymerase II transcription factor activity -> RNA polymerase II transcription factor activity	nucleus -> nucleus	NRG1
YLR308W	CDA2	spore wall assembly (sensu Saccharomyces) -> sporulation	chitin deacetylase activity -> chitin deacetylase activity	chitosan layer of spore wall -> cell wall	REB1, SUM1
\|YMR204C\|	NO SYMBOL				STE12
YMR001C	CDC5	DNA dependent DNA replication, protein amino acid phosphorylation -> phosphorus metabolism, cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	protein serine/threonine kinase activity -> protein serine/threonine kinase activity	nucleus, spindle pole, bud neck -> nucleus, cytoplasm, site of polarized growth (sensu Fungi)	NDD1, REB1, SWI6
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.44)	structural constituent of cell wall (0.14)	cytoplasm (0.43)	STE12 (0.27)
Score:		0.36	0.00	0.33	0.182
P-value:		4.087E-01 (microtubule cytoskeleton organization and biogenesis)	1.148E+00 (structural molecule activity)	1.882E-01 (spindle pole)	5.856E-02 (STE12)

ndt80(MSE)(1) AND SFF'(1) AND MCM1'(1) => SimExpr(YGL116W) OR SimExpr(other) : 11 5

EXPR: (0.250) ndt80(MSE) (P < 0.575) SFF' (P < 0.000) MCM1' (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YKL104C	GFA1	cell wall chitin biosynthesis -> cell organization and biogenesis, biosynthesis, polysaccharide metabolism, carbohydrate metabolism	glucosamine-fructose-6-phosphate aminotransferase (isomerizing) activity -> glucosamine-fructose-6-phosphate aminotransferase (isomerizing) activity		REB1
YNR034W	SOL1	tRNA processing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			YFL044C
YKL096W	CWP1	cell wall organization and biogenesis -> cell organization and biogenesis	structural molecule activity -> structural molecule activity	cell wall (sensu Fungi) -> cell wall	RLM1, SMP1, STE12, SWI4
YFR023W	PES4	DNA dependent DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			DIG1, FKH1, FKH2, GLN3, HAP3, MCM1, MSN2, RIM101, RLM1, RTG3, STE12, SUM1, THI2, YAP1
\|YMR111C\|	NO SYMBOL				GRF10(Pho2)
\|YPL109C\|	NO SYMBOL
YGL116W	CDC20	mitotic spindle elongation, ubiquitin-dependent protein catabolism, mitotic metaphase/anaphase transition, mitotic chromosome segregation, cyclin catabolism -> cell organization and biogenesis, catabolism, cell proliferation, cell cycle, protein metabolism	enzyme activator activity -> enzyme activator activity	anaphase-promoting complex -> nucleus, ubiquitin ligase complex	DIG1, FKH2, INO2, INO4, IXR1, MCM1, NDD1
YJR007W	SUI2	translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity -> translation initiation factor activity	ribosome, cytoplasm -> cytoplasm, ribonucleoprotein complex	GLN3, HAP3, HIR1, RCS1
YGL230C	NO SYMBOL				HIR1, MATa1
\|YOR388C\|	FDH1	formate catabolism, NADH regeneration -> catabolism, coenzymes and prosthetic group metabolism, one-carbon compound metabolism, vitamin metabolism, organic acid metabolism	formate dehydrogenase activity -> formate dehydrogenase activity	cytosol -> cytoplasm	MCM1, YJL206C
YPL255W	BBP1	microtubule nucleation -> cell organization and biogenesis	structural molecule activity -> structural molecule activity	spindle pole body -> cytoplasm	STB1, SWI4
YGL170C	SPO74	sporulation (sensu Saccharomyces) -> sporulation	structural molecule activity -> structural molecule activity	spindle pole body -> cytoplasm	MOT3, MSS11, SUM1
\|YOL028C\|	YAP7	positive regulation of transcription from Pol II promoter -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	RNA polymerase II transcription factor activity -> RNA polymerase II transcription factor activity	nucleus -> nucleus	NRG1
YLR308W	CDA2	spore wall assembly (sensu Saccharomyces) -> sporulation	chitin deacetylase activity -> chitin deacetylase activity	chitosan layer of spore wall -> cell wall	REB1, SUM1
\|YMR204C\|	NO SYMBOL				STE12
YMR001C	CDC5	DNA dependent DNA replication, protein amino acid phosphorylation -> phosphorus metabolism, cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	protein serine/threonine kinase activity -> protein serine/threonine kinase activity	nucleus, spindle pole, bud neck -> nucleus, cytoplasm, site of polarized growth (sensu Fungi)	NDD1, REB1, SWI6
Main:		cell organization and biogenesis (0.33)	structural molecule activity (0.30)	cytoplasm (0.56)	REB1 SUM1 STE12 MCM1 (0.20)
Score:		0.29	0.07	0.39	0.152
P-value:		1.143E+00 (microtubule cytoskeleton organization and biogenesis)	9.729E-01 (structural molecule activity)	3.374E-02 (spindle pole)	9.953E-02 (SUM1)

MCM1(1) AND ndt80(MSE)(1) => SimExpr(YGL116W) : 5

EXPR: (0.134) ndt80(MSE) (P < 0.050) MCM1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YKL104C	GFA1	cell wall chitin biosynthesis -> cell organization and biogenesis, biosynthesis, polysaccharide metabolism, carbohydrate metabolism	glucosamine-fructose-6-phosphate aminotransferase (isomerizing) activity -> glucosamine-fructose-6-phosphate aminotransferase (isomerizing) activity		REB1
YGL116W	CDC20	mitotic spindle elongation, ubiquitin-dependent protein catabolism, mitotic metaphase/anaphase transition, mitotic chromosome segregation, cyclin catabolism -> cell organization and biogenesis, catabolism, cell proliferation, cell cycle, protein metabolism	enzyme activator activity -> enzyme activator activity	anaphase-promoting complex -> anaphase-promoting complex	DIG1, FKH2, INO2, INO4, IXR1, MCM1, NDD1
YDR273W	DON1	meiosis, spore wall assembly (sensu Saccharomyces) -> cell proliferation, sporulation		spindle, prospore membrane -> spindle, prospore membrane
YPL255W	BBP1	microtubule nucleation -> cell organization and biogenesis	structural constituent of cytoskeleton -> structural constituent of cytoskeleton	spindle pole body -> spindle, microtubule organizing center	STB1, SWI4
YBR069C	TAT1	amino acid transport -> transport	amino acid transporter activity -> amino acid transporter activity	plasma membrane -> plasma membrane	CIN5, DAL81, PHD1, SWI4
Main:		cell organization and biogenesis (0.60)	glucosamine-fructose-6-phosphate aminotransferase (isomerizing) activity (0.25)	spindle (0.50)	SWI4 (0.50)
Score:		0.40	0.00	0.17	0.167
P-value:		5.823E-02 (microtubule cytoskeleton organization and biogenesis)	2.000E+00 (molecular_function)	3.508E-02 (spindle)	1.941E-01 (SWI4)

ndt80(MSE)(1) AND SFF'(1) AND SWI5(1) AND MCM1'(1) => SimExpr(YGL116W) : 5

EXPR: (0.115) ndt80(MSE) (P < 0.020) SFF' (P < 0.000) SWI5 (P < 0.000) MCM1' (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YKL104C	GFA1	cell wall chitin biosynthesis -> cell organization and biogenesis, biosynthesis, polysaccharide metabolism, carbohydrate metabolism	glucosamine-fructose-6-phosphate aminotransferase (isomerizing) activity -> glucosamine-fructose-6-phosphate aminotransferase (isomerizing) activity		REB1
YFR023W	PES4	DNA dependent DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			DIG1, FKH1, FKH2, GLN3, HAP3, MCM1, MSN2, RIM101, RLM1, RTG3, STE12, SUM1, THI2, YAP1
YGL116W	CDC20	mitotic spindle elongation, ubiquitin-dependent protein catabolism, mitotic metaphase/anaphase transition, mitotic chromosome segregation, cyclin catabolism -> cell organization and biogenesis, catabolism, cell proliferation, cell cycle, protein metabolism	enzyme activator activity -> enzyme activator activity	anaphase-promoting complex -> nucleus, ubiquitin ligase complex	DIG1, FKH2, INO2, INO4, IXR1, MCM1, NDD1
YJR007W	SUI2	translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity -> translation initiation factor activity	ribosome, cytoplasm -> cytoplasm, ribonucleoprotein complex	GLN3, HAP3, HIR1, RCS1
YMR001C	CDC5	DNA dependent DNA replication, protein amino acid phosphorylation -> phosphorus metabolism, cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	protein serine/threonine kinase activity -> protein serine/threonine kinase activity	nucleus, spindle pole, bud neck -> nucleus, cytoplasm, site of polarized growth (sensu Fungi)	NDD1, REB1, SWI6
Main:		cell proliferation (0.60)	translation initiation factor activity (0.25)	cytoplasm (0.67)	HAP3 GLN3 FKH2 REB1 DIG1 NDD1 MCM1 (0.40)
Score:		0.70	0.00	0.67	0.400
P-value:		2.974E-02 (DNA replication and chromosome cycle)	7.327E-01 (transferase activity)	3.357E+00 (nucleus)	3.787E-02 (GLN3)

HSE(1) AND MCM1'(1) AND SCB(1) => SimExpr(YLL010C) OR SimExpr(other) : 5 2

EXPR: (0.291) HSE (P < 0.007) MCM1' (P < 0.001) SCB (P < 0.004)

ORF	SYMBOL	P	F	C	TF
\|YHL008C\|	NO SYMBOL				RFX1, RTG1, YJL206C
YDR116C	MRPL1	protein biosynthesis, meiosis, aerobic respiration -> protein biosynthesis, M phase, cellular respiration	structural constituent of ribosome -> structural constituent of ribosome	mitochondrial large ribosomal subunit -> cytoplasm, ribonucleoprotein complex	CHA4, GRF10(Pho2)
\|YGR142W\|	BTN2	regulation of pH, intracellular protein transport -> cation homeostasis, intracellular protein transport		cytosol -> cytoplasm	HSF1, MSN4
YLL010C	PSR1	response to stress -> response to stress	protein phosphatase activity -> protein phosphatase activity	plasma membrane -> plasma membrane	CBF1
YKL185W	ASH1	regulation of transcription\, mating-type specific, pseudohyphal growth -> mating-type determination, growth pattern, regulation of transcription, transcription\, DNA-dependent	specific transcriptional repressor activity -> specific transcriptional repressor activity	nucleus -> nucleus	SMP1, SWI5
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent	RNA binding -> RNA binding	nucleolus -> nucleus
YOR086C	NO SYMBOL				ABF1, STE12
Main:		transcription\, DNA-dependent (0.40)	RNA binding (0.25)	cytoplasm (0.40)	ABF1 (0.17)
Score:		0.10	0.00	0.20	0.000
P-value:		1.864E+00 (transcription\, DNA-dependent)	2.000E+00	4.535E+00 (nucleus)	9.217E-01 (CHA4)

ALPHA1'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YGR280C) OR SimExpr(other) : 32 15

EXPR: (0.240) ALPHA1' (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.001)

