Skip to main content

Table 2 Representative functional predictions of hypothetical proteins with high confidence.

From: Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory

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  
  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  
  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  
  1. The function of the listed hypothetical proteins was not clearly understood. However, many of our predictions were supported by existing experimental evidence from other laboratories (see last column), which was cited and summarized in the Saccharomyces Genome Database or TIGR's S. oneidensis or E. coli annotation database [59].
  2. ND: not determined.