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Table 1 Statistically significant associations between annotated complexes and known regulons

From: Transcriptional regulation of protein complexes in yeast

(a) Associations between the annotated complexes and annotated regulons

 

Annotated complex

Annotated regulon

Components in complex

Genes in regulon

Common genes

E-value

Total overlap

Permanent

19-22S regulator

Rpn4

18

11

6

2E-11

6

 

Cytochrome bc1 complex

Hap4

9

14

3

1E-04

2

 

Nucleosomal protein complex

Hir1

8

4

4

2E-10

7

  

Hir3

 

3

3

3E-07

 
  

Hta2

 

2

2

3E-04

 
  

Hta1

 

2

2

3E-04

 
  

Hir2

 

2

2

3E-04

 
  

Spt10

 

3

2

9E-04

 
  

Spt21

 

3

2

9E-04

 
 

RNA polymerase II

Abf1

13

37

3

1E-02

3

 

RNA polymerase III

Abf1

13

37

3

1E-02

3

Transient

2 oxoglutarate dehydrogenase

Hap2

3

14

2

3E-03

2

  

Hap3

 

15

2

3E-03

 
 

Alpha alpha trehalose phosphate synthase

Msn2

4

56

3

5E-04

3

  

Msn4

 

58

3

6E-04

 
 

Anthranilate synthase

Gcn4

2

40

2

8E-03

2

 

Fatty acid synthetase cytoplasmic

Reb1

2

19

2

2E-03

2

  

Ino2

 

19

2

2E-03

 
  

Ino4

 

19

2

2E-03

 
 

GAL80 complex

Mig1

3

26

2

1E-02

2

 

Glycine decarboxylase

Fau1

4

3

3

2E-08

3

 

Isocitrate dehydrogenase

Rtg3

2

6

2

2E-04

2

  

Rtg1

 

12

2

7E-04

 
 

Ribonucleoside diphosphate reductase

Dun1

4

3

3

2E-08

4

  

Rfx1

 

5

3

2E-07

 
  

Tup1

 

7

3

7E-07

 
  

Yku70

 

2

2

6E-05

 
  

Rad9

 

2

2

6E-05

 
  

Mbp1

 

6

2

9E-04

 

Others

Cdc28p complexes

Ndt80

10

11

5

3E-10

10

  

Xbp1

 

5

3

6E-06

 
  

Swi6

 

10

3

7E-05

 
  

Mcm1

 

14

3

2E-04

 
  

Azf1

 

2

2

5E-04

 
  

Sit4

 

2

2

5E-04

 
  

Spt16

 

2

2

5E-04

 
  

Far1

 

2

2

5E-04

 
  

Cln3

 

2

2

5E-04

 
  

Bck2

 

2

2

5E-04

 
 

Glucan synthases

Swi4

5

8

2

3E-03

2

(b) Associations between annotated complexes and high-throughput regulons, identified by a genome-wide location analysis [16]

 

Annotated complex

High-throughput regulon

Components in complex

Genes in regulon

Common genes

E-value

Total overlap

Permanent

Respiration chain complexes

      
 

   Cytochrome bc1 complex

Hap4

9

69

7

5E-11

7

 

   Cytochrome c oxidase

Hap4

8

69

8

2E-14

8

 

   F0-F1 ATP synthase

Hap4

15

69

10

4E-15

10

 

Cytoplasmic ribosomes

      
 

   Cytoplasmic ribosomal large subunit

Fhl1

81

194

67

4E-90

67

  

Rap1

 

209

46

3E-46

 
  

Yap5

 

107

10

1E-04

 
  

Pdr1

 

69

8

3E-04

 
 

   Cytoplasmic ribosomal small subunit

Fhl1

57

194

53

2E-76

53

  

Rap1

 

209

30

4E-28

 
  

Yap5

 

107

8

5E-04

 
 

Nucleosomal-protein-complex

Hir2

8

21

6

2E-12

6

  

Hir1

 

30

6

2E-11

 

Transient

Fatty acid synthetase cytoplasmic

Ino2

2

11

2

3E-04

2

  

Ino4

 

19

2

9E-04

 
 

Glycine decarboxylase

Bas1

4

44

3

1E-04

3

 

Ribonucleoside diphosphate reductase

Rfx1

4

32

3

5E-05

3

Others

Replication complexes

Mbp1

49

112

7

2E-03

7

  1. Only the most statistically significant associations (E-value ≤ 0.01) between complexes and regulons are listed (see Additional data file 1 (Figure S2a-b) for a complete list). Each line lists the association detected between a multiprotein complex denoted by its CYGD name (column 2) and a regulon denoted by its common name (column 3). Column 4 lists the number of genes in the complex and column 5 lists the number of genes in the regulon. Column 6 lists the number of common genes between the regulon and complex, and column 7 lists the statistical significance criterion (E-value) for the detected overlap (see Materials and methods). The far right column lists the total number of genes in the complex that are common between it and all the regulons that map into it. Complexes have been subdivided into three categories, 'permanent', 'transient' or 'others', as indicated in column 1, and described in Materials and methods. When a smaller complex is completely included within a larger one and detected associations map into it, only the smaller complex is listed. For example, the larger assembly 'Cyclin-CDK complexes' is not listed because the detected association is with one of its components the 'Cdc28p complexes' only. When associations are detected with more than one complex of a larger assembly, as is the case for the small and large subunits of the cytoplasmic ribosomes, the name of the larger assembly is given first, with no details of the identified associations. But those are listed for each of the component complexes. Information on the annotated regulons in (a) was obtained from the TRANSFAC and aMAZE databases, from the list compiled by Young and colleagues [16, 48] and from the recent literature.