ORF	SYMBOL	P	F	C	TF
YAL059W	ECM1	cell wall organization and biogenesis -> cell growth and/or maintenance			MOT3
YNL132W	KRE33
\|YOL022C\|	NO SYMBOL				MAC1, MOT3, RTS2
YFR001W	LOC1	ribosomal large subunit biogenesis -> cell growth and/or maintenance	mRNA binding -> RNA binding	nucleus -> nucleus	ARG80, GAL4, GTS1, HAP4, HIR1, LEU3, MSN2, MSN4, RCS1, RLM1, SWI4
YDR496C	PUF6				RFX1
\|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
\|YGL169W\|	SUA5	cell growth and/or maintenance -> cell growth and/or maintenance			ABF1
YLR002C	NOC3	DNA replication initiation, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	chromatin binding, protein binding -> DNA binding, protein binding	nucleus, nucleolus -> nucleus	HIR1, IXR1, RCS1
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
YCR072C	NO SYMBOL				YFL044C
\|YHR128W\|	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups		CIN5
YNL175C	NOP13		RNA binding -> RNA binding	nucleolus, nucleoplasm -> nucleus	INO2, INO4
\|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
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
YKL014C	NO SYMBOL				ABF1
YDR184C	ATC1	response to stress, polar budding -> response to stress, asexual reproduction		nucleus -> nucleus	ARO80, GLN3, SIP4, SKO1
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
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
\|YNR024W\|	NO SYMBOL
YBR104W	YMC2	transport -> cell growth and/or maintenance	transporter activity -> transporter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	FKH1, FKH2
\|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
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
YMR049C	ERB1	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			RTG3
\|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
YNL112W	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
\|YCR090C\|	NO SYMBOL
\|YNL308C\|	KRI1	ribosome biogenesis -> cell growth and/or maintenance		nucleolus -> nucleus
YGR245C	SDA1	actin cytoskeleton organization and biogenesis, start control point of mitotic cell cycle -> cell growth and/or maintenance		nucleus -> nucleus
\|YCL059C\|	KRR1	ribosome biogenesis, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
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
\|YNL292W\|	PUS4	tRNA modification -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pseudouridylate synthase activity -> carbon-oxygen lyase activity	mitochondrion, nucleus -> cytoplasm, nucleus	RCS1
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
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
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
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
\|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
YJR070C	NO SYMBOL				GAT3, YAP5
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
YGR162W	TIF4631	translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	HSF1
YOR359W	VTS1	protein-vacuolar targeting -> protein metabolism, cell growth and/or maintenance	intracellular transporter activity -> transporter activity	cytosol -> cytoplasm	RAP1
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, SWI6
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
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
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
YOR272W	YTM1	chromosome organization and biogenesis (sensu Eukarya), ribosomal large subunit biogenesis -> cell growth and/or maintenance		nucleus, nucleolus -> nucleus	LEU3, PUT3, REB1
\|YCR016W\|	NO SYMBOL
Main:		cell growth and/or maintenance (0.77)	RNA binding (0.56)	nucleus (0.78)	ABF1 (0.15)
Score:		0.73	0.33	0.65	0.066
P-value:		2.029E-17 (ribosome biogenesis)	8.994E-08 (snoRNA binding)	3.877E-18 (nucleolus)	6.159E-01 (RCS1)

ALPHA1'(1) AND SWI5(1) AND PAC(1) AND SCB(1) => SimExpr(YGR280C) OR SimExpr(other) : 5 2

EXPR: (0.220) ALPHA1' (P < 0.000) SWI5 (P < 0.000) PAC (P < 0.059) SCB (P < 0.000)

ORF	SYMBOL	P	F	C	TF
\|YKL120W\|	OAC1	oxaloacetate transport, sulfate transport -> transport	oxaloacetate carrier activity, sulfate porter activity -> electrochemical potential-driven transporter activity, anion transporter activity, organic cation transporter activity, carboxylic acid transporter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	LEU3, MTH1
YLL010C	PSR1	response to stress -> response to stress	protein phosphatase activity -> hydrolase activity\, acting on ester bonds	plasma membrane -> plasma membrane	CBF1
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
\|YIL066C\|	RNR3	DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ribonucleoside-diphosphate reductase activity -> oxidoreductase activity\, acting on CH2 groups	cytoplasm -> cytoplasm	RFX1, STB1
YOR294W	RRS1	ribosome biogenesis, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleus -> nucleus	STB1
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
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.71)	RNA binding (0.40)	nucleus (0.57)	STB1 (0.40)
Score:		0.48	0.10	0.33	0.100
P-value:		3.816E-04 (rRNA processing)	5.233E-01 (RNA binding)	8.698E-03 (small nucleolar ribonucleoprotein complex)	2.235E-02 (STB1)

ALPHA1'(1) AND mRRPE(1) AND SWI5(1) AND PAC(1) => SimExpr(YGR280C) OR SimExpr(other) : 7 3

EXPR: (0.248) ALPHA1' (P < 0.000) mRRPE (P < 0.026) SWI5 (P < 0.000) PAC (P < 0.100)

ORF	SYMBOL	P	F	C	TF
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
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
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
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
\|YNR024W\|	NO SYMBOL
YGR245C	SDA1	actin cytoskeleton organization and biogenesis, start control point of mitotic cell cycle -> cell organization and biogenesis, cell proliferation		nucleus -> nucleus
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
\|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
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
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:		1.784E-04 (transcription from Pol I promoter)	5.899E-03 (snoRNA binding)	1.234E-04 (nucleolus)	4.198E-01 (RLM1)

SFF(1) AND ndt80(MSE)(1) => SimExpr(YLR049C) OR SimExpr(other) : 25 12

EXPR: (0.239) SFF (P < 0.000) ndt80(MSE) (P < 0.139)

ORF	SYMBOL	P	F	C	TF
\|YLR154C\|	RNH203				RLM1
YDR042C	NO SYMBOL				ARG80, ARG81, AZF1, CIN5, CUP9, DIG1, FZF1, GCR2, HAL9, HAP2, HAP4, HAP5, HIR2, HMS1, IXR1, LEU3, MBP1, MCM1, MET31, NRG1, PDR1, RLM1, RME1, ROX1, RTG1, RTG3, SRD1, STE12, SUM1, YAP6, ZAP1
\|YNL196C\|	NO SYMBOL
YDR522C	SPS2	sporulation (sensu Saccharomyces) -> sporulation		cell wall (sensu Fungi) -> cell wall	ARG81, HAL9, HAP5, HIR2, HMS1, LEU3, MET31, RTG3, SUM1
YFL040W	NO SYMBOL				SUM1
YNR034W	SOL1	tRNA processing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			YFL044C
YDL028C	MPS1	mitotic spindle checkpoint, spindle pole body duplication (sensu Saccharomyces) -> cell organization and biogenesis, cell cycle	protein threonine/tyrosine kinase activity -> protein kinase activity	spindle pole body, condensed nuclear chromosome kinetochore -> cytoplasm, chromosome\, pericentric region, condensed chromosome, chromosome, nucleus	SUM1
YKL096W	CWP1	cell wall organization and biogenesis -> cell organization and biogenesis	structural constituent of cell wall -> structural molecule activity	cell wall (sensu Fungi) -> cell wall	RLM1, SMP1, STE12, SWI4
YNL034W	NO SYMBOL				MAC1, MET4, NDD1, RME1
YFR023W	PES4	DNA dependent DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			DIG1, FKH1, FKH2, GLN3, HAP3, MCM1, MSN2, RIM101, RLM1, RTG3, STE12, SUM1, THI2, YAP1
YHR184W	SSP1	spore wall assembly (sensu Saccharomyces), protein complex assembly -> protein metabolism, sporulation		prospore membrane -> prospore	SUM1
YGR059W	SPR3	cellular morphogenesis, cell wall organization and biogenesis, spore wall assembly (sensu Saccharomyces), cellular morphogenesis during conjugation with cellular fusion -> cell organization and biogenesis, conjugation with cellular fusion, perception of external stimulus, sporulation, sensory perception, response to abiotic stimulus	structural constituent of cytoskeleton -> structural molecule activity	septin ring (sensu Saccharomyces), spore wall (sensu Fungi), prospore membrane -> site of polarized growth (sensu Fungi), cell wall, prospore, cell cortex, cytoskeleton	ABF1, RFX1, SUM1
\|YOR191W\|	RIS1	chromatin assembly/disassembly, mating-type switching/recombination -> cell organization and biogenesis, mating-type determination, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	DNA dependent ATPase activity -> ATP binding, hydrolase activity\, acting on acid anhydrides\, in phosphorus-containing anhydrides	nucleus -> nucleus
YOL132W	GAS4			cell wall (sensu Fungi) -> cell wall
YGL116W	CDC20	mitotic spindle elongation, ubiquitin-dependent protein catabolism, mitotic metaphase/anaphase transition, mitotic chromosome segregation, cyclin catabolism -> cell organization and biogenesis, catabolism, cell proliferation, cell cycle, protein metabolism	enzyme activator activity -> enzyme activator activity	anaphase-promoting complex -> nucleus, ubiquitin ligase complex	DIG1, FKH2, INO2, INO4, IXR1, MCM1, NDD1
\|YJR007W\|	SUI2	translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity -> translation initiation factor activity	ribosome, cytoplasm -> cytoplasm, ribonucleoprotein complex	GLN3, HAP3, HIR1, RCS1
YLR227C	ADY4	sporulation -> sporulation	structural molecule activity -> structural molecule activity	spindle pole body -> cytoplasm	AZF1
YMR252C	NO SYMBOL				SKN7
\|YML050W\|	NO SYMBOL				FKH2, MCM1, NDD1, SKN7
YDR281C	PHM6				PHO4, SUM1
YGL230C	NO SYMBOL				HIR1, MATa1
\|YHL043W\|	ECM34	cell wall organization and biogenesis -> cell organization and biogenesis
YBR115C	LYS2	lysine biosynthesis\, aminoadipic pathway -> amine metabolism, amino acid and derivative metabolism, organic acid metabolism, biosynthesis	aminoadipate-semialdehyde dehydrogenase activity -> aminoadipate-semialdehyde dehydrogenase activity	cytoplasm -> cytoplasm	DAL81, GCN4
YPL255W	BBP1	microtubule nucleation -> cell organization and biogenesis	structural constituent of cytoskeleton -> structural molecule activity	spindle pole body -> cytoplasm	STB1, SWI4
YLR049C	NO SYMBOL				MBP1, SWI5
YBR250W	NO SYMBOL				CBF1, GCN4
\|YDR438W\|	NO SYMBOL				CBF1
YDR218C	SPR28	cellular morphogenesis, cell wall organization and biogenesis -> cell organization and biogenesis	structural constituent of cytoskeleton -> structural molecule activity	septin ring (sensu Saccharomyces) -> site of polarized growth (sensu Fungi), cell cortex, cytoskeleton	YAP6
\|YGL121C\|	GPG1	signal transduction -> signal transduction	signal transducer activity -> signal transducer activity		CHA4
\|YOL028C\|	YAP7	positive regulation of transcription from Pol II promoter -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	RNA polymerase II transcription factor activity -> RNA polymerase II transcription factor activity	nucleus -> nucleus	NRG1
YOR214C	NO SYMBOL				BAS1
\|YGL046W\|	NO SYMBOL
\|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 -> RNA polymerase II transcription factor activity	nucleus -> nucleus	ABF1, REB1
YLR308W	CDA2	spore wall assembly (sensu Saccharomyces) -> sporulation	chitin deacetylase activity -> chitin deacetylase activity	chitosan layer of spore wall -> cell wall	REB1, SUM1
\|YMR204C\|	NO SYMBOL				STE12
YMR001C	CDC5	DNA dependent DNA replication, protein amino acid phosphorylation -> phosphorus metabolism, cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	protein serine/threonine kinase activity -> protein kinase activity	nucleus, spindle pole, bud neck -> nucleus, cytoplasm, site of polarized growth (sensu Fungi)	NDD1, REB1, SWI6
YFR012W	NO SYMBOL				DAL81
Main:		cell organization and biogenesis (0.40)	structural molecule activity (0.33)	cytoplasm (0.35)	SUM1 (0.28)
Score:		0.33	0.11	0.32	0.141
P-value:		9.263E-02 (sporulation)	1.851E-01 (structural constituent of cytoskeleton)	5.972E-02 (cell wall (sensu Fungi))	8.984E-07 (SUM1)

ndt80(MSE)(1) AND CCA(1) => SimExpr(YLR049C) OR SimExpr(other) : 5 1

EXPR: (0.148) ndt80(MSE) (P < 0.008) CCA (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YPR122W	AXL1	axial budding, bud site selection, conjugation with cellular fusion, peptide pheromone maturation -> budding, conjugation with cellular fusion, protein modification, cytokinesis, cytoplasm organization and biogenesis	metalloendopeptidase activity -> metalloendopeptidase activity	integral to membrane, bud neck, shmoo tip -> integral to membrane, bud neck, shmoo tip	CIN5
YMR252C	NO SYMBOL				SKN7
YGL230C	NO SYMBOL				HIR1, MATa1
YLR049C	NO SYMBOL				MBP1, SWI5
\|YIL151C\|	NO SYMBOL				RGT1, THI2
YOR339C	UBC11	protein polyubiquitination, protein monoubiquitination -> macromolecule catabolism, protein modification, protein metabolism	ubiquitin conjugating enzyme activity -> ubiquitin conjugating enzyme activity	cytoplasm -> cytoplasm	HAP2, IXR1
Main:		protein modification (1.00)	metalloendopeptidase activity (0.50)	cytoplasm (0.50)	SWI5 (0.17)
Score:		1.00	0.00	0.00	0.000
P-value:		5.515E-01 (protein modification)	2.737E+00 (enzyme activity)	3.000E+00 (cell)	3.357E-01 (THI2)

