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Table 1 Overview of the uncovered modules

From: Exploiting combinatorial cultivation conditions to infer transcriptional regulation

Module Disc.Expr.Pattern TF binding Motif Discovery Annotation
   Aer Ana         
no. # genes C N P S C N P S Ox TFs TFpairs Motif Ass.TFs GO MIPS KEGG
1 57 1 0 0 0 1 0 0 0 1 Hap4   CCAATCA Hap5, Hap2/3/4, Mcm1 GO: Oxidative phosphorylation
              ATTGG Hap5, Hap2/3/4, Mcm1, ... MIPS: Respiration
                KEGG: Oxidative phosphorylation
2 70 0 1 0 0 0 1 0 0 0 Dal82 Gln3-Dal82 AGATAAG Gzf3, Dal80, Gat1 GO: Catabolism
            Gln3   CTTATC Gat1, Gzf3, Dal82, ... MIPS: Nitrogen and sulfur utilization
                KEGG: Cyanoamino acid metabolism
3 211 0 0 0 0 0 0 0 0 1 Hap1       
4 70 0 0 0 1 0 0 0 1 0 Cbf1 Met32-Cbf1 CACGTGA Cbf1, Tye7, Ino4, ... GO: Sulfur metabolism
            Met32 Yap7-Yap1 GCCACA Met4, Rpn4 MIPS: Amino acid metabolism
            Yap7     KEGG: Sulfur metabolism
5 44 0 0 1 0 0 0 1 0 0 Pho4 Pho4-Cbf1 ACGTGC Pho4, Cbf1, Ino2, ... GO: Anion transport
              CACGTGG Pho4, Tye7, Cbf1, ...    
6 15 0 0 0 1 0 0 0 1 1 Met32   GCCAC Rpn4, Met4, R. car1, ...    
              CTGTGGC Met4, Rfx1    
7 169 1 0 0 0 1 0 0 0 x Hap4   GGGGTA Mig1, Rap1 GO: Oxidative phosphorylation
              ACCCC Mig1, Adr1, Msn4, ... MIPS: Respiration
                KEGG: Oxidative phosphorylation
8 100 0 1 0 0 0 1 0 0 x Dal82 Gln3-Dal82 CTTATC Gat1, Gzf3, Dal82, ... GO: Amine transport
            Gln3   AGATAAG Gzf3, Dal80, Gat1 MIPS: Nitrogen and sulfur utilization
9 93 0 0 0 1 0 0 0 1 x Cad1 Met32-Cbf1 GCCACA Met4, Rpn4 GO: Sulfur metabolism
            Cbf1 Met32-Met31 CACGTGA Cbf1, Tye7, Ino4, ... MIPS: Metabolism of methionine
            Met31 Tye7-Cbf1 CTGTGGC Met4, Rfx1 KEGG: Sulfur metabolism
            Met32       
            Met4       
            Yap7       
10 52 0 0 1 0 0 0 1 0 x Cbf1 Pho4-Cbf1 ACGTGC Pho4, Cbf1, Ino2, ... GO: Anion transport
            Pho4   CACGTGG Pho4, Tye7, Cbf1, ...    
11 638 x x x x x x x x 1 Hap1   CCGATA Hap1 GO: Oxidative phosphorylation
            Hap4     MIPS: Respiration
                KEGG: Oxidative phosphorylation
12 383 x x x x x x x x -1 Dig1 Cin5-Aft2 ACAATAG Yox1, Rox1 GO: Lipid metabolism
            Rox1 Rox1-Cin5 TGCTTT Upc2 MIPS: Metabolism
            Ste12 Swi4-Mcm1      
            Swi4 Tec1-Dig1      
            Tec1 Tec1-Ste12      
             Yap6-Cin5      
13 3883 0 0 0 0 0 0 0 0 0 Fhl1 Rap1-Fhl1 AAAAT Rlr1, Spt23    
             Sfp1-Fhl1 GAAAA Rlr1, Ume1, Azf1, ...    
              AAAAA Azf1, Sig1, Met4    
              TGAAA Ste12, Dig1, Ume1, ...    
              AAATA Smp1, Rlm1, Azf1, ...    
              AAATT Pho2, Spt23    
  1. Detailed information for all modules that are significantly related to at least one TF(-pair). Besides the discretized expression pattern and the significant TFs from binding data, the table reports overrepresented motifs through motif discovery as well as TFs associated to these motifs. Also, the most highly enriched GO, MIPS and KEGG category for each module is given (if significant).
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