How biologically relevant are interaction-based modules in protein networks?

Table 4 Statistical significance of the overall analysis of coexpression, common 5' regulatory motifs, homogeneity in dispensability and lethality for the phylogenetically distinct module cores

Function	P-exp	P-mot	P-hom	P-let	p-core	p-net
Cell fate	<0.05	-	-	<0.05	0.28	0.08
Energy	-	<.005	-	-	0	0.05
Metabolism	<0.0005	<0.05	-	<0.01	0.14	0.08
Cellular transport	-	-	< 0.01	-	None	0.28
Cell cycle	<0.05	-	< 0.05	0.0001	0.35	0.29
Protein fate	<0.0005	-	-	-	0.41	0.16
Transport facilitation	-	-	-	-	0.5	0.15
Cell environment	-	-	-	<0.05	0	0.06
Protein synthesis	<0.05	-	< 0.0005	0.0001	0.2	0.06
Cell rescue	<0.05	-	-	-	0	0.12
Signaling	-	-	-	-	0	0.12
Cell organization	<0.01	<0.05	-	-	0.08	0.12
Transcription	<0.05	<0.01	<0.01	<0.001	0.68	0.3

Statistical significance (P-values), of the overall analysis of coexpression (P-exp), common 5' regulatory motifs (P-mot), homogeneity in dispensability (P-hom) and lethality (P-let), for the phylogenetically distinct module cores (see text and Materials and methods for details). Not significant statistical results are denoted by -. p-core is the probability of finding lethal genes in the set of proteins without human homolog belonging to the significant cores. p-net is the probability of finding lethal genes in those proteins not found in humans which are part of each full network.

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