LYS14(1) AND ndt80(MSE)(1) => SimExpr(YLR049C) OR SimExpr(other) : 6 2

EXPR: (0.249) LYS14 (P < 0.001) ndt80(MSE) (P < 0.419)

ORF	SYMBOL	P	F	C	TF
\|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
YHR124W	NDT80	meiosis, transcription -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	transcription factor activity -> transcription factor activity	nuclear chromosome -> chromosome, nucleus	SUM1
YDR317W	NO SYMBOL				HAL9, RLM1
YBR115C	LYS2	lysine biosynthesis\, aminoadipic pathway -> amine metabolism, amino acid and derivative metabolism, organic acid metabolism, biosynthesis	aminoadipate-semialdehyde dehydrogenase activity -> aminoadipate-semialdehyde dehydrogenase activity	cytoplasm -> cytoplasm	DAL81, GCN4
YLR049C	NO SYMBOL				MBP1, SWI5
YDR218C	SPR28	cellular morphogenesis, cell wall organization and biogenesis -> cell organization and biogenesis	structural constituent of cytoskeleton -> structural constituent of cytoskeleton	septin ring (sensu Saccharomyces) -> site of polarized growth (sensu Fungi), cell cortex, cytoskeleton	YAP6
\|YGL046W\|	NO SYMBOL
YLR308W	CDA2	spore wall assembly (sensu Saccharomyces) -> sporulation	chitin deacetylase activity -> chitin deacetylase activity	chitosan layer of spore wall -> cell wall	REB1, SUM1
Main:		biosynthesis (0.40)	transcription factor activity (0.20)	cytoplasm (0.40)	SWI5 SUM1 (0.29)
Score:		0.10	0.00	0.10	0.095
P-value:		3.657E+00 (biosynthesis)	5.241E-01 (oxidoreductase activity)	4.615E+00 (cytoplasm)	1.215E-01 (SUM1)

ndt80(MSE)(1) AND SWI5(1) => SimExpr(YKL104C) OR SimExpr(other) : 16 7

ALPHA1'(1) AND ndt80(MSE)(1) AND SWI5(1) => SimExpr(YKL104C) OR SimExpr(other) : 10 4

EXPR: (0.229) ALPHA1' (P < 0.000) ndt80(MSE) (P < 0.285) SWI5 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
\|YLR154C\|	RNH203				RLM1
YKL104C	GFA1	cell wall chitin biosynthesis -> cell organization and biogenesis, biosynthesis, polysaccharide metabolism, carbohydrate metabolism	glucosamine-fructose-6-phosphate aminotransferase (isomerizing) activity -> glucosamine-fructose-6-phosphate aminotransferase (isomerizing) activity		REB1
YPR122W	AXL1	axial budding, bud site selection, conjugation with cellular fusion, peptide pheromone maturation -> asexual reproduction, conjugation, protein metabolism, cell proliferation, cell organization and biogenesis, sexual reproduction	metalloendopeptidase activity -> metalloendopeptidase activity	integral to membrane, bud neck, shmoo tip -> integral to membrane, site of polarized growth (sensu Fungi)	CIN5
YDR042C	NO SYMBOL				ARG80, ARG81, AZF1, CIN5, CUP9, DIG1, FZF1, GCR2, HAL9, HAP2, HAP4, HAP5, HIR2, HMS1, IXR1, LEU3, MBP1, MCM1, MET31, NRG1, PDR1, RLM1, RME1, ROX1, RTG1, RTG3, SRD1, STE12, SUM1, YAP6, ZAP1
YNL196C	NO SYMBOL
YHR124W	NDT80	meiosis, transcription -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	transcription factor activity -> transcription factor activity	nuclear chromosome -> chromosome, nucleus	SUM1
YNL034W	NO SYMBOL				MAC1, MET4, NDD1, RME1
\|YBR159W\|	NO SYMBOL				ACE2, ARG81, GCR2, HIR2, LEU3, MOT3, PDR1, PHD1, SKN7, USV1
YOL132W	GAS4			cell wall (sensu Fungi) -> cell wall
YGL116W	CDC20	mitotic spindle elongation, ubiquitin-dependent protein catabolism, mitotic metaphase/anaphase transition, mitotic chromosome segregation, cyclin catabolism -> cell organization and biogenesis, catabolism, cell proliferation, cell cycle, protein metabolism	enzyme activator activity -> enzyme activator activity	anaphase-promoting complex -> nucleus, ubiquitin ligase complex	DIG1, FKH2, INO2, INO4, IXR1, MCM1, NDD1
\|YHL043W\|	ECM34	cell wall organization and biogenesis -> cell organization and biogenesis
YFR032C	NO SYMBOL				PUT3, SUM1
YOR214C	NO SYMBOL				BAS1
\|YMR280C\|	CAT8	gluconeogenesis, positive regulation of transcription from Pol II promoter -> alcohol metabolism, monosaccharide metabolism, carbohydrate metabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, biosynthesis, energy pathways	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> nucleus	ABF1, REB1
Main:		cell organization and biogenesis (0.67)	metalloendopeptidase activity (0.20)	nucleus (0.60)	SUM1 (0.27)
Score:		0.67	0.00	0.30	0.182
P-value:		6.517E-01 (carbohydrate biosynthesis)	1.375E+00 (transcription regulator activity)	4.547E+00 (nucleus)	9.556E-02 (SUM1)

ndt80(MSE)(1) AND mRRPE(1) => SimExpr(YJR007W) OR SimExpr(other) : 6 1

EXPR: (0.196) ndt80(MSE) (P < 0.008) mRRPE (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YFR023W	PES4	DNA dependent DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			DIG1, FKH1, FKH2, GLN3, HAP3, MCM1, MSN2, RIM101, RLM1, RTG3, STE12, SUM1, THI2, YAP1
YHR184W	SSP1	spore wall assembly (sensu Saccharomyces), protein complex assembly -> protein metabolism, sporulation		prospore membrane -> prospore	SUM1
\|YGL253W\|	HXK2	fructose metabolism -> alcohol metabolism, carbohydrate metabolism	hexokinase activity -> hexokinase activity	nucleus, cytosol -> nucleus, cytoplasm	ABF1, CIN5, HSF1, SWI4
YJR007W	SUI2	translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity -> translation initiation factor activity	ribosome, cytoplasm -> cytoplasm, ribonucleoprotein complex	GLN3, HAP3, HIR1, RCS1
YOL091W	SPO21	spore wall assembly (sensu Saccharomyces), meiosis -> cell proliferation, sporulation	structural molecule activity -> structural molecule activity	spindle pole body -> cytoplasm	HAP5, SUM1
YOR338W	NO SYMBOL				RAP1
YOR339C	UBC11	protein polyubiquitination, protein monoubiquitination -> catabolism, protein metabolism	ubiquitin conjugating enzyme activity -> ubiquitin conjugating enzyme activity	cytoplasm -> cytoplasm	HAP2, IXR1
Main:		protein metabolism (0.50)	ubiquitin conjugating enzyme activity (0.25)	cytoplasm (0.80)	SUM1 (0.43)
Score:		0.33	0.00	0.60	0.190
P-value:		2.092E-02 (spore wall assembly (sensu Saccharomyces))	2.857E+00 (enzyme activity)	3.171E+00 (cytoplasm)	5.273E-03 (SUM1)

CSRE(1) AND ndt80(MSE)(1) => SimExpr(YKL096W) OR SimExpr(other) : 6 1

EXPR: (0.190) ndt80(MSE) (P < 0.031) CSRE (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YHR124W	NDT80	meiosis, transcription -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	transcription factor activity -> transcription factor activity	nuclear chromosome -> chromosome, nucleus	SUM1
YKL096W	CWP1	cell wall organization and biogenesis -> cell organization and biogenesis	structural constituent of cell wall -> structural constituent of cell wall	cell wall (sensu Fungi) -> cell wall	RLM1, SMP1, STE12, SWI4
\|YGL253W\|	HXK2	fructose metabolism -> alcohol metabolism, carbohydrate metabolism	hexokinase activity -> hexokinase activity	nucleus, cytosol -> nucleus, cytoplasm	ABF1, CIN5, HSF1, SWI4
YML050W	NO SYMBOL				FKH2, MCM1, NDD1, SKN7
YPL255W	BBP1	microtubule nucleation -> cell organization and biogenesis	structural constituent of cytoskeleton -> structural constituent of cytoskeleton	spindle pole body -> cytoplasm	STB1, SWI4
YLR049C	NO SYMBOL				MBP1, SWI5
YBR069C	TAT1	amino acid transport -> transport	amino acid transporter activity -> amino acid transporter activity	plasma membrane -> plasma membrane	CIN5, DAL81, PHD1, SWI4
Main:		cell organization and biogenesis (0.40)	structural constituent of cell wall (0.20)	cytoplasm (0.40)	SWI4 (0.57)
Score:		0.10	0.00	0.20	0.286
P-value:		4.052E+00 (cell growth and/or maintenance)	4.212E-01 (structural molecule activity)	4.535E+00 (nucleus)	1.369E-03 (SWI4)

