Table 3.
Ingenuity Pathway Analysis of gene clusters.
| LST clustera | Significant b functions (F) and canonical pathways (C) | Genes included in the function |
|---|---|---|
| LIVR (143/212) | glycerophospholipid metabolism (C) | LYPLA1, PGS1, PLCE1, PLCL2 |
| cancer (F) | FABP5, GLRX, GRRP1, MET, MLH1, PLCE1, PLXNB2, ASB2, KCTD11, CDK3 | |
| repair of DNA (F) | CDC5L, ERCC1, MLH1, NHEJ1, NTHL1, POLI, XRCC1 | |
| immune response of organism (F) | CD48, GATA3, MX1 | |
| development of epidermis (F) | ALDH3A2, FABP5, GJB5 | |
| PLAC (64/116) | Wnt/beta-catenin signaling (C) | CDH1, CSNK1G2, DKK1, TLE4 |
| acute-phase response signaling(C) | FOS, HMOX2, PTPN11, SOD2 | |
| tissue morphology--size (F) | CDKN1C, DLX5, IGF2, STC1, PTGS2, FOS, CDH1 | |
| small molecule biochemistry- transport of amino acids and synthesis of prostaglandin (F) | SLC7A3, STX1A, COMT, PTGS2, IGF2, FOS, IGFBP7, CYP4A22, BCAT, STC1, MAN2A1, PTPN11, TFPI, SOD2 | |
| embryonic development-- proliferation and formation of embryonic tissue (F) | ESM1, MED28, PTGS2, CDH1, DKK1, FOS, HAND1 | |
| development of embryonic and trophoblast cells (F) | CDKN1C, HAND1, IGF2, PTPN11 | |
| cell cycle--entry into cell stage (F) | CDH1, CDKN1C, FOS, MAD2L1, PTPN11, SOD2 | |
| lipid Metabolism | CYP4A22, IGF2, IGFBP7, PTGS2, STC1, PTPN11, COMT | |
| cell adhesion (F) | CASK, CD151, CDH1, IGFBP7, MAD2L1, MAN2A1, PTPN11, PVRL2, TFPI | |
| transcription (F) | CASK, CDH1, CDKN1C, DKK1, DLX5, FADD, FOS, GATAD2A, HAND1, IGF2, MED28, MSX1, PTPN11, RP13-122B23.3, SNAPC2, SOD2, SPEN, TARBP2, THOC4, TLE4, UBTF, ZNF281 | |
| cancer--cell death of tumor cell lines(F) | CDH1, CDKN1C, DKK1, FADD, FOS, IGF2, IGFBP7, IHPK2, MAD2L1, MSX1, PTGS2, PTPN11, SOD2, UBTF | |
| THYM (18/32) | cellular growth and proliferation (F) | BTG1, CDCA7, ELF1, HMGB1, NCOR2, PCNA, PTK2, TCF12, ZFP36L2, ASXL1 |
| cell death (F) | PCNA, TRAP1, PLA2G7, BTG1, NCOR2, HMGB1, PTK2, TCF12, ZFP36L2 | |
| gene expression--transcription and transactivation (F) | HMGB1, HMGB2, PCNA, ELF1, ASXL1, NCOR2, ZBTB7A, BTG1, PTK2, TCF12, NXF1 | |
| immune and lymphatic system development and function (F) | HMGB1, TCF12, PTK2, CDCA7, NCOR2 |
a Numbers in parentheses indicate count of genes with IPA functions/cluster size; LIVR cluster, [5BP, 39NG, 237NG, 266NG] and 208 other genes; PLAC cluster, [104JE, 22JE, 34FL] and 113 other genes; THYM cluster, [383NG, 21PW] and 30 other genes.
b All P-values were < 0.05