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Table 1 Detailed cluster analysis: differential and statistically significant biological functions in clusters C1-C7

From: Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer

Cluster no. Number of transcripts/ProbeSets (PS) Reference Pattern Biology Example genes
1 391 Global Up (A/M/T); down (S) RNA post-transcriptional modification, cell cycle, DNA replication/recombination/repair, molecular transport, post-translational modification, cellular assembly and organization, cellular movement, cardiovascular system development and function, connective tissue development and function, cancer Cell cycle progression (Cdk4, Ctnnb1, Id1, Id3, Myc, Pcna, Tcf3), replication of DNA (Idi1, Mcm2, Myc, Orc4l, Pcna, Polb, Set), checkpoint control (Bub3, Myc, Rae1, Smc1l1), invasion of mammary epithelial cells (Ezh2), recovery of ATP (Hspd1, Hspe1), hyperplasia of secretory structure (Cdk4, Ctnnb1, Ptpre, Sdc1), cell proliferation (Id1, Id3, Myc, Pcna)
2 663 Global Up (A/M); down (S/T) Cell cycle, cellular response to therapeutics, cellular assembly and organization, molecular transport, connective tissue development and function, genetic disorder, gastrointestinal disease, cancer, Wnt-signaling pathway Contact growth inhibition of connective tissue cells (Metap2, Pcyox1), mitosis of tumor cells (Mif, Plk1), cell cycle progression (Id2, Tp53), checkpoint control (Mad2l1, Tp53), DNA modification (Apex1, Dnmt3a, Dnmt3b), infiltrating duct carcinoma (Esr1, Ing4), mitosis of tumor cells (Mif, Plk1), myotonic dystrophy (Dmpk, Znf9), Wnt-signaling (Csnk1d, Csnk1e, Lef1, Nlk, Tcf3, Tcf4, Wif1)
3 170 Global Up (A/S); down (M/T) Cancer, cell death, cellular development, cellular growth and proliferation, cell cycle Apoptosis of colon carcinoma cells (Tnfsf10), sarcoma (Ewsr1, Mdm2, Tnfsf10), hyperpoliferation (Map2k7), survival (Mdm2, Nras, Tnfsf10), tumorigenesis (Ewsr1, Mdm2, Nras, Tnfsf10), fibroblast proliferation (Arid5b, E4f1, Map2k7, Mdm2, Nras), mitosis of embryonic cells (E4f1)
4 142 Global Up (M/S); down (A/T) Cellular movement, hematological system development and function, immune response, hematological disease, immune and lymphatic system development and function, organ morphology, cell-to-cell signaling and interaction, cell death, molecular transport Cell movement/chemotaxis (Alox5AP, C3, Ctsb, Cxcl12, Dcn, Fcgr3a, Fgfr1, Hif1a, Igf2, Itgb2, Lsp1, S100A9, Slp1), invasion of tumor cell lines (Cbx5, Ctsb, Cxcl12, Fstl1, Hif1a, Ighg1, Igf2, Itgb2), chemotaxis/migration of leukocytes (C3, Cxcl12, Icam2, Itgb2, Lgals1, Lsp1, S100a9, Slpi), growth of tumor (Fgfr1, Hif1a, Igf2, Igfbp5, Ighg1), invasion of tumor cell lines (Cbx5, Ctsb, Cxcl12, Fstl1, Hif1a, Igf2, Ighg1, Itgb2)
5 432 Global Up (S/T); down (A/M) Cell death, neurological disease, drug metabolism, endocrine system development and function, cancer, drug metabolism, lipid metabolism, gastrointestinal disease, organismal functions, organismal injury and abnormalities Gut epithelium differentiation (Chgb, Klf4, Klf6, Sst), cell death/apoptosis of microglia (Btg1, Casp3, Casp9, Cx3cl1, Grin1, Myd88), uptake of prostaglandin E2 (Slco2a1), tumorigenesis of brain tumor (Nf2, Stat2), tumorigenesis of polyp (Asph, Smad4), aggregatability of colon cancer cell lines (Cd82), cell spreading of colon cancer cell lines (Smad4), contact inhibition of colon cancer cell lines (Prkg1)
6 904 Global Up (A/M); down (S/T) Cell proliferation, cell cycle progression and mitosis, DNA replication/recombination/repair, molecular transport, RNA post-transcriptional modification, post-translational modification, cellular growth and proliferation, connective tissue development and function, cancer, gastrointestinal disease, digestive system development and function Cell cycle progression/proliferation (Cdk4, Clu, Id2, Mki67, Magoh, Myc, Pcna, Tcf3, Tp53), tumor cell mitosis (Mif, Plk1), DNA excision repair (Apex1, Ddb1, Hmgb1, Polb), DNA methylation (Dnmt3a, Dnmt3b), accumulation of colonocytes (Clu, Myc), tumorigenesis (Cd44, Cdk4, Ctnnb1, Esr1, Myc, Prkar1a, Tp53), Wnt-signaling pathway (Csnk1a1, Cskn1d, Cskn1e, Ctnnb1, Lef1, Myc, Nlk, Ppp2cb, Tcf3, Tcf4, Wif1)
7 361 Global Up (S/T); down (A/M) Cell death, neurological disease, cancer, drug metabolism, embryonic development, endocrine system development and function, lipid metabolism, organismal injury and abnormalities, infectious disease, immune response, immunological disease, hematological disease; gastrointestinal disease; antigen +presentation pathway Antigen presentation (B2m, Cd74, H2-D1, HLA-DMA, HLA-DRB, Psmb8, Tap2), embryonic development (C3, Celsr1, Erbb3, Impk, Mcl1), infectious disease (B2m, Ifngr1, Irf1, Myd88, Nr3c1), mast cell chemotaxis (C3, Cx3cl1), apoptosis of microglia (Btg1, Casp3, Cx3cl1, Myd88), tumorigenesis of polyp (Asph, Smad4), transport of prostaglandin E2 (Slco2a1), quantity of colonocytes (Guca2a), gastrointestinal disease (Asph, Cd84, Smad4)
  1. A, AOM-induced; M, ApcMin/+; S, Smad3-/-; T, Tgfb1-/-; Rag2-/-.