mRRPE(1) AND PAC(1) => SimExpr(YOR310C) OR SimExpr(other) : 59 24

EXPR: (0.227) mRRPE (P < 0.000) PAC (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YPL043W	NOP4	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus
\|YMR310C\|	NO SYMBOL
YAL059W	ECM1	cell wall organization and biogenesis -> cell growth and/or maintenance			MOT3
YNL132W	KRE33
\|YML125C\|	NO SYMBOL				MAL13, MSN4, NDD1, RME1, SWI5
\|YOL022C\|	NO SYMBOL				MAC1, MOT3, RTS2
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
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
YDR496C	PUF6				RFX1
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
\|YGL169W\|	SUA5	cell growth and/or maintenance -> cell growth and/or maintenance			ABF1
YLR002C	NOC3	DNA replication initiation, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	chromatin binding, protein binding -> DNA binding, protein binding	nucleus, nucleolus -> nucleus	HIR1, IXR1, RCS1
YBR267W	NO SYMBOL
YKL172W	EBP2	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus	ABF1, FZF1, RFX1
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
YCR072C	NO SYMBOL				YFL044C
\|YHR128W\|	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups		CIN5
YMR290C	HAS1			nucleolus, nuclear membrane -> nucleus, endomembrane system	RAP1
YNL175C	NOP13		RNA binding -> RNA binding	nucleolus, nucleoplasm -> nucleus	INO2, INO4
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
\|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
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
YKL014C	NO SYMBOL				ABF1
YHR089C	GAR1	rRNA modification, 35S primary transcript processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	RNA binding -> RNA binding	nucleolus, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	CBF1, FZF1
YPR144C	NOC4	ribosome biogenesis -> cell growth and/or maintenance		nucleus -> nucleus	HIR1
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
YKL056C	NO SYMBOL
YDR184C	ATC1	response to stress, polar budding -> response to stress, asexual reproduction		nucleus -> nucleus	ARO80, GLN3, SIP4, SKO1
\|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
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
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
YNL110C	NOP15	ribosomal large subunit biogenesis -> cell growth and/or maintenance		nucleus, nucleolus -> nucleus
YMR131C	RRB1	ribosome biogenesis -> cell growth and/or maintenance		nucleolus -> nucleus	FZF1, MATa1, RGT1
YDR365C	NO SYMBOL				ABF1, MSS11, YJL206C
YGR145W	ENP2
\|YNR024W\|	NO SYMBOL
\|YBR104W\|	YMC2	transport -> cell growth and/or maintenance	transporter activity -> transporter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	FKH1, FKH2
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 binding	cytoplasm, nuclear pore -> cytoplasm, nucleus, integral to membrane, endomembrane system	MSN2
\|YGR272C\|	NO SYMBOL				REB1, STP2
YJL069C	UTP18				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
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
YMR049C	ERB1	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			RTG3
\|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
YNL112W	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
\|YCR090C\|	NO SYMBOL
YDR101C	ARX1	ribosomal large subunit biogenesis -> cell growth and/or maintenance		nucleoplasm, cytoplasm -> nucleus, cytoplasm	IXR1, RFX1
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
YNL308C	KRI1	ribosome biogenesis -> cell growth and/or maintenance		nucleolus -> nucleus
YGR245C	SDA1	actin cytoskeleton organization and biogenesis, start control point of mitotic cell cycle -> cell growth and/or maintenance		nucleus -> nucleus
\|YCL059C\|	KRR1	ribosome biogenesis, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
YMR239C	RNT1	35S primary transcript processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ribonuclease III activity -> hydrolase activity\, acting on ester bonds, RNA binding	nucleolus -> nucleus
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
\|YNL292W\|	PUS4	tRNA modification -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pseudouridylate synthase activity -> carbon-oxygen lyase activity	mitochondrion, nucleus -> cytoplasm, nucleus	RCS1
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
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
\|YDR161W\|	NO SYMBOL
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
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
\|YMR259C\|	NO SYMBOL				ARG80, GCR2, GTS1, HIR1, SRD1
\|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
\|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
YJR070C	NO SYMBOL				GAT3, YAP5
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
YGR162W	TIF4631	translational initiation -> biosynthesis, protein metabolism	translation initiation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	HSF1
YGR187C	HGH1				ABF1, HAP3, HIR1, RCS1, RTG1
\|YOR359W\|	VTS1	protein-vacuolar targeting -> protein metabolism, cell growth and/or maintenance	intracellular transporter activity -> transporter activity	cytosol -> cytoplasm	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 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
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
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
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
\|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
YOR272W	YTM1	chromosome organization and biogenesis (sensu Eukarya), ribosomal large subunit biogenesis -> cell growth and/or maintenance		nucleus, nucleolus -> nucleus	LEU3, PUT3, REB1
YCR016W	NO SYMBOL
\|YNR046W\|	NO SYMBOL				ABF1
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
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
YMR014W	BUD22	bud site selection -> cell growth and/or maintenance		nucleus -> nucleus	CUP9, HAL9, HIR2, LEU3, NDD1, RLM1, ROX1, SMP1, YAP6
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
Main:		cell growth and/or maintenance (0.78)	RNA binding (0.55)	nucleus (0.82)	ABF1 (0.20)
Score:		0.73	0.33	0.73	0.101
P-value:		2.929E-31 (ribosome biogenesis)	2.998E-08 (snoRNA binding)	1.266E-32 (nucleolus)	8.516E-01 (LEU3)

mRRPE(1) AND PAC(1) AND MCM1'(1) => SimExpr(YOR310C) OR SimExpr(other) : 12 5

EXPR: (0.223) mRRPE (P < 0.000) PAC (P < 0.012) MCM1' (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YPL043W	NOP4	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus
\|YML125C\|	NO SYMBOL				MAL13, MSN4, NDD1, RME1, SWI5
\|YGL169W\|	SUA5	cell growth and/or maintenance -> cell growth and/or maintenance			ABF1
YBR267W	NO SYMBOL
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
\|YHR128W\|	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups		CIN5
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
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
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
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
YMR049C	ERB1	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			RTG3
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleus
\|YDR399W\|	HPT1	purine nucleotide biosynthesis -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	hypoxanthine phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups
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
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
YCR016W	NO SYMBOL
Main:		cell growth and/or maintenance (0.75)	RNA binding (0.50)	nucleus (1.00)	ABF1 (0.33)
Score:		0.77	0.25	1.00	0.167
P-value:		3.753E-06 (rRNA processing)	2.619E-02 (transferase activity\, transferring pentosyl groups)	1.787E-04 (nucleolus)	1.000E+00

mRRPE(1) AND PAC(1) AND SCB(1) => SimExpr(YOR310C) OR SimExpr(other) : 15 6

EXPR: (0.216) mRRPE (P < 0.000) PAC (P < 0.002) SCB (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YGR159C	NSR1	ribosomal small subunit assembly and maintenance, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	single-stranded DNA binding, RNA binding -> DNA binding, RNA binding	nucleolus, nucleus -> nucleus
\|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
YPR144C	NOC4	ribosome biogenesis -> cell organization and biogenesis		nucleus -> nucleus	HIR1
YKL056C	NO SYMBOL
YDR184C	ATC1	response to stress, polar budding -> response to stress, asexual reproduction		nucleus -> nucleus	ARO80, GLN3, SIP4, SKO1
YMR131C	RRB1	ribosome biogenesis -> cell organization and biogenesis		nucleolus -> nucleus	FZF1, MATa1, RGT1
\|YBR104W\|	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	FKH1, FKH2
YJL069C	UTP18				ABF1
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
YNL112W	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
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
\|YCL059C\|	KRR1	ribosome biogenesis, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
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
\|YNL292W\|	PUS4	tRNA modification -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pseudouridylate synthase activity -> carbon-oxygen lyase activity	mitochondrion, nucleus -> cytoplasm, nucleus	RCS1
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
\|YMR259C\|	NO SYMBOL				ARG80, GCR2, GTS1, HIR1, SRD1
\|YDR399W\|	HPT1	purine nucleotide biosynthesis -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	hypoxanthine phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups
YJR070C	NO SYMBOL				GAT3, YAP5
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
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
Main:		cell organization and biogenesis (0.62)	RNA binding (0.64)	nucleus (0.75)	ABF1 (0.23)
Score:		0.54	0.40	0.67	0.064
P-value:		2.390E-08 (ribosome biogenesis)	5.021E-03 (RNA binding)	2.473E-07 (nucleolus)	5.263E-01 (SKO1)

ALPHA1'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YOR310C) OR SimExpr(other) : 33 14

SFF'(1) AND mRRPE(1) AND PAC(1) AND MCM1'(1) => SimExpr(YOR310C) OR SimExpr(other) : 6 2

EXPR: (0.247) SFF' (P < 0.000) mRRPE (P < 0.034) PAC (P < 0.152) MCM1' (P < 0.000)

ORF	SYMBOL	P	F	C	TF
\|YML125C\|	NO SYMBOL				MAL13, MSN4, NDD1, RME1, SWI5
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
YIL122W	POG1	re-entry into mitotic cell cycle after pheromone arrest -> re-entry into mitotic cell cycle, conjugation with cellular fusion, response to pheromone	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> nucleus	ASH1, CIN5, NRG1, RLM1, SMP1, YAP6
YOR095C	RKI1	pentose-phosphate shunt -> glucose catabolism, main pathways of carbohydrate metabolism, nicotinamide metabolism	ribose-5-phosphate isomerase activity -> ribose-5-phosphate isomerase activity		FHL1, FKH2, RAP1
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> rRNA processing, snRNA processing	RNA binding -> RNA binding	nucleolus -> nucleus
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> rRNA modification, rRNA processing		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	ABF1, SWI6
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis, rRNA processing		nucleolus -> nucleus
YCR016W	NO SYMBOL
Main:		rRNA processing (0.60)	RNA binding (0.33)	nucleus (1.00)	RLM1 SWI6 (0.40)
Score:		0.30	0.00	1.00	0.200
P-value:		2.047E-02 (rRNA processing)	2.000E+00	1.578E-02 (nucleolus)	2.443E-01 (RLM1)

ALPHA1'(1) AND mRRPE(1) AND PAC(1) AND MCM1'(1) => SimExpr(YOR310C) OR SimExpr(other) : 7 3

EXPR: (0.212) ALPHA1' (P < 0.000) mRRPE (P < 0.001) PAC (P < 0.017) MCM1' (P < 0.000)

ORF	SYMBOL	P	F	C	TF
\|YGL169W\|	SUA5	cell growth and/or maintenance -> cell growth and/or maintenance			ABF1
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
\|YHR128W\|	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups		CIN5
YML093W	UTP14	processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex -> nucleolus, ribonucleoprotein complex
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
YMR049C	ERB1	rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			RTG3
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleolus
YOR310C	NOP58	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription		small nuclear ribonucleoprotein complex, small nucleolar ribonucleoprotein complex -> small nuclear ribonucleoprotein complex, nucleolus, ribonucleoprotein complex	ABF1, SWI6
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> cell growth and/or maintenance, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleolus
YCR016W	NO SYMBOL
Main:		cell growth and/or maintenance (0.75)	RNA binding (0.50)	nucleolus (1.00)	ABF1 SWI6 (0.33)
Score:		0.71	0.17	1.00	0.133
P-value:		7.004E-05 (rRNA processing)	9.731E-01 (RNA binding)	2.786E-03 (nucleolus)	3.698E-01 (SWI6)

SFF'(1) AND mRRPE(1) AND PAC(1) AND SCB(1) => SimExpr(YOR310C) OR SimExpr(other) : 8 4

EXPR: (0.242) SFF' (P < 0.000) mRRPE (P < 0.007) PAC (P < 0.099) SCB (P < 0.000)

ORF	SYMBOL	P	F	C	TF
\|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
YKL056C	NO SYMBOL
\|YBR104W\|	YMC2	transport -> transport	transporter activity -> transporter activity	mitochondrial inner membrane -> cytoplasm, inner membrane	FKH1, FKH2
YJL069C	UTP18				ABF1
YNL112W	DBP2		RNA helicase activity -> RNA binding	bud neck -> site of polarized growth (sensu Fungi)
YJL138C	TIF2	translational initiation, regulation of translational initiation -> protein biosynthesis	translation initiation factor activity, RNA helicase activity -> translation factor activity\, nucleic acid binding, RNA binding	ribosome, cytoplasm -> cytoplasm, ribonucleoprotein complex	PHD1
\|YCL059C\|	KRR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent		nucleolus -> nucleus
\|YNL292W\|	PUS4	tRNA modification -> RNA processing, tRNA metabolism	pseudouridylate synthase activity -> carbon-oxygen lyase activity	mitochondrion, nucleus -> cytoplasm, nucleus	RCS1
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
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent	RNA binding -> RNA binding	nucleolus -> nucleus
YLR249W	YEF3	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
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 (0.67)	RNA binding (0.62)	nucleus (0.60)	ABF1 (0.43)
Score:		0.44	0.39	0.60	0.143
P-value:		2.661E-04 (rRNA processing)	1.098E-02 (RNA binding)	5.025E-04 (nucleolus)	4.564E-01 (ABF1)

ALPHA1'(1) AND mRRPE(1) AND SWI5(1) AND PAC(1) => SimExpr(YOR310C) OR SimExpr(other) : 7 3

CSRE(1) AND ndt80(MSE)(1) => SimExpr(YHR124W) OR SimExpr(other) : 6 1

CSRE(1) AND ndt80(MSE)(1) => SimExpr(YPL255W) OR SimExpr(other) : 5 2

CSRE(1) AND ndt80(MSE)(1) => SimExpr(YML050W) OR SimExpr(other) : 5 2

MCM1(1) AND mRRPE(1) AND PAC(1) => SimExpr(YDR184C) OR SimExpr(other) : 5 1

EXPR: (0.205) mRRPE (P < 0.000) PAC (P < 0.007) MCM1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YBR267W	NO SYMBOL
\|YDR279W\|	RNH202				GCR2, MBP1, RIM101, RLM1, SWI6, THI2
YIL122W	POG1	re-entry into mitotic cell cycle after pheromone arrest -> re-entry into mitotic cell cycle, conjugation with cellular fusion, response to pheromone	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> nucleus	ASH1, CIN5, NRG1, RLM1, SMP1, YAP6
YDR184C	ATC1	response to stress, polar budding -> response to stress, polar budding		nucleus -> nucleus	ARO80, GLN3, SIP4, SKO1
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> rRNA processing, snRNA processing	RNA binding -> RNA binding	nucleolus -> nucleus
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis, rRNA processing		nucleolus -> nucleus
Main:		rRNA processing (0.50)	RNA binding (0.50)	nucleus (1.00)	RLM1 (0.67)
Score:		0.17	0.00	1.00	0.333
P-value:		2.148E-01 (rRNA processing)	2.000E+00	1.182E-01 (nucleolus)	1.010E-01 (RLM1)

