Species | Module | Gene Designation | Predicted biological pathway/localization | Identified by other methods? | Experimental verification in this paper | Experimental supporting evidences from annotation databases |
---|---|---|---|---|---|---|
Yeast | Module 9 | YLR183C | cell cycle | yes [19, 63] | ND | transcription factor regulating several promoters of genes involved in pheromone response and cell cycle; |
 | Module 9 | YOL007C | cell cycle | yes [19, 63] | ND | structural component of the chitin synthase 3 complex |
 | Module 9 | YLR190W | cytokinesis | yes [19] | Consistent with prediction | localized to small buds, bud neck, and incipient bud sites; mRNA is targeted to the bud via the mRNA transport system involving She2p |
 | Module 9 | YNL058C | cell cycle | yes [18, 19] | ND | potential Cdc28p substrate |
 | Module 15 | YHL021C | Stress response | yes [19, 63] | ND |  |
 | Module 15 | YGR160W | ribosome biogenesis | yes [19, 63] | Consistent with prediction |  |
 | Module 15 | YIL127C | ribosome biogenesis | yes [63] | ND |  |
 | Module 15 | YJL122W | ribosome biogenesis | yes [63] | Consistent with prediction |  |
 | Module 15 | YLR196W | ribosome biogenesis | yes [19, 63] | ND | nucleolar protein |
 | Module 15 | YLR400W | ribosome biogenesis | no | Consistent with prediction |  |
 | Module 15 | YML074C | ribosome biogenesis | yes [19] | Consistent with prediction | nucleolar peptidyl-prolyl cis-trans isomerase (PPIase); FK506 binding protein; phosphorylated by casein kinase II (Cka1p-Cka2p-Ckb1p-Ckb2p) and dephosphorylated by Ptp1p |
 | Module 15 | YMR269W | ribosome biogenesis | no | Consistent with prediction | nucleolar protein [40]; protein possibly involved in protein synthesis [64] |
 | Module 15 | YNL050C | ribosome biogenesis | no | Consistent with prediction |  |
 | Module 15 | YOR146W | ribosome biogenesis | no | ND |  |
 | Module 15 | YOR154W | ribosome biogenesis | no | Consistent with prediction |  |
 | Module 15 | YCR016W | ribosome biogenesis | yes [63] | Consistent with prediction | nucleolar protein |
 | Module 15 | YPR169W | ribosome biogenesis | no | ND | nucleolar protein [40] |
 | Module 15 | YCR072C | ribosome biogenesis | yes [19, 63] | ND | present in several complexes involved in protein synthesis and RNA turnover metabolism [38]; co-purified with the 60S ribosomal subunit [39]. |
 | Module 15 | YDL063C | ribosome biogenesis | yes [19] | ND |  |
S. oneidensis | Module 4 | SO3725 | central intermediate metabolism; protein modification | no | ND | Â |
 | Module 5 | SO2017 | heat shcok response | yes [42]. | Consistent with prediction |  |
 | Module 5 | SO2042 | heat shcok response |  |  |  |
 | Module 5 | SO2375 | metabolism |  |  |  |
 | Module 5 | SO3298 | metabolism | no | ND |  |
 | Module 5 | DsbD | metabolism | no | ND | thiol:disulfide interchange protein |
E. c | Module 143 | yaeC | metabolism, cell surface transporter | no | ND | Â |
 | Module 143 | ybgF | protein synthesis | no | ND |  |
 | Module 141 | envR | function related to cell surface structure | no | ND |  |
 | Module 2531 | b1505 | transport protein | no | ND |  |
 | Module 2531 | yqcB | energy metabolism | no | ND |  |