Table 2.

Representative functional predictions of hypothetical proteins with high confidence.

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

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].

ND: not determined.