ALPHA1'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YGL029W) OR SimExpr(other) : 33 14

ALPHA1'(1) AND mRRPE(1) AND PAC(1) AND MCM1'(1) => SimExpr(YGL029W) OR SimExpr(other) : 8 2

ALPHA1(1) AND mRRPE(1) AND PAC(1) => SimExpr(YGL029W) OR SimExpr(other) : 18 6

EXPR: (0.225) mRRPE (P < 0.000) PAC (P < 0.007) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
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
YCR072C	NO SYMBOL				YFL044C
\|YHR128W\|	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups		CIN5
YMR290C	HAS1			nucleolus, nuclear membrane -> nucleus, endomembrane system	RAP1
\|YKL056C\|	NO SYMBOL
\|YPL266W\|	DIM1	rRNA modification, 35S primary transcript processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	rRNA (adenine-N6\,N6-)-dimethyltransferase activity -> transferase activity\, transferring one-carbon groups	nucleolus -> nucleus	ARG81, STP2
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
YMR131C	RRB1	ribosome biogenesis -> cell organization and biogenesis		nucleolus -> nucleus	FZF1, MATa1, RGT1
YJL069C	UTP18				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
\|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
YNL075W	IMP4	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	rRNA primary transcript binding -> RNA binding	small nucleolar ribonucleoprotein complex, small nuclear ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	USV1
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
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
YHR196W	UTP9	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex, nucleolus, nucleus -> nucleus, ribonucleoprotein complex
YMR259C	NO SYMBOL				ARG80, GCR2, GTS1, HIR1, SRD1
\|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
YJR070C	NO SYMBOL				GAT3, YAP5
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
\|YHR169W\|	DBP8	35S primary transcript processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ATP dependent RNA helicase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleus
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
YOR381W	FRE3	iron-siderochrome transport, iron ion homeostasis -> transport, cell homeostasis	ferric-chelate reductase activity -> oxidoreductase activity\, oxidizing metal ions	plasma membrane, integral to membrane -> plasma membrane, integral to membrane	CIN5, PDR1, YAP6
Main:		cell organization and biogenesis (0.71)	RNA binding (0.57)	nucleus (0.81)	RAP1 (0.18)
Score:		0.58	0.32	0.70	0.044
P-value:		1.939E-10 (ribosome biogenesis)	2.350E-03 (snoRNA binding)	7.819E-11 (nucleolus)	1.000E+00

ALPHA1(1) AND SFF(1) AND mRRPE(1) AND PAC(1) => SimExpr(YGL029W) OR SimExpr(other) : 9 3

EXPR: (0.230) SFF (P < 0.000) mRRPE (P < 0.003) PAC (P < 0.058) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
YCR072C	NO SYMBOL				YFL044C
YMR290C	HAS1			nucleolus, nuclear membrane -> nucleus, endomembrane system	RAP1
YJL069C	UTP18				ABF1
\|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
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
YMR259C	NO SYMBOL				ARG80, GCR2, GTS1, HIR1, SRD1
\|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
YLR249W	YEF3	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
\|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
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent		nucleolus -> nucleus
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
Main:		RNA processing (0.57)	RNA binding (0.50)	nucleus (0.62)	GCR2 (0.11)
Score:		0.33	0.20	0.46	0.000
P-value:		5.611E-03 (rRNA processing)	2.860E-02 (ATP dependent RNA helicase activity)	4.568E-04 (nucleolus)	1.000E+00

ALPHA1(1) AND SFF'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YGL029W) OR SimExpr(other) : 10 4

EXPR: (0.232) SFF' (P < 0.000) mRRPE (P < 0.001) PAC (P < 0.039) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
YCR072C	NO SYMBOL				YFL044C
YMR290C	HAS1			nucleolus, nuclear membrane -> nucleus, endomembrane system	RAP1
\|YKL056C\|	NO SYMBOL
YJL069C	UTP18				ABF1
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
\|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
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
\|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
YLR249W	YEF3	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
\|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
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent		nucleolus -> nucleus
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
Main:		RNA processing (0.56)	RNA binding (0.50)	nucleus (0.67)	USV1 RAP1 (0.20)
Score:		0.31	0.21	0.53	0.044
P-value:		6.168E-04 (rRNA processing)	3.923E-02 (ATP dependent RNA helicase activity)	6.528E-05 (nucleolus)	1.874E-01 (USV1)

SFF(1) AND SWI5(1) AND AFT1(1) AND SCB(1) => SimExpr(YMR253C) OR SimExpr(other) : 5 1

EXPR: (0.200) SFF (P < 0.001) SWI5 (P < 0.000) AFT1 (P < 0.000) SCB (P < 0.001)

ORF	SYMBOL	P	F	C	TF
YHR085W	IPI1	rRNA processing -> cytoplasm organization and biogenesis, RNA metabolism, transcription			FZF1
YMR253C	NO SYMBOL				MCM1
YLR229C	CDC42	exocytosis, apical bud growth, isotropic bud growth, pseudohyphal growth, invasive growth, Rho protein signal transduction, signal transduction during conjugation with cellular fusion, establishment of cell polarity (sensu Saccharomyces) -> secretory pathway, budding, growth pattern, cellular morphogenesis, intracellular signaling cascade, cell surface receptor linked signal transduction, conjugation with cellular fusion, cytoplasm organization and biogenesis, perception of abiotic stimulus, sensory perception, vesicle-mediated transport	Rho small monomeric GTPase activity, signal transducer activity -> Rho small monomeric GTPase activity, signal transducer activity	soluble fraction, plasma membrane, bud tip, bud neck, shmoo tip -> soluble fraction, plasma membrane, bud tip, bud neck, shmoo tip	ABF1, FZF1, INO2, RTS2
YOL132W	GAS4			cell wall (sensu Fungi) -> cell wall (sensu Fungi)
YDR297W	SUR2	sphingolipid metabolism, sphingolipid biosynthesis -> membrane lipid metabolism, lipid biosynthesis	sphingosine hydroxylase activity -> sphingosine hydroxylase activity	endoplasmic reticulum -> endoplasmic reticulum	CBF1, MTH1
\|YPR185W\|	APG13	protein-vacuolar targeting, autophagy -> cytoplasm organization and biogenesis, autophagy, intracellular transport, protein metabolism, protein transport	protein binding -> protein binding	extrinsic to membrane -> extrinsic to membrane	MET4, SWI6
Main:		cytoplasm organization and biogenesis (0.75)	protein binding (0.33)	endoplasmic reticulum (0.25)	FZF1 (0.40)
Score:		0.50	0.00	0.00	0.100
P-value:		7.326E-01 (cytoplasm organization and biogenesis)	2.356E+00 (binding)	1.742E+00 (membrane)	4.289E-02 (FZF1)

LYS14(1) AND mRRPE(1) AND PAC(1) => SimExpr(YNL110C) OR SimExpr(other) : 6 2

EXPR: (0.162) LYS14 (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.005)

ORF	SYMBOL	P	F	C	TF
\|YHR128W\|	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups		CIN5
YMR290C	HAS1			nucleolus, nuclear membrane -> nucleolus, nuclear membrane	RAP1
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 -> nucleolus, ribonucleoprotein complex
YNL110C	NOP15	ribosomal large subunit biogenesis -> cell organization and biogenesis		nucleus, nucleolus -> nucleus, nucleolus
YGR280C	PXR1	35S primary transcript processing, snRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	RNA binding -> RNA binding	nucleolus -> nucleolus
\|YMR259C\|	NO SYMBOL				ARG80, GCR2, GTS1, HIR1, SRD1
YJR070C	NO SYMBOL				GAT3, YAP5
YGL099W	LSG1	conjugation with cellular fusion, sporulation (sensu Saccharomyces), ribosome nucleus export -> conjugation, sporulation, cell organization and biogenesis, protein metabolism, transport, sexual reproduction	GTPase activity -> purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	cytoplasm -> cytoplasm	PHO4
Main:		cell organization and biogenesis (0.80)	RNA binding (0.50)	nucleolus (0.80)	GCR2 (0.20)
Score:		0.80	0.17	0.60	0.000
P-value:		2.107E-03 (ribosome biogenesis)	6.653E-01 (RNA binding)	7.382E-04 (nucleolus)	1.000E+00

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

EXPR: (0.224) MCM1' (P < 0.000) RAP1 (P < 0.033)

ORF	SYMBOL	P	F	C	TF
YPL090C	RPS6A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, INO4, RAP1, YAP5
\|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
YGR254W	ENO1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphopyruvate hydratase activity -> carbon-oxygen lyase activity	phosphopyruvate hydratase complex, cytoplasm -> cytoplasm	FKH2, MSN4, PDR1, SWI5, YAP5
YLR061W	RPL22A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	BAS1, FHL1, HIR1, PDR1, RAP1, RCS1, RME1, ZAP1
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
\|YPL180W\|	BIT89	glycerol metabolism -> alcohol metabolism, glycerol ether metabolism, lipid metabolism			REB1, RGT1, SIG1
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
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
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
\|YJR139C\|	HOM6	homoserine biosynthesis, methionine metabolism, threonine metabolism -> amine metabolism, sulfur metabolism, biosynthesis, amino acid and derivative metabolism, organic acid metabolism	homoserine dehydrogenase activity -> oxidoreductase activity\, acting on CH-OH group of donors		HMS1, RAP1
\|YHL038C\|	CBP2	RNA splicing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	pre-mRNA splicing factor activity -> RNA binding	mitochondrion -> cytoplasm	RAP1
YGL147C	RPL9A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, MBP1, RAP1, SWI4
\|YLR146C\|	SPE4	pantothenate biosynthesis, spermine biosynthesis -> biosynthesis, amine metabolism, coenzymes and prosthetic group metabolism, amino acid and derivative metabolism, secondary metabolism	spermine synthase activity -> transferase activity\, transferring alkyl or aryl (other than methyl) groups
YGR214W	RPS0A	protein biosynthesis, ribosomal small subunit assembly and maintenance -> biosynthesis, cell organization and biogenesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, RAP1
YDL130W	RPP1B	protein biosynthesis, translational elongation -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAL4, RAP1, RFX1
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
YIL018W	RPL2B	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic large ribosomal subunit (sensu Eukarya) -> cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, SWI5, YAP5
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
YKL152C	GPM1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphoglycerate mutase activity -> intramolecular transferase activity	cytosol -> cytoplasm	GCR1, GCR2, HSF1, RAP1
\|YKL033W\|	NO SYMBOL				RPH1
YBR117C	TKL2	pentose-phosphate shunt -> coenzymes and prosthetic group metabolism, alcohol metabolism, water-soluble vitamin metabolism, carbohydrate metabolism, energy derivation by oxidation of organic compounds, catabolism	transketolase activity -> transferase activity\, transferring aldehyde or ketonic groups		FHL1, RAP1
Main:		biosynthesis (0.85)	structural constituent of ribosome (0.68)	cytoplasm (1.00)	RAP1 (0.80)
Score:		0.75	0.47	1.00	0.732
P-value:		2.321E-07 (biosynthesis)	4.470E-11 (structural constituent of ribosome)	1.734E-12 (cytosolic ribosome (sensu Eukarya))	1.498E-16 (FHL1)

RAP1(1) AND SWI5(1) AND MCM1'(1) => SimExpr(YKL006W) OR SimExpr(other) : 5 1

EXPR: (0.178) SWI5 (P < 0.000) MCM1' (P < 0.000) RAP1 (P < 0.055)

