Table 2.

Composition of active modules containing one or more of the identified genes of interest listed in Table 1 (in bold) with genes upregulated in red and genes downregulated in blue, representative enrichment and role of differentially expressed genes (DEGs) in cancers.

Module Number and Composition	Representative Enrichment	Role of the DEGs in Cancer
1 ASPN, COL5A1, COL25A1, COL3A1, SFRP4	Extracellular matrix organization	CSC maintenance, EMT
2 ANXA6, ANXA1, ANXA2, ANXA2R, GREG1, FUCA1, PADi2, S100A10, S100A11	Vesicle transport, cell adhesion	Cancer development and progression, poorer prognosis
4 and 8 ADCY2, S1PR3, S1PR5, EDNRA, GNB4, GNG4, GRK5, GNAT3, GPR37L1, PTGER3, SSTR3, ECE1, GRPR, HCRTR2, PROK1	Signaling by GPCR	Regulation of CSC, cancer cell survival, metastasis, poor prognosis
5 NFATC1, SNAI2, ATF3, EGR1, FOSL2, GBP1, GBP2, GBP3, IFIT3, IRF1, IRF6, JUN, XAF1	Regulation of cell population proliferation	Maintenance of mesenchymal phenotype, invasive migration, metastasis, poor prognosis, chemotherapy resistance
16 TMSB4X, ACTN4, ISLR, SERPINE1	Platelet degranulation	EMT induction and metastasis
17 and 165 PTCH1, SHH, GLI2, CTNNA2, GAS1, BOC, CDON, MEF2D, TNNT1, ZIC1, ACTA2, ACTG2, MTSS1	Hedgehog signaling, cell differentiation, cell fate specification, development	Hedgehog pathway activation, CSC maintenance, tumor cell survival
20 GFRA2, GRB10, GRB7	RET signaling	Stem cell self-renewal
29 ABCG2, CYP26B1 ALDH1A1, CYP2S1	Retinoic acid metabolic process	Chemotherapy resistance, CSC, poor prognosis
51 EHBP1, GAPVD1, RAB5A, RAB31, EHD3, MYOF, RAB11, FIP2, RAB38	Endosome membrane, endocytosis	Membrane trafficking, endocytosis, cancer cell motility and invasiveness, cancer development and progression, metastasis
77 DLX6, GREB1, HIST1, H2AC, CBFB, H2AFZ, ITGBL1, PHC1, RUNX1, ZFPM1	Negative regulation of differentiation	Poor patient survival, malignant phenotype and metastasis, tumor progression and development, cell proliferation, migration and EMT
79 CLTCL1, DNM1, HIP1, SYT2, DNM3	Endocytosis, membrane trafficking	Proliferation, migration and invasion, cancer progression and metastasis, poor prognosis
85 CEP85 SOX13 SOX5	Transcription factors, cell-cycle progression	CSC maintenance, EMT, invasion, metastasis
89 CALCR, FOXE1, GPR176, PTHLH, TSHR, VIPR1	G protein-coupled receptor activity	Stem cell maintenance
98 CDH10, CDH2, CDH12, CDH24, JUP	Cell–cell adhesion	EMT, cell migration and invasion, poor prognosis
104 CERS4, CERS6, UGCG, GBA, SMPD4	Sphingolipid metabolism	Multidrug resistance, proliferation of cancer cells, cell migration and metastasis
106 MITF, PMEL, POU3F2	Melanoma phenotype switching	Enrichment of stem cells, de-differentiated state and invasiveness
127 GBAS, NDUFA8 NDUFS1 PAAF1 UQCRC1 ZNF713, ANKFY1, NDUFA10 TSPAN11	Mitochondrial respiratory chain complex	Malignant behavior of cancer cells, cell cycle progression
178 SLC22A4 SLC29A4 SLC47A1	SLC-mediated transmembrane transport	Cell proliferation, epithelial-to-mesenchymal transition