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 | Â | Â | Â | Â | Â | Â |
 |    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 |