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
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
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
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 (1.00)	structural constituent of ribosome (1.00)	cytosolic ribosome (sensu Eukarya) (1.00)	RAP1 FHL1 (1.00)
Score:		1.00	1.00	1.00	1.000
P-value:		1.267E-05 (protein biosynthesis)	2.262E-07 (structural constituent of ribosome)	6.453E-08 (cytosolic ribosome (sensu Eukarya))	4.049E-09 (FHL1)

ALPHA1(1) AND SFF'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YLR249W) OR SimExpr(other) : 10 4

RAP1(1) AND PDR(1) => SimExpr(YNL096C) : 6

EXPR: (0.164) PDR (P < 0.000) RAP1 (P < 0.004)

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 -> acetyltransferase activity	nuclear chromosome\, telomeric region, nuclear chromatin -> chromosome, nuclear chromosome	GRF10(Pho2), SUM1
YGR254W	ENO1	gluconeogenesis, glycolysis -> alcohol metabolism, carbohydrate biosynthesis, carbohydrate metabolism, energy derivation by oxidation of organic compounds, biosynthesis, catabolism	phosphopyruvate hydratase activity -> phosphopyruvate hydratase activity	phosphopyruvate hydratase complex, cytoplasm -> cytoplasm	FKH2, MSN4, PDR1, SWI5, YAP5
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
YNL096C	RPS7B	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, SFP1
YDR406W	PDR15	transport -> transport	ATP-binding cassette (ABC) transporter activity -> ATP-binding cassette (ABC) transporter activity	integral to membrane -> integral to membrane
YPR080W	TEF1	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation elongation factor activity	ribosome -> cytoplasm, ribonucleoprotein complex	FHL1, PDR1, RAP1, YAP5
Main:		biosynthesis (0.67)	structural constituent of ribosome (0.33)	cytoplasm (0.67)	RAP1 FHL1 YAP5 (0.60)
Score:		0.40	0.07	0.40	0.500
P-value:		1.961E-01 (biosynthesis)	2.565E-01 (structural constituent of ribosome)	5.038E-02 (cytosolic small ribosomal subunit (sensu Eukarya))	8.067E-04 (YAP5)

ndt80(MSE)(1) AND SWI5(1) => SimExpr(YFR023W) OR SimExpr(other) : 16 7

ndt80(MSE)(1) AND mRRPE(1) => SimExpr(YFR023W) OR SimExpr(other) : 6 1

SFF(1) AND ndt80(MSE)(1) AND MCM1'(1) => SimExpr(YFR023W) OR SimExpr(other) : 9 2

ndt80(MSE)(1) AND SFF'(1) AND SWI5(1) AND MCM1'(1) => SimExpr(YFR023W) : 5

LYS14(1) AND mRRPE(1) AND PAC(1) => SimExpr(YMR290C) OR SimExpr(other) : 6 2

ndt80(MSE)(1) AND SWI5(1) => SimExpr(YPR122W) OR SimExpr(other) : 16 7

ndt80(MSE)(1) AND CCA(1) => SimExpr(YPR122W) OR SimExpr(other) : 5 1

ALPHA1(1) AND SFF'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YJL069C) OR SimExpr(other) : 10 4

ALPHA1'(1) AND SWI5(1) AND Ume6(URS1)(1) => SimExpr(YDR285W) OR SimExpr(other) : 5 2

EXPR: (0.213) ALPHA1' (P < 0.000) SWI5 (P < 0.000) Ume6(URS1) (P < 0.084)

ORF	SYMBOL	P	F	C	TF
YNL196C	NO SYMBOL
YDR285W	ZIP1	meiosis, synapsis -> cell proliferation	binding -> binding	synaptonemal complex -> chromosome, nucleus	ABF1, FKH1, GCR2, GLN3, GTS1, RIM101, RTG1, SWI6
YHL024W	RIM4	sporulation, meiosis, premeiotic DNA synthesis, meiotic recombination -> sporulation, M phase, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, cell proliferation	binding -> binding	cytoplasm -> cytoplasm	FKH2, PHD1
YPR007C	SPO69	meiosis, sister chromatid cohesion -> cell proliferation	binding -> binding	condensed nuclear chromosome\, pericentric region, nuclear cohesin complex -> chromosome, nuclear chromosome	MCM1
YDR180W	SCC2	mitotic sister chromatid cohesion -> cell proliferation, cell cycle	protein kinase activity -> protein kinase activity	nuclear cohesin complex -> chromosome, nucleus	GLN3, MSN4, ROX1
\|YMR280C\|	CAT8	gluconeogenesis, positive regulation of transcription from Pol II promoter -> alcohol metabolism, monosaccharide metabolism, carbohydrate metabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, biosynthesis, energy pathways	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> nucleus	ABF1, REB1
\|YDR091C\|	RLI1		binding -> binding
Main:		cell proliferation (0.80)	binding (0.67)	nucleus (0.60)	ABF1 GLN3 (0.40)
Score:		0.70	0.40	0.50	0.200
P-value:		4.464E-03 (sister chromatid cohesion)	3.930E-01 (binding)	1.718E-03 (condensed chromosome)	4.976E-02 (GLN3)

ALPHA1(1) AND mRRPE(1) AND PAC(1) AND SCB(1) => SimExpr(YJL109C) OR SimExpr(other) : 6 2

EXPR: (0.169) mRRPE (P < 0.001) PAC (P < 0.013) SCB (P < 0.000) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
\|YKL056C\|	NO SYMBOL
YMR131C	RRB1	ribosome biogenesis -> ribosome biogenesis		nucleolus -> nucleus	FZF1, MATa1, RGT1
YJL069C	UTP18				ABF1
YMR239C	RNT1	35S primary transcript processing -> ribosome biogenesis, RNA processing, transcription from Pol I promoter	ribonuclease III activity -> hydrolase activity\, acting on ester bonds, RNA binding	nucleolus -> nucleus
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
\|YMR259C\|	NO SYMBOL				ARG80, GCR2, GTS1, HIR1, SRD1
YJR070C	NO SYMBOL				GAT3, YAP5
YLR249W	YEF3	translational elongation -> translational elongation	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
Main:		ribosome biogenesis (0.75)	RNA binding (0.67)	nucleus (0.75)	GCR2 (0.20)
Score:		0.50	0.33	0.67	0.000
P-value:		4.481E-02 (ribosome biogenesis)	5.544E-01 (RNA binding)	1.842E-02 (nucleolus)	1.000E+00

ALPHA1(1) AND SFF(1) AND mRRPE(1) AND PAC(1) => SimExpr(YJL109C) OR SimExpr(other) : 9 3

ALPHA1'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YJL109C) OR SimExpr(other) : 38 9

ALPHA1(1) AND SFF'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YJL109C) OR SimExpr(other) : 11 3

ALPHA1(1) AND ALPHA1'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YJL109C) OR SimExpr(other) : 13 2

EXPR: (0.185) ALPHA1' (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.005) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
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
YCR072C	NO SYMBOL				YFL044C
YHR128W	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups		CIN5
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
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
\|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
YNL075W	IMP4	rRNA modification, 35S primary transcript processing, processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, transcription	rRNA primary transcript binding -> RNA binding	small nucleolar ribonucleoprotein complex, small nuclear ribonucleoprotein complex -> nucleus, ribonucleoprotein complex	USV1
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
YHR196W	UTP9	processing of 20S pre-rRNA -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	snoRNA binding -> RNA binding	small nucleolar ribonucleoprotein complex, nucleolus, nucleus -> nucleus, ribonucleoprotein complex
\|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
YJR070C	NO SYMBOL				GAT3, YAP5
YHR169W	DBP8	35S primary transcript processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	ATP dependent RNA helicase activity -> RNA binding, purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	nucleolus -> nucleus
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
YOR381W	FRE3	iron-siderochrome transport, iron ion homeostasis -> transport, cell homeostasis	ferric-chelate reductase activity -> oxidoreductase activity\, oxidizing metal ions	plasma membrane, integral to membrane -> plasma membrane, integral to membrane	CIN5, PDR1, YAP6
Main:		cell organization and biogenesis (0.67)	RNA binding (0.64)	nucleus (0.80)	USV1 RAP1 CIN5 FHL1 (0.18)
Score:		0.55	0.40	0.62	0.055
P-value:		3.282E-07 (ribosome biogenesis)	5.374E-04 (snoRNA binding)	3.980E-06 (nucleolus)	3.487E-01 (USV1)

ALPHA1'(1) AND mRRPE(1) AND SWI5(1) AND PAC(1) => SimExpr(YJL109C) OR SimExpr(other) : 7 3

ALPHA1(1) AND SFF(1) AND SFF'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YJL109C) OR SimExpr(other) : 9 2

EXPR: (0.205) SFF (P < 0.000) SFF' (P < 0.000) mRRPE (P < 0.002) PAC (P < 0.044) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YOL022C	NO SYMBOL				MAC1, MOT3, RTS2
YCR072C	NO SYMBOL				YFL044C
YMR290C	HAS1			nucleolus, nuclear membrane -> nucleus, endomembrane system	RAP1
YJL069C	UTP18				ABF1
\|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
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
\|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
YLR249W	YEF3	translational elongation -> protein biosynthesis	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
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
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> ribosome biogenesis and assembly, RNA processing, transcription\, DNA-dependent		nucleolus -> nucleus
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
Main:		RNA processing (0.57)	RNA binding (0.50)	nucleus (0.62)	ABF1 (0.12)
Score:		0.33	0.20	0.46	0.000
P-value:		3.822E-03 (rRNA processing)	2.389E-02 (ATP dependent RNA helicase activity)	2.746E-04 (nucleolus)	1.000E+00

ALPHA2(1) AND mRRPE(1) AND PAC(1) => SimExpr(YJR070C) OR SimExpr(other) : 6 3

EXPR: (0.213) ALPHA2 (P < 0.000) mRRPE (P < 0.003) PAC (P < 0.066)

ORF	SYMBOL	P	F	C	TF
YKL172W	EBP2	rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus	ABF1, FZF1, RFX1
YHR128W	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups		CIN5
YMR049C	ERB1	rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			RTG3
\|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
\|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
YJR070C	NO SYMBOL				GAT3, YAP5
YLR249W	YEF3	translational elongation -> biosynthesis, protein metabolism	translation elongation factor activity -> translation factor activity\, nucleic acid binding	ribosome -> cytoplasm, ribonucleoprotein complex	INO2, INO4
YGL029W	CGR1	ribosome biogenesis, rRNA processing -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleolus -> nucleus
\|YNR046W\|	NO SYMBOL				ABF1
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.71)	transferase activity\, transferring glycosyl groups (0.50)	nucleus (0.60)	ABF1 (0.25)
Score:		0.62	0.17	0.40	0.036
P-value:		1.454E-03 (rRNA processing)	1.462E-01 (transferase activity\, transferring glycosyl groups)	2.687E-02 (nucleolus)	1.000E+00

LYS14(1) AND ALPHA1'(1) AND PAC(1) => SimExpr(YJR070C) OR SimExpr(other) : 7 2

EXPR: (0.234) LYS14 (P < 0.001) ALPHA1' (P < 0.000) PAC (P < 0.169)

ORF	SYMBOL	P	F	C	TF
\|YOL075C\|	NO SYMBOL				CRZ1, DAL82, SIP4
YHR128W	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups		CIN5
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
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
YJR070C	NO SYMBOL				GAT3, YAP5
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
YDR361C	BCP1				ABF1, ARO80, GLN3, HAP5, IXR1, YAP1
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
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.67)	RNA binding (0.40)	nucleus (0.60)	CIN5 YAP1 GLN3 (0.29)
Score:		0.60	0.10	0.40	0.095
P-value:		6.921E-02 (ribosome biogenesis)	8.159E-01 (RNA binding)	3.071E-01 (nucleolus)	1.198E-01 (GLN3)

ALPHA1(1) AND ALPHA1'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YJR070C) OR SimExpr(other) : 13 2

