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Table 3 Ingenuity Pathway Analysis of gene clusters.

From: Functional annotation of novel lineage-specific genes using co-expression and promoter analysis

LST clustera

Significantbfunctions (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

  1. 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.
  2. b All P-values were < 0.05