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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.