Table 4.

Pathways

CFinder	module ID	Protein IDs	Pathways
High	Int-2	-	na
	Int-3	-	na
	Int-4	-	na
	Int-7	POLR3G POLR3A POLR3 H POLR1A ZNRD1 POLR1D POLR2C POLR2E POLR2 H POLR2L POLR1B POLR3GL POLR1C	hsa03020 RNA polymerase
	Lit-2	-	na
	Lit-5	POLR2A POLR2C POLR2 D POLR2E POLR2G POLR2 H POLR2L	hsa03020 RNA polymerase
	Lit-9	LSM1 LSM2 LSM3 LSM4 LSM5 LSM6 LSM7 LSM1 LSM2 LSM3 LSM4 LSM5 LSM6 LSM7	hsa03018 RNA degradation hsa03040 Spliceosome
	Lit-11	SKIV2L2 EXOSC2 EXOSC4 EXOSC5 EXOSC6 EXOSC7 EXOSC8 EXOSC9	hsa03018 RNA degradation
	Ortho-8	POLR3G POLR3A POLR3 H POLR1A ZNRD1 POLR1 D POLR2E POLR2F POLR2 H POLR2L POLR1B POLR3GL POLR1C	hsa03020 RNA polymerase
	Ortho-12	PSMA1 PSMA2 PSMA4 PSMA6 PSMA7 PSMB1 PSMB2 PSMB3 PSMB5	hsa03050 Proteasome
Medium	Int-18	PSMA1 PSMB2 PSMC2 PSMC3 PSMD11 PSMD12 PSMD13 PSMD6	hsa03050 Proteasome
	Ortho-18	PSMA1 PSMB2 PSMC2 PSMC3 PSMD11 PSMD12 PSMD13 PSMD6	hsa03050 Proteasome
Low	Int-13	TAF1 TAF2 TAF4 TAF5 TAF6 TAF7 TAF9 TAF10 TAF12 TAF13 TBP	hsa03022 Basal transcription factors
	Lit-4	MYC RUVBL1	hsa04310 Wnt signaling pathway
	Lit-14	TAF1 TAF2 TAF4 TAF5 TAF6 TAF7 TAF9 TAF10 TAF12	hsa03022 Basal transcription factors
	Ortho-7	EXOSC2 EXOSC3 EXOSC4 EXOSC5	hsa03018 RNA degradation
MCODE	module ID	Protein IDs	Pathways
High	Int-5	-	na
	Lit-4	-	na
	Ortho-4	DDX6 LSM1 LSM2	hsa03018 RNA degradation
	Ortho-5	RPL3 RPL12 RPL27A RPS2	hsa03010 Ribosome
Low	Lit-11	-.	na
	Lit-13	TAF1 TAF2 TAF4 TAF5 TAF6 TAF7 TAF9 TAF10 TAF12 HDAC1 HDAC2	hsa03022 Basal transcription factors hsa04110 Cell cycle
	Ortho-2	TAF9B TAF5 TAF6 TAF12	hsa03022 Basal transcription factors
	Ortho-10	PPP1CA PPP1CB	hsa04720 Long-term potentiation hsa03018 RNA degradation hsa04810 Regulation of actin cytoskeleton hsa04910 Insulin signaling pathway hsa04510 Focal adhesion

Pathways results for CFinder and MCODE High, Medium and Low confidence modules (KEGG source [55], na: not annotated). See also: Figure 9-12.