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Table 4 Detailed cluster analysis: differential and statistically significant biological functions in clusters C18-C23

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

Cluster no. Number of PS Reference Pattern Biology Example genes
18 258 Adult colon Down (D); down (CRC); down (A/M/S/T) Lipid metabolism, molecular transport, cell death, cancer, cellular movement, drug metabolism, lipid metabolism, digestive system development and function, small molecule biochemistry, endocrine system development and function, neurological disease Gut epithelium differentiation (CA4, CA12, CBR1, CHGB, KLF4, KLF9, MCOLN2, SST, TFF3), apoptosis/cell death (CYCS, GSN, KITLG, SST, TFF3, TGFA), cytolisis/crypt damage (ABCB1, KLKR1, PTGER4), formation of aberrant crypt foci (NR5A2, PTGER4), drug transport (ABCB1, ABCG2), migration of tumor cells (EDG2, KITLG, SST, TGFA), quantity of colonocytes (GUCA2A)
19 42 Adult colon Up (D); down (CRC); down (A/M/S/T) Digestive system development and function, cancer, small molecule biochemistry, reproductive system development and function, organ morphology Colon and midgut development (EDNRB), gastrointestinal stromal tumor (KIT), apoptosis of mesothelioma cells (KIT), melanocyte differentiation (EDNRB, KIT), inhibition and morphology of melanoma cells (HSPE, LSP1), adhesion of lymphoma cells (HSPE)
20 91 Adult colon Up (D); down (CRC); up (A/M/S/T) Cell death, hematological disease, immunological disease, cell-to-cell signaling and interaction, hematological system development and function, immune response, cancer, cell morphology, tissue development, gastrointestinal disease Apoptosis of colon carcinoma, cells (BCL2), apoptosis of lymphoma cell lines (BCL2, IGFBP4, MAP4K1, PDGFRA), cell-cell contact of endothelial cells (STAB1), lymphocyte quantity (BCL2, CCR7, CD28, ITGB7, ITK, MUC1, WNT4), proliferation of lymphocytes (CD28, ITK), gastrointestinal stromal tumor (PDGFRA), metastasis (CD28, ENPP2, FKBP1A), transmembrane potential of mitochondria (BCL2, CD28, EYA2, LGALS2, MUC1)
21 313 Adult colon Down (D); up (CRC); down (A/M/S/T) Cell death, nervous system development and function, drug metabolism, small molecule biochemistry, cancer, cell cycle, cellular growth and proliferation, tissue development Melanocyte survival (RB1), proliferation of neuronal progenitor cells (ATM, VEGF), heparin binding (PRNP, TNC, VEGF), dopamine formation (TH), drug resistance (ABCC1), quantity of tumor cell lines (LIF, PIK3R1, RB1, TIMP3, VEGF), transformation (FOXO3A), malignancy of astrocytoma (TNC), tumor vascularization (PTEGS, VEGF), growth of sarcoma cell lines (TIMP3), tissue proliferation (GRP, KRIT1, RB1, RBL2)
22 860 Adult colon Up (D); up (CRC); up (A/M/S/T) Cell proliferation, cancer, DNA replication/recombination/repair, cell cycle progression and mitosis, cellular movement, connective tissue development and function, tumor morphology; purine and pyrimidine metabolism, folate metabolism Cell transformation (Myc), mismatch repair (HMGB1, MSH2, MSH6, PCNA), arrest in mitosis (BIRC5, BUB1B, CDC2.CHEK1, CSE1L, MAD2L1, MIF, PLK1), migration/cytokinesis (ANLN, CDC42, FN1, ITGB5, MSF, SPARC, TOP2A), survival (AKT2, APEX1, BIRC5), gastric carcinoma progression (COL1A1, FUS), folate metabolism (MTHFD1, MTHFD2)
23 142 Adult colon Down (D); up (CRC); up (A/M/S/T) Connective tissue development and function, cell-to-cell signaling, development disorder, organismal injury and abnormalities, tumor morphology, hematological system development and function, immune and lymphatic system development and function, cancer Cell transformation (ESR1, SRC), basal membrane disruption (MMP7), cell extension (ATF3, CD82, IL6, SRC), contact growth inhibition (JUN, IL6), osteocyte differentiation (IL6, JUN, SMAD6, SRC), cell cycle progression (ESR1, IER3, IL6, PSEN2), ERK/MAPK signaling (ESR1, ETS2, PPP1R10, PPP2R5C), development of tumor (CXCL6, ESR1, IER3, IL6, JUN), invasion of colon cancer cell lines (CD82, SRC), colon cancer (JUN, PDGFRL, SRC)
  1. A, AOM-induced; M, ApcMin/+; PS, ProbeSets; S, Smad3-/-; T, Tgfb1-/-; Rag2-/-.