Supplementary information

1. Module 1
2. Module 2
3. Module 3
4. Module 4
5. Module 5
6. Module 6

An overview of the modules involved in the cell cycle is given in the Figure below. Cell cycle dependency of the identified modules was identified by their seed profiles showing an oscillating behavior and the overrepresented functional classes in the respective modules being related to cell cycle. For each module the corresponding expression profile is indicated in the same color (e.g. red profile belongs to module 1 (Mbp1, Swi4, Swi6, Stb1). These different modules are known to be essential at the different phases of the cell cycle as indicated by the bar. This is also illustrated by the shifted peaking of their different profiles.

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Parameters used


An overview of the parameters used to infer the regulatory modules is given in the table below. +: module detected, /: module not detected


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Motif Logos


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Motif logos of the motifs correlated with the detected motifs.
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Module 1

Genes and Motifs




Genes	Mbp1, Swi4, Swi6, Stb1
Motifs	M_18 (Mbp1), M_12(Mbp1), M_11 (Swi4), M_67(Swi4)




p-values




Seed profile	p-value ChIP	p-value Motif
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Functional Overrepresentation





Detected Genes

Gene	Name	AccessionNr	Description
YDL003W	MCD1	NC_001136	YDL003W Mcd1p Mitotic Chromosome Determinant; similar to S. pombe RAD21; may function in chromosome morphogenesis from S phase through mitosis
YER001W	MNN1	NC_001137	YER001W Mnn1p Alpha-1,3-mannosyltransferase
YGR109C	CLB6	NC_001139	YGR109C Clb6p role in DNA replication during S phase
YGR189C	CRH1	NC_001139	YGR189C Crh1p congo red hypersensitive
YGR221C	TOS2	NC_001139	YGR221C Tos2p Hypothetical ORF
YHR149C	YHR149C	NC_001140	Yhr149cp Hypothetical ORF
YER070W	RNR1	NC_001137	YER070W Rnr1p ribonucleotide reductase
YPL256C	CLN2	NC_001148	YPL256C Cln2p role in cell cycle START
YNL300W	TOS6	NC_001146	YNL300W Tos6p Hypothetical ORF
YPL163C	SVS1	NC_001148	YPL163C Svs1p involved in vanadate resistance
YPL267W	YPL267W	NC_001148	Ypl267wp Hypothetical ORF
YPR120C	CLB5	NC_001148	YPR120C Clb5p role in DNA replication during S phase; additional functional role in formation of mitotic spindles along with Clb3 and Clb4
YMR199W	CLN1	NC_001145	YMR199W Cln1p role in cell cycle START
YMR179W	SPT21	NC_001145	YMR179W Spt21p involved in trascriptional regulation of Ty1 LTRs
YML027W	YOX1	NC_001145	YML027W Yox1p Homeodomain protein that binds leu-tRNA gene
YKL113C	RAD27	NC_001143	YKL113C Rad27p DNA repair protein that belongs to the RAD2(pombe)*FEN1 subfamily




Correlation between genes


66 genes were correlated with the seed profile (minimal correlation of 0.7). In 18 of the 66 genes, the complete module consisting of all 4 motifs and 4 regulators was present (Table 2). Based on the functional categories that were significantly overrepresented in this subset of 18 genes, this module was clearly involved in cell cycle, DNA synthesis and replication. Note that if the complete module (consisting of all regulators with their respective putative motifs) would be responsible for the observed expression pattern, a large overlap between the genes recruited using the stringent conditions (presence of all regulators and motifs) versus the recruitment based on the correlation only is to be expected. This not being the case (in this example we only recovered 18 genes of the 66) can, to some extent, be explained by the presence of a large number of false negative measurements in the respective datasets. Alternatively the large module consisting of 4 regulators might only be present in a subset of genes correlated with the seed profile (in 18 genes in this case). The other 48 genes might contain different combinations of the same subset of regulators and motifs. Indeed we also found strong evidence for the presence of modules containing regulator combinations (Swi4, Swi6), (Mbp1, Swi4), (Mbp1, Swi6), (Stb1, Swi4) and (Mbp1, Swi4, Swi6). Therefore, we verified which combination of regulators occurred most frequently in this set of 66 genes, correlated with the seed profile. These appeared to be the combination (Mbp1, Swi4, Swi6, Stb1) and (Mbp1, Swi6). Therefore, we could hypothesize that a subset of the genes with a profile correlated to the seed profile (18) are regulated by all 4 regulators, for other genes the presence of only 2 or 3 regulators would be sufficient. These detected dependencies seemed to be biologically relevant as it is known that SBF and MBF are both heteromeric transcription factors that are involved in the transcriptional activation during G1. Both regulators share a common regulatory subunit Swi6 that is tethered to DNA via its binding partners Swi4 and Mbp1 in SBF and MBF respectively. The distinction between SBF and MBF mediated transcriptional control is not absolute and partially redundant as Mbp1 and Swi4 would share 34% of their target genes.

