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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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BMC Genomics

ISSN: 1471-2164

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