LYS14(1) AND ALPHA1'(1) AND mRRPE(1) AND PAC(1) => SimExpr(YJR070C) : 5

EXPR: (0.133) LYS14 (P < 0.000) ALPHA1' (P < 0.000) mRRPE (P < 0.000) PAC (P < 0.001)

ORF	SYMBOL	P	F	C	TF
YHR128W	FUR1	pyrimidine salvage -> biosynthesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	uracil phosphoribosyltransferase activity -> transferase activity\, transferring glycosyl groups		CIN5
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 -> nucleolus, 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 -> nucleolus
YJR070C	NO SYMBOL				GAT3, YAP5
YGL099W	LSG1	conjugation with cellular fusion, sporulation (sensu Saccharomyces), ribosome nucleus export -> conjugation, sporulation, cell organization and biogenesis, protein metabolism, transport, sexual reproduction	GTPase activity -> purine nucleotide binding, hydrolase activity\, acting on acid anhydrides	cytoplasm -> cytoplasm	PHO4
Main:		cell organization and biogenesis (0.75)	RNA binding (0.50)	nucleolus (0.67)	GAT3 (0.33)
Score:		0.83	0.17	0.33	0.000
P-value:		8.699E-03 (ribosome biogenesis)	2.743E-01 (RNA binding)	8.076E-02 (nucleolus)	3.025E-01 (GAT3)

SFF(1) AND ndt80(MSE)(1) => SimExpr(YMR001C) OR SimExpr(other) : 27 10

ALPHA1(1) AND ndt80(MSE)(1) AND SFF'(1) => SimExpr(YMR001C) OR SimExpr(other) : 13 6

EXPR: (0.248) ndt80(MSE) (P < 0.455) SFF' (P < 0.000) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YJL160C	NO SYMBOL				ACE2, HIR2, MCM1, SWI5
YPR122W	AXL1	axial budding, bud site selection, conjugation with cellular fusion, peptide pheromone maturation -> asexual reproduction, conjugation, protein metabolism, cell proliferation, cell organization and biogenesis, sexual reproduction	metalloendopeptidase activity -> endopeptidase activity, metallopeptidase activity	integral to membrane, bud neck, shmoo tip -> integral to membrane, site of polarized growth (sensu Fungi)	CIN5
\|YHR207C\|	SET5				LEU3, PHO4
\|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
YNR034W	SOL1	tRNA processing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			YFL044C
YNL034W	NO SYMBOL				MAC1, MET4, NDD1, RME1
YFR023W	PES4	DNA dependent DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			DIG1, FKH1, FKH2, GLN3, HAP3, MCM1, MSN2, RIM101, RLM1, RTG3, STE12, SUM1, THI2, YAP1
YMR125W	STO1	mRNA splicing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	mRNA binding -> mRNA binding	commitment complex, snRNA cap binding complex -> nucleus, cytoplasm, ribonucleoprotein complex	ABF1, FZF1, HAP3, MET31, RTG1, SRD1, SUM1, YAP6, ZAP1
YOL132W	GAS4			cell wall (sensu Fungi) -> cell wall
YGL116W	CDC20	mitotic spindle elongation, ubiquitin-dependent protein catabolism, mitotic metaphase/anaphase transition, mitotic chromosome segregation, cyclin catabolism -> cell organization and biogenesis, catabolism, cell proliferation, cell cycle, protein metabolism	enzyme activator activity -> enzyme activator activity	anaphase-promoting complex -> nucleus, ubiquitin ligase complex	DIG1, FKH2, INO2, INO4, IXR1, MCM1, NDD1
\|YOR388C\|	FDH1	formate catabolism, NADH regeneration -> catabolism, coenzymes and prosthetic group metabolism, one-carbon compound metabolism, vitamin metabolism, organic acid metabolism	formate dehydrogenase activity -> oxidoreductase activity\, acting on the aldehyde or oxo group of donors\, NAD or NADP as acceptor	cytosol -> cytoplasm	MCM1, YJL206C
YBR115C	LYS2	lysine biosynthesis\, aminoadipic pathway -> amine metabolism, amino acid and derivative metabolism, organic acid metabolism, biosynthesis	aminoadipate-semialdehyde dehydrogenase activity -> oxidoreductase activity\, acting on the aldehyde or oxo group of donors\, NAD or NADP as acceptor	cytoplasm -> cytoplasm	DAL81, GCN4
YDR438W	NO SYMBOL				CBF1
\|YGL189C\|	RPS26A	protein biosynthesis -> biosynthesis, protein metabolism	structural constituent of ribosome -> structural constituent of ribosome	cytosolic small ribosomal subunit (sensu Eukarya) -> eukaryotic 48S initiation complex, cytoplasm, ribonucleoprotein complex	FHL1, GAT3, PDR1, RAP1, RGM1, YAP5
YDR218C	SPR28	cellular morphogenesis, cell wall organization and biogenesis -> cell organization and biogenesis	structural constituent of cytoskeleton -> structural constituent of cytoskeleton	septin ring (sensu Saccharomyces) -> site of polarized growth (sensu Fungi), cell cortex, cytoskeleton	YAP6
\|YGL121C\|	GPG1	signal transduction -> signal transduction	signal transducer activity -> signal transducer activity		CHA4
YOR214C	NO SYMBOL				BAS1
\|YMR280C\|	CAT8	gluconeogenesis, positive regulation of transcription from Pol II promoter -> alcohol metabolism, monosaccharide metabolism, carbohydrate metabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, biosynthesis, energy pathways	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> nucleus	ABF1, REB1
YMR001C	CDC5	DNA dependent DNA replication, protein amino acid phosphorylation -> phosphorus metabolism, cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	protein serine/threonine kinase activity -> phosphotransferase activity\, alcohol group as acceptor	nucleus, spindle pole, bud neck -> nucleus, cytoplasm, site of polarized growth (sensu Fungi)	NDD1, REB1, SWI6
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.38)	oxidoreductase activity\, acting on the aldehyde or oxo group of donors\, NAD or NADP as acceptor (0.18)	cytoplasm (0.55)	NDD1 MCM1 (0.22)
Score:		0.36	0.02	0.42	0.111
P-value:		1.825E+00 (DNA dependent DNA replication)	4.899E-02 (oxidoreductase activity\, acting on the aldehyde or oxo group of donors\, NAD or NADP as acceptor)	1.555E-01 (bud neck)	7.065E-02 (NDD1)

ALPHA1(1) AND SFF(1) AND ndt80(MSE)(1) => SimExpr(YMR001C) OR SimExpr(other) : 11 2

EXPR: (0.198) SFF (P < 0.000) ndt80(MSE) (P < 0.097) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YNR034W	SOL1	tRNA processing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			YFL044C
YNL034W	NO SYMBOL				MAC1, MET4, NDD1, RME1
YFR023W	PES4	DNA dependent DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			DIG1, FKH1, FKH2, GLN3, HAP3, MCM1, MSN2, RIM101, RLM1, RTG3, STE12, SUM1, THI2, YAP1
YOL132W	GAS4			cell wall (sensu Fungi) -> cell wall
YGL116W	CDC20	mitotic spindle elongation, ubiquitin-dependent protein catabolism, mitotic metaphase/anaphase transition, mitotic chromosome segregation, cyclin catabolism -> cell organization and biogenesis, catabolism, cell proliferation, cell cycle, protein metabolism	enzyme activator activity -> enzyme activator activity	anaphase-promoting complex -> nucleus, ubiquitin ligase complex	DIG1, FKH2, INO2, INO4, IXR1, MCM1, NDD1
YBR115C	LYS2	lysine biosynthesis\, aminoadipic pathway -> amine metabolism, amino acid and derivative metabolism, organic acid metabolism, biosynthesis	aminoadipate-semialdehyde dehydrogenase activity -> aminoadipate-semialdehyde dehydrogenase activity	cytoplasm -> cytoplasm	DAL81, GCN4
YLR049C	NO SYMBOL				MBP1, SWI5
YDR438W	NO SYMBOL				CBF1
YDR218C	SPR28	cellular morphogenesis, cell wall organization and biogenesis -> cell organization and biogenesis	structural constituent of cytoskeleton -> structural constituent of cytoskeleton	septin ring (sensu Saccharomyces) -> site of polarized growth (sensu Fungi), cell cortex, cytoskeleton	YAP6
\|YGL121C\|	GPG1	signal transduction -> signal transduction	signal transducer activity -> signal transducer activity		CHA4
YOR214C	NO SYMBOL				BAS1
\|YMR280C\|	CAT8	gluconeogenesis, positive regulation of transcription from Pol II promoter -> alcohol metabolism, monosaccharide metabolism, carbohydrate metabolism, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, biosynthesis, energy pathways	specific RNA polymerase II transcription factor activity -> specific RNA polymerase II transcription factor activity	nucleus -> nucleus	ABF1, REB1
YMR001C	CDC5	DNA dependent DNA replication, protein amino acid phosphorylation -> phosphorus metabolism, cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	protein serine/threonine kinase activity -> protein serine/threonine kinase activity	nucleus, spindle pole, bud neck -> nucleus, cytoplasm, site of polarized growth (sensu Fungi)	NDD1, REB1, SWI6
Main:		nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism (0.50)	signal transducer activity (0.17)	nucleus (0.50)	NDD1 (0.25)
Score:		0.36	0.00	0.33	0.076
P-value:		5.608E-01 (DNA dependent DNA replication)	2.997E+00 (enzyme activity)	4.713E-01 (bud neck)	1.459E-01 (NDD1)

ALPHA1(1) AND ndt80(MSE)(1) AND MCM1'(1) => SimExpr(YMR001C) OR SimExpr(other) : 6 2

EXPR: (0.177) ndt80(MSE) (P < 0.068) MCM1' (P < 0.000) ALPHA1 (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YNR034W	SOL1	tRNA processing -> nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			YFL044C
YFR023W	PES4	DNA dependent DNA replication -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism			DIG1, FKH1, FKH2, GLN3, HAP3, MCM1, MSN2, RIM101, RLM1, RTG3, STE12, SUM1, THI2, YAP1
YGL116W	CDC20	mitotic spindle elongation, ubiquitin-dependent protein catabolism, mitotic metaphase/anaphase transition, mitotic chromosome segregation, cyclin catabolism -> cell organization and biogenesis, catabolism, cell proliferation, cell cycle, protein metabolism	enzyme activator activity -> enzyme activator activity	anaphase-promoting complex -> nucleus, ubiquitin ligase complex	DIG1, FKH2, INO2, INO4, IXR1, MCM1, NDD1
YDR273W	DON1	meiosis, spore wall assembly (sensu Saccharomyces) -> cell proliferation, sporulation		spindle, prospore membrane -> cytoplasm, prospore
YPL130W	SPO19	meiosis -> cell proliferation		cell wall (sensu Fungi) -> cell wall	GRF10(Pho2), HAP2, MOT3
\|YOR388C\|	FDH1	formate catabolism, NADH regeneration -> catabolism, coenzymes and prosthetic group metabolism, one-carbon compound metabolism, vitamin metabolism, organic acid metabolism	formate dehydrogenase activity -> formate dehydrogenase activity	cytosol -> cytoplasm	MCM1, YJL206C
\|YBR069C\|	TAT1	amino acid transport -> transport	amino acid transporter activity -> amino acid transporter activity	plasma membrane -> plasma membrane	CIN5, DAL81, PHD1, SWI4
YMR001C	CDC5	DNA dependent DNA replication, protein amino acid phosphorylation -> phosphorus metabolism, cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism, protein metabolism	protein serine/threonine kinase activity -> protein serine/threonine kinase activity	nucleus, spindle pole, bud neck -> nucleus, cytoplasm, site of polarized growth (sensu Fungi)	NDD1, REB1, SWI6
Main:		cell proliferation (0.62)	protein serine/threonine kinase activity (0.25)	cytoplasm (0.50)	MCM1 (0.43)
Score:		0.46	0.00	0.27	0.190
P-value:		2.166E-02 (cell cycle)	2.924E+00 (enzyme activity)	1.050E-01 (spindle)	5.811E-02 (MCM1)