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Module 2




Genes and Motifs




Genes	Mbp1, Swi4, Swi6, Fkh2
Motifs	M_18 (Mbp1), M_12(Mbp1), M_11 (Swi4), M_8(Mcm)




p-values




Seed profile	p-value ChIP	p-value Motif
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Functional Overrepresentation





Detected Genes

Gene	Name	AccessionNr	Description
YDL003W	MCD1	NC_001136	YDL003W Mcd1p Mitotic Chromosome Determinant; similar to S. pombe RAD21; may function in chromosome morphogenesis from S phase through mitosis
YGR143W	SKN1	NC_001139	YGR143W Skn1p Involved in (1->6)-beta-glucan biosynthesis
YIL123W	SIM1	NC_001141	YIL123W Sim1p (putative) invovled in control of DNA replication
YHR061C	GIC1	NC_001140	YHR061C Gic1p Gtpase-interacting component 1
YDR451C	YHP1	NC_001136	YDR451C Yhp1p
YBR078W	ECM33	NC_001134	YBR078W Ecm33p ExtraCellular Mutant
YDR261C	EXG2	NC_001136	YDR261C Exg2p Exo-1,3-b-glucanase
YJL080C	SCP160	NC_001142	YJL080C Scp160p May be required during cell division for faithful partitioning of the ER-nuclear envelope membranes, involved in control of mitotic chromsome transmission
YLR300W	EXG1	NC_001144	YLR300W Exg1p Exo-1,3-beta-glucanase
YLR380W	CSR1	NC_001144	YLR380W Csr1p chs5 spa2 rescue; isolated as a multicopy suppressor of the lethality of chs5 spa2 double mutant at 37 degrees.
YLR342W	FKS1	NC_001144	YLR342W Fks1p Required for viability of calcineurin mutants
YLR437C	YLR437C	NC_001144	Ylr437cp Hypothetical ORF
YOR114W	YOR114W	NC_001147	Yor114wp Hypothetical ORF
YPL127C	HHO1	NC_001148	YPL127C Hho1p Histone H1
YNL089C	YNL089C	NC_001146	Ynl089cp Hypothetical ORF
YJL187C	SWE1	NC_001142	YJL187C Swe1p protein kinase homolog
YNR009W	YNR009W	NC_001146	Ynr009wp Hypothetical ORF
YPL163C	SVS1	NC_001148	YPL163C Svs1p involved in vanadate resistance
YMR199W	CLN1	NC_001145	YMR199W Cln1p role in cell cycle START
YMR215W	YMR215W	NC_001145	Ymr215wp Hypothetical ORF
YJL186W	MNN5	NC_001142	YJL186W Mnn5p mannan synthesis
YOR247W	SRL1	NC_001147	YOR247W Srl1p Suppressor of rad53 lethality
YNL238W	KEX2	NC_001146	YNL238W Kex2p prohormone processing; golgi localization marker, dispensable for meiotic recombination but partially required for meiosis I and*or meiosis II
YLR056W	ERG3	NC_001144	YLR056W Erg3p C-5 sterol desaturase
YJL092W	HPR5	NC_001142	YJL092W Hpr5p Required for proper timing of committment to meiotic recombination and the transition from Meiosis I to Meiosis II
YKL096W	CWP1	NC_001143	YKL096W Cwp1p cell wall protein, involved in O and N glycosylation, acceptor of B1-6 glucan.
YLR297W	YLR297W	NC_001144	Ylr297wp Hypothetical ORF
YML027W	YOX1	NC_001145	YML027W Yox1p Homeodomain protein that binds leu-tRNA gene
YJL158C	CIS3	NC_001142	YJL158C Cis3p cik1 suppressor




Module 3

Genes and Motifs




Genes	NDD1, FKH2, Mcm1
Motifs	M_8 (Mcm1), M_30(Mcm1)




p-values




Seed profile	p-value ChIP	p-value Motif
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Functional Overrepresentation





