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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.