SFF(1) AND ndt80(MSE)(1) AND MCM1'(1) => SimExpr(YMR001C) OR SimExpr(other) : 9 2

ndt80(MSE)(1) AND SFF'(1) AND SWI5(1) AND MCM1'(1) => SimExpr(YMR001C) : 5

ALPHA1(1) AND SFF(1) AND ndt80(MSE)(1) => SimExpr(YNR034W) OR SimExpr(other) : 11 2

ALPHA2(1) AND ALPHA1'(1) AND RPN4(1) => SimExpr(YOL038W) OR SimExpr(other) : 5 2

EXPR: (0.235) ALPHA2 (P < 0.000) ALPHA1' (P < 0.000) RPN4 (P < 0.092)

ORF	SYMBOL	P	F	C	TF
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
YOL038W	PRE6	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity -> peptidase activity	proteasome core complex (sensu Eukarya) -> cytoplasm, nucleus
\|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
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
\|YBL022C\|	PIM1	proteolysis and peptidolysis, response to heat -> catabolism, response to abiotic stimulus, protein metabolism	ATP-dependent peptidase activity -> peptidase activity	mitochondrial matrix -> cytoplasm	RAP1
YDR212W	TCP1	protein folding, cytoskeleton organization and biogenesis -> protein metabolism, cell organization and biogenesis	chaperone activity -> chaperone activity	cytoplasm, cytoskeleton -> cytoplasm
YKL054C	DEF1	response to DNA damage, ubiquitin-dependent protein catabolism -> response to biotic stimulus, catabolism, protein metabolism		nucleus -> nucleus
Main:		protein metabolism (0.86)	peptidase activity (0.33)	cytoplasm (0.86)	SWI4 (0.25)
Score:		0.71	0.07	0.86	0.000
P-value:		1.376E-05 (proteolysis and peptidolysis)	8.873E-02 (peptidase activity)	7.428E-03 (endoplasmic reticulum)	4.110E-01 (MAL33)

mRRPE(1) AND PAC(1) => SimExpr(YKL172W) OR SimExpr(other) : 60 23

mRRPE(1) AND PAC(1) => SimExpr(YGR187C) OR SimExpr(other) : 59 24

ALPHA1'(1) AND SWI5(1) AND Ume6(URS1)(1) => SimExpr(YHL024W) OR SimExpr(other) : 5 2

LYS14(1) AND mRRPE(1) AND PAC(1) => SimExpr(YML093W) OR SimExpr(other) : 6 2

LYS14(1) AND RPN4(1) => SimExpr(YNL012W) OR SimExpr(other) : 9 3

EXPR: (0.212) LYS14 (P < 0.000) RPN4 (P < 0.012)

ORF	SYMBOL	P	F	C	TF
YNL097C	PHO23	chromatin modification -> cell organization and biogenesis, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism		nucleus -> nucleus	MAC1
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
YIL075C	RPN2	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	receptor activity, endopeptidase activity -> receptor activity, endopeptidase activity	proteasome regulatory particle (sensu Eukarya) -> cytoplasm, nucleus	MSS11, REB1, SFL1
\|YJL045W\|	NO SYMBOL				MBP1, ROX1
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
YNL012W	SPO1	meiosis -> cell proliferation	phospholipase activity -> phospholipase activity	nucleus -> nucleus	ARO80, SRD1
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
\|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 -> glucose-6-phosphate 1-dehydrogenase activity	cytoplasm -> cytoplasm	ACE2, ADR1, FKH2, HIR1, IME4, MBP1, NDD1, PHO4, RCS1, SFP1, SKN7, SWI5
YER021W	RPN3	ubiquitin-dependent protein catabolism -> catabolism, protein metabolism	endopeptidase activity -> endopeptidase activity	proteasome regulatory particle (sensu Eukarya) -> cytoplasm, nucleus
YGL201C	MCM6	DNA unwinding, DNA replication initiation -> cell proliferation, nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	chromatin binding, ATP dependent DNA helicase activity -> chromatin binding, ATP dependent DNA helicase activity	cytoplasm, nucleus, pre-replicative complex -> cytoplasm, nucleus	MCM1
\|YKL054C\|	DEF1	response to DNA damage, ubiquitin-dependent protein catabolism -> response to biotic stimulus, catabolism, protein metabolism		nucleus -> nucleus
YOR052C	NO SYMBOL
Main:		catabolism (0.50)	endopeptidase activity (0.38)	nucleus (0.80)	NDD1 PHO4 SWI5 MBP1 (0.22)
Score:		0.33	0.11	0.82	0.083
P-value:		5.589E-03 (ubiquitin-dependent protein catabolism)	2.690E-03 (endopeptidase activity)	3.129E-03 (proteasome complex (sensu Eukarya))	7.289E-01 (PHO4)

ndt80(MSE)(1) AND mRRPE(1) => SimExpr(YOL091W) OR SimExpr(other) : 6 1

ALPHA1'(1) AND SWI5(1) AND Ume6(URS1)(1) => SimExpr(YPR007C) OR SimExpr(other) : 5 2

ndt80(MSE)(1) AND PDR(1) => SimExpr(YDR281C) OR SimExpr(other) : 5 2

EXPR: (0.180) ndt80(MSE) (P < 0.023) PDR (P < 0.000)

ORF	SYMBOL	P	F	C	TF
YKL096W	CWP1	cell wall organization and biogenesis -> cell wall organization and biogenesis	structural constituent of cell wall -> structural constituent of cell wall	cell wall (sensu Fungi) -> cell wall (sensu Fungi)	RLM1, SMP1, STE12, SWI4
\|YCR045C\|	NO SYMBOL
\|YBR159W\|	NO SYMBOL				ACE2, ARG81, GCR2, HIR2, LEU3, MOT3, PDR1, PHD1, SKN7, USV1
YDR317W	NO SYMBOL				HAL9, RLM1
YMR252C	NO SYMBOL				SKN7
YDR281C	PHM6				PHO4, SUM1
YOR338W	NO SYMBOL				RAP1
Main:		cell wall organization and biogenesis (1.00)	structural constituent of cell wall (1.00)	cell wall (sensu Fungi) (1.00)	RLM1 SKN7 (0.33)
Score:		0.00	0.00	0.00	0.133
P-value:		0.000E+00	0.000E+00	0.000E+00	1.672E-01 (RLM1)

ndt80(MSE)(1) AND CCA(1) => SimExpr(YGL230C) OR SimExpr(other) : 5 1

SFF(1) AND ndt80(MSE)(1) => SimExpr(YHR184W) OR SimExpr(other) : 25 12

ndt80(MSE)(1) AND mRRPE(1) => SimExpr(YOR339C) OR SimExpr(other) : 6 1

ndt80(MSE)(1) AND mRRPE(1) => SimExpr(YOR338W) OR SimExpr(other) : 6 1

GCN4(1) AND Leu3(1) => SimExpr(YJR016C) OR SimExpr(other) : 5 1

EXPR: (0.210) GCN4 (P < 0.003) Leu3 (P < 0.004)

ORF	SYMBOL	P	F	C	TF
YLR355C	ILV5	branched chain family amino acid biosynthesis, mitochondrial genome maintenance -> amino acid biosynthesis, mitochondrion organization and biogenesis, branched chain family amino acid metabolism	ketol-acid reductoisomerase activity -> oxidoreductase activity\, acting on the CH-OH group of donors\, NAD or NADP as acceptor	mitochondrion -> cytoplasm	GCN4, MET4
YOR108W	LEU9	leucine biosynthesis -> amino acid biosynthesis, branched chain family amino acid metabolism	2-isopropylmalate synthase activity -> oxo-acid-lyase activity	mitochondrion -> cytoplasm	AZF1, GCN4, LEU3
\|YDL194W\|	SNF3	signal transduction, response to glucose stimulus -> signal transduction, response to glucose stimulus	receptor activity, glucose binding, glucose transporter activity -> receptor activity, monosaccharide binding, hexose transporter activity	plasma membrane -> plasma membrane
YGL009C	LEU1	leucine biosynthesis -> amino acid biosynthesis, branched chain family amino acid metabolism	3-isopropylmalate dehydratase activity -> hydro-lyase activity	cytosol -> cytoplasm	LEU3
YDR158W	HOM2	homoserine biosynthesis, threonine metabolism, methionine metabolism -> amino acid biosynthesis, aspartate family amino acid metabolism, homoserine metabolism, serine family amino acid metabolism, sulfur amino acid metabolism	aspartate-semialdehyde dehydrogenase activity -> oxidoreductase activity\, acting on the aldehyde or oxo group of donors\, NAD or NADP as acceptor		ACE2, HSF1, NDD1, REB1, SKN7, SWI5
YJR016C	ILV3	branched chain family amino acid biosynthesis -> amino acid biosynthesis, branched chain family amino acid metabolism	dihydroxy-acid dehydratase activity -> hydro-lyase activity	mitochondrion -> cytoplasm
Main:		amino acid biosynthesis (0.83)	hydro-lyase activity (0.33)	cytoplasm (0.80)	LEU3 GCN4 (0.50)
Score:		0.67	0.07	0.60	0.333
P-value:		6.193E-08 (branched chain family amino acid biosynthesis)	4.845E-03 (lyase activity)	1.878E-01 (mitochondrion)	1.596E-02 (LEU3)

SFF'(1) AND GCN4(1) AND Leu3(1) => SimExpr(YJR016C) : 5

EXPR: (0.139) SFF' (P < 0.000) GCN4 (P < 0.000) Leu3 (P < 0.002)

ORF	SYMBOL	P	F	C	TF
YLR355C	ILV5	branched chain family amino acid biosynthesis, mitochondrial genome maintenance -> amino acid biosynthesis, mitochondrion organization and biogenesis, branched chain family amino acid metabolism	ketol-acid reductoisomerase activity -> oxidoreductase activity\, acting on the CH-OH group of donors\, NAD or NADP as acceptor	mitochondrion -> cytoplasm	GCN4, MET4
YOR108W	LEU9	leucine biosynthesis -> amino acid biosynthesis, branched chain family amino acid metabolism	2-isopropylmalate synthase activity -> oxo-acid-lyase activity	mitochondrion -> cytoplasm	AZF1, GCN4, LEU3
YGL009C	LEU1	leucine biosynthesis -> amino acid biosynthesis, branched chain family amino acid metabolism	3-isopropylmalate dehydratase activity -> hydro-lyase activity	cytosol -> cytoplasm	LEU3
YDR158W	HOM2	homoserine biosynthesis, threonine metabolism, methionine metabolism -> amino acid biosynthesis, aspartate family amino acid metabolism, homoserine metabolism, serine family amino acid metabolism, sulfur amino acid metabolism	aspartate-semialdehyde dehydrogenase activity -> oxidoreductase activity\, acting on the aldehyde or oxo group of donors\, NAD or NADP as acceptor		ACE2, HSF1, NDD1, REB1, SKN7, SWI5
YJR016C	ILV3	branched chain family amino acid biosynthesis -> amino acid biosynthesis, branched chain family amino acid metabolism	dihydroxy-acid dehydratase activity -> hydro-lyase activity	mitochondrion -> cytoplasm
Main:		amino acid biosynthesis (1.00)	hydro-lyase activity (0.40)	cytoplasm (1.00)	LEU3 GCN4 (0.50)
Score:		1.00	0.10	1.00	0.333
P-value:		1.947E-08 (branched chain family amino acid biosynthesis)	2.482E-03 (lyase activity)	1.037E-01 (mitochondrion)	1.071E-02 (LEU3)

AVERAGE SCORES:

P
  SCORE: 0.515 (Part of genes covered by "Main": 0.643) (No. rules=43/45)
  P-VALUE: 0.535
F
  SCORE: 0.169 (Part of genes covered by "Main": 0.419) (No. rules=42/45)
  P-VALUE: 0.262
C
  SCORE: 0.550 (Part of genes covered by "Main": 0.685) (No. rules=43/45)
  P-VALUE: 0.442
TF
  SCORE: 0.166 (Part of genes covered by "Main": 0.338) (No. rules=45/45)
  P-VALUE: 0.133
EXPRESSION: 0.578 (45)

Discovering regulatory binding-site modules using rule-based learning

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