Detected Genes

Gene	Name	AccessionNr	Description
YDR033W	MRH1	NC_001136	YDR033W Mrh1p Membrane protein related to Hsp30p; Localized by immunofluorescence to membranes, mainly the plasma membr. punctuate immunofluorescence pattern observed in buds. The nuclear envelope, but not vacuole or mitochondrial membranes also stained
YAR018C	KIN3	NC_001133	YAR018C Kin3p protein kinase
YDR146C	SWI5	NC_001136	YDR146C Swi5p transcriptional activator
YIL158W	YIL158W	NC_001141	Yil158wp Hypothetical ORF
YGL116W	CDC20	NC_001139	YGL116W Cdc20p Required for onset of anaphase
YJL051W	YJL051W	NC_001142	Yjl051wp Hypothetical ORF
YGL021W	ALK1	NC_001139	YGL021W Alk1p
YGR143W	SKN1	NC_001139	YGR143W Skn1p Involved in (1->6)-beta-glucan biosynthesis
YHR023W	MYO1	NC_001140	YHR023W Myo1p myosin class II
YBR038W	CHS2	NC_001134	YBR038W Chs2p chitin synthase 2
YCR024C-A	PMP1	NC_001135	YCR024C-A Pmp1p May regulate plasma membrane H(+)-ATPase
YLR084C	RAX2	NC_001144	YLR084C Rax2p Involved in the maintenance of bipolar pattern
YMR001C	CDC5	NC_001145	YMR001C Cdc5p CDC5 is dispensable for premeiotic DNA synthesis and recombination, but required for tripartite synaptonemal complexes, haploidization, and spores
YML119W	YML119W	NC_001145	Yml119wp Hypothetical ORF
YLR190W	YLR190W	NC_001144	Ylr190wp Hypothetical ORF
YPR119W	CLB2	NC_001148	YPR119W Clb2p Involved in mitotic induction
YPL141C	YPL141C	NC_001148	Ypl141cp Hypothetical ORF
YJR092W	BUD4	NC_001142	YJR092W Bud4p co-assembles with Bud3p at bud sites
YLR131C	ACE2	NC_001144	YLR131C Ace2p involved in transcriptional regulation of CUP1


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Module 4

Genes and Motifs




Genes	Swi5 (ace2)
Motifs	M_8 (Mcm1)




p-values




Seed profile	p-value ChIP	p-value Motif
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Functional Overrepresentation





Detected Genes

Gene	Name	AccessionNr	Description
YIL009W	FAA3	NC_001141	YIL009W Faa3p acyl-CoA synthetase (long-chain fatty acid CoA ligase) (fatty acid activator 3), activates endogenous but not imported fatty acids and provides substrates for N-myristoylation
YDL117W	CYK3	NC_001136	YDL117W Cyk3p involved in CYtoKinesis
YDR055W	PST1	NC_001136	YDR055W Pst1p Protoplasts-secreted
YJL159W	HSP150	NC_001142	YJL159W Hsp150p Heat shock protein, secretory glycoprotein
YKL163W	PIR3	NC_001143	YKL163W Pir3p Protein containing tandem internal repeats
YKL164C	PIR1	NC_001143	YKL164C Pir1p Protein containing tandem internal repeats
YNL327W	EGT2	NC_001146	YNL327W Egt2p cell-cycle regulation protein, may be involved in the correct timing of cell separation after cytokinesis
YOR066W	YOR066W	NC_001147	Yor066wp Hypothetical ORF
YNL078W	JIP1	NC_001146	YNL078W Jip1p Hypothetical ORF
YKL185W	ASH1	NC_001143	YKL185W Ash1p Zinc-finger inhibitor of HO transcription which is asymmetrically localized to the daughter cell nucleus


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Module 5

Genes and Motifs




Genes	FKL1, Yap5, Rap1
Motifs	M_54




p-values




Seed profile	p-value ChIP	p-value Motif
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Functional Overrepresentation





Detected Genes

Gene	Name	AccessionNr	Description
YDL136W	RPL35B	NC_001136	YDL136W Rpl35bp Homology to rat L35
YDL130W	RPP1B	NC_001136	YDL130W Rpp1bp Homology to rat P1, human P1, and E. coli L12eIIB
YDL083C	RPS16B	NC_001136	YDL083C Rps16bp Homology to rat S16
YGR148C	RPL24B	NC_001139	YGR148C Rpl24bp Homology to rat L24
YDR450W	RPS18A	NC_001136	YDR450W Rps18ap Homology to rat S18 and E. coli S13
YGL189C	RPS26A	NC_001139	YGL189C Rps26ap Homology to rat S26
YER056C-A	RPL34A	NC_001137	YER056C-A Rpl34ap Homology to rat L34
YER131W	RPS26B	NC_001137	YER131W Rps26bp Homology to rat S26
YGL031C	RPL24A	NC_001139	YGL031C Rpl24ap Homology to rat L24
YGL103W	RPL28	NC_001139	YGL103W Rpl28p Homology to rat, mouse L27a
YER102W	RPS8B	NC_001137	YER102W Rps8bp Homology to mammalian S8
YBL072C	RPS8A	NC_001134	YBL072C Rps8ap Homology to mammalian S8
YCR031C	RPS14A	NC_001135	YCR031C Rps14ap Homology to mammalian S14, E. coli S11
YBR118W	TEF2	NC_001134	YBR118W Tef2p translational elongation factor EF-1 alpha
YBR189W	RPS9B	NC_001134	YBR189W Rps9bp Homology to rat S9 and E. coli S4
YLR167W	RPS31	NC_001144	YLR167W Rps31p Homology to rat S27a
YLR061W	RPL22A	NC_001144	YLR061W Rpl22ap Homology to rat L22
YLR333C	RPS25B	NC_001144	YLR333C Rps25bp Homology to rat S25; belongs to the S25E family of ribosomal proteins
YOL127W	RPL25	NC_001147	YOL127W Rpl25p Homology to E. coli L23 and rat L23a
YOL040C	RPS15	NC_001147	YOL040C Rps15p Homology to rat S15 and E. coli S19
YOR293W	RPS10A	NC_001147	YOR293W Rps10ap Homology to rat S10
YPL090C	RPS6A	NC_001148	YPL090C Rps6ap Homology to rat, mouse, and human S6
YPL220W	RPL1A	NC_001148	YPL220W Rpl1ap Homology to rat L10a, eubacterial L1, and archaebacterial L1; identical to S. cerevisiae L1B (Ssm2p)
YOR096W	RPS7A	NC_001147	YOR096W Rps7ap Homology to human S7 and Xenopus S8
YLR344W	RPL26A	NC_001144	YLR344W Rpl26ap Homology to rat L26
YLR441C	RPS1A	NC_001144	YLR441C Rps1ap Homologous to rat S3A

Module 6

Genes and Motifs




Genes	/
Motifs	ESR1, ESR2




p-values




Seed profile	p-value ChIP	p-value Motif
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Functional Overrepresentation





Detected Genes

Gene	Name	AccessionNr	Description
YCR057C	PWP2	NC_001135	YCR057C Pwp2p Eight WD-repeats with homology with G protein beta subunits flanked by nonhomologous N-terminal and C-terminal extensions
YCR091W	KIN82	NC_001135	YCR091W Kin82p Putative serine*threonine protein kinase most similar to cyclic nucleotide-dependent protein kinase subfamily and the protein kinase C subfamily
YDR184C	ATC1	NC_001136	YDR184C Atc1p interacts with AIP3, localized to the nucleus
YAL025C	MAK16	NC_001133	YAL025C Mak16p putative nuclear protein
YDR083W	RRP8	NC_001136	YDR083W Rrp8p
YDR449C	YDR449C	NC_001136	Ydr449cp Protein required for cell viability
YER127W	LCP5	NC_001137	YER127W Lcp5p Lethal with conditional pap1 allele
YGL099W	KRE35	NC_001139	YGL099W Kre35p Killer toxin REsistant
YGL171W	ROK1	NC_001139	YGL171W Rok1p contains domains found in the DEAD protein family of ATP-dependent RNA helicases; high-copy suppressor of kem1 null mutant
YHR196W	YHR196W	NC_001140	Yhr196wp Protein required for cell viability
YIL103W	YIL103W	NC_001141	Yil103wp Hypothetical ORF
YIL127C	YIL127C	NC_001141	Yil127cp Hypothetical ORF
YHR065C	RRP3	NC_001140	YHR065C Rrp3p Required for maturation of the 35S primary transcript of pre-rRNA and is required for cleavages leading to mature 18S RNA
YGR128C	YGR128C	NC_001139	Ygr128cp Protein required for cell viability
YBR155W	CNS1	NC_001134	YBR155W Cns1p cyclophilin seven suppressor
YGL120C	PRP43	NC_001139	YGL120C Prp43p Pre-mRNA processing factor involved in disassembly of spliceosomes after the release of mature mRNA
YGR145W	YGR145W	NC_001139	Ygr145wp Protein required for cell viability
YIL091C	YIL091C	NC_001141	Yil091cp Protein required for cell viability
YER006W	NUG1	NC_001137	YER006W Nug1p NUclear GTPase
YCR016W	YCR016W	NC_001135	Ycr016wp Hypothetical ORF
YER126C	NSA2	NC_001137	YER126C Nsa2p Killer toxin Resistant; Nop seven associated protein 2
YHR085W	YHR085W	NC_001140	Yhr085wp Protein required for cell viability
YAL059W	ECM1	NC_001133	YAL059W Ecm1p putative transmembrane domain protein involved in cell wall biogenesis
YCL054W	SPB1	NC_001135	YCL054W Spb1p Suppressor of PaB1 mutant; involved in 60S ribosomal subunit biogenesis
YDR165W	YDR165W	NC_001136	Ydr165wp Hypothetical ORF
YCR072C	YCR072C	NC_001135	Ycr072cp Protein required for cell viability
YKR025W	RPC37	NC_001143	YKR025W Rpc37p RNA Polymerase C (III) 37 kDa subunit; interacts with C53 subunit. C37 is an RNA polymerase III specific subunit.
YKR081C	RPF2	NC_001143	YKR081C Rpf2p Hypothetical ORF
YLR196W	PWP1	NC_001144	YLR196W Pwp1p Protein with periodic trytophan residues that resembles members of beta-transducin superfamily because of presence of WD-40 repeats
YKL099C	YKL099C	NC_001143	Ykl099cp Protein required for cell viability
YLR197W	SIK1	NC_001144	YLR197W Sik1p homology to microtubule binding proteins and to X90565_5.cds
YMR049C	ERB1	NC_001145	YMR049C Erb1p Eukaryotic Ribosome Biogenesis
YKL172W	EBP2	NC_001143	YKL172W Ebp2p EBNA1-binding protein homolog
YOR001W	RRP6	NC_001147	YOR001W Rrp6p Ribosomal RNA Processing
YML093W	YML093W	NC_001145	Yml093wp Protein required for cell viability
YNL248C	RPA49	NC_001146	YNL248C Rpa49p 49-kDa alpha subunit of RNA polymerase A
YOL144W	NOP8	NC_001147	YOL144W Nop8p Nucleolar protein required for 60S ribosome biogenesis
YNR046W	YNR046W	NC_001146	Ynr046wp Protein required for cell viability
YOL041C	NOP12	NC_001147	YOL041C Nop12p Nucleolar Protein; isolated as a mutant exhibiting synthetic lethality with a nop2 ts allele.
YOR091W	YOR091W	NC_001147	Yor091wp Hypothetical ORF
YPL217C	BMS1	NC_001148	YPL217C Bms1p BMH1 sensitive
YMR269W	YMR269W	NC_001145	Ymr269wp protein possibly involved in protein synthesis
YOR277C	YOR277C	NC_001147	Yor277cp Hypothetical ORF
YOR340C	RPA43	NC_001147	YOR340C Rpa43p DNA-dependent RNA polymerase I subunit A43
YNL132W	KRE33	NC_001146	YNL132W Kre33p Killer toxin REsistant
YOR206W	NOC2	NC_001147	YOR206W Noc2p NucleOlar Complex 2; involved in nuclear export of pre-ribosomes
YPL211W	NIP7	NC_001148	YPL211W Nip7p Nip7p is required for 60S ribosome subunit biogenesis
YNL061W	NOP2	NC_001146	YNL061W Nop2p May participate in nucleolar function during the transition from stationary phase to rapid growth
YNL110C	NOP15	NC_001146	YNL110C Nop15p Nucleolar protein 15
YJR002W	MPP10	NC_001142	YJR002W Mpp10p Protein component of the U3 small nucleolar ribonucleoprotein (snoRNP)
YMR128W	ECM16	NC_001145	YMR128W Ecm16p ExtraCellular Mutant
YLR129W	DIP2	NC_001144	YLR129W Dip2p DOM34 Interacting Protein
YMR014W	BUD22	NC_001145	YMR014W Bud22p
YJL109C	YJL109C	NC_001142	Yjl109cp Protein required for cell viability
YKL144C	RPC25	NC_001143	YKL144C Rpc25p Subunit of RNA polymerase III
YLR074C	BUD20	NC_001144	YLR074C Bud20p
YLR449W	FPR4	NC_001144	YLR449W Fpr4p Homolog of homolog of the nucleolar FKBP, Fpr3
YKL082C	YKL082C	NC_001143	Ykl082cp Protein required for cell viability
YKR024C	DBP7	NC_001143	YKR024C Dbp7p Dead-box protein
YLR051C	YLR051C	NC_001144	Ylr051cp Protein required for cell viability