Table 2

Enriched GSEA pathways and gene sets for both up- and down-regulated genes. ‘NES’ represents normalized enrichment score
Pathways and gene sets enriched by up-regulated genes NES FDR q-val Genes
Breast cancer estrogen signaling 2.217 0.002 SCGB2A1, TFF1, SCGB2A2, SCGB1D2, STC2, GATA3, SERPINB5, SERPINA3, AZGP1, TP53, CCNA2, CCNE2, EGFR, PTEN, DLC1, FHL5
HSA01430 cell communication 1.711 0.075 KRT15, DSC3, DSG3, KRT5, COL4A6, KRT17, KRT14, LAMC2, LAMA3, LAMB3, THBS3, LAMA5,LAMC1, GJA4, LAMA4, VWF, COL4A1, COL4A2
MRNA processing reactome 1.626 0.093 METTL3, HNRPD, HNRPA2B1, PRPF4B, SFRS7, CLK4, SFRS5, PABPN1, CSTF3, HNRPU, RBM5, SNRP70, SFRS14, SNRPA1, CLK2, NXF1, SFRS8, SFRS2, PTBP2, FUS, SFRS6, SFRS16, SF3B1, HNRPA3, SNRPB, PRPF3, SFRS12, U2AF1, PHF5A, TXNL4A, CUGBP2
Pathways and gene sets enriched by down-regulated genes NES FDR q-val Genes
HSA04910 insulin signaling pathway −2.242 0.004 CALML3, SHC4, IKBKB, PKM2, PIK3CD, PHKA1, CALM1, CBL, MAPK9, GSK3B, SKIP, MAP2K1, PIK3R3, CRK, IRS2, SORBS1, SOS1, PDE3A, PDE3B, PRKAR2B, MAPK10, PCK1
HSA04080 neuroactive ligand receptor interaction −2.148 0.007 NPY2R, OXTR, PARD3, GABBR1, LTB4R, NR3C1, EDNRA, EDNRB, EDG1, CALCRL, ADRB2, AGTRL1, ADRA2A, GHR, PTGER3, ADRA1A
HSA04530 tight junction −2.053 0.012 CGN, INADL, EXOC3, LLGL2, PARD3, PARD6G, TJP1, EPB41L1, ZAK, PPP2R1B, PTEN, GNAI1, RRAS2, CTNNA1, MAGI1, CLDN10
HSA04010 MAPK signaling pathway −2.018 0.013 NTF5, FGFR3, CACNA1D, RASGRP1, MAP3K14, TP53, CACNA1G, FAS, PDGFA, IKBKB, CACNA2D2, DAXX, GNA12, MAPK9, EGFR, GADD45A, DUSP10, CHP, DUSP3, MAP2K1, CRK, MEF2C, ZAK, EVI1, TGFBR1, SOS1, FGF10, RAPGEF2, RRAS2, RASGRF2, MAPK10, ACVR1C
HSA05210 colorectal cancer −1.972 0.013 TP53, IGF1R, FZD8, RALGDS, PIK3CD, FZD6, CYCS, MAPK9, EGFR, GSK3B, MAP2K1, PIK3R3, TGFBR1, SOS1, TCF7L2, FZD4, MAPK10, ACVR1C
HSA04510 focal adhesion −1.913 0.016 PAK7, COL4A6, LAMC2, LAMA3, SHC4, PAK6, ITGA10, LAMB3, ITGA4, PDGFA, IGF1R, THBS3, LAMA5, ZYX, PPP1R12A, ITGA2, PIK3CD, MAPK9, CAV1, EGFR, PARVA, GSK3B, LAMC1, MAP2K1, PIK3R3, CRK, FLT1, FYN, CCND2, PTEN, LAMA4, SOS1, VWF, IGF1, CAV2, TLN2, COL4A1, PDGFC, COL4A2, MAPK10
Integrin mediated cell adhesion KEGG −1.661 0.062 CAPN3, PAK6, ITGA10, ITGA4, ZYX, ITGA2, CAV1, MAP2K1, CRK, SORBS1, FYN, SOS1, CAV2, TNS1, MAPK10
HSA04310 WNT signaling pathway −1.423 0.161 CSNK1A1, NFATC3, TP53, WNT5A, VANGL2, FZD8, FZD6, MAPK9, GSK3B, CHP, DAAM1, DAAM2, SOX17, PPP2R1B, CCND2, TCF7L2, FZD4, MAPK10
ST INTEGRIN SIGNALING PATHWAY −1.400 0.160 PAK7, PAK6, ITGA10, ITGA4, ZYX, ITGA2, MAPK9, CAV1, CRK, ARHGEF7, FYN, PTEN, SOS1, TLN2, MAPK10
HSA04060 cytokine cytokine receptor interaction −1.383 0.152 CXCL6, IL28RA, CCL5, IFNGR2, FAS, IL4R, TNFSF15, PF4V1, TNFRSF14, IL2RB, IFNAR1, EGFR, LIFR, FLT1, BMPR2, TGFBR1, PDGFC, GHR, BMP2.

Peri et al.

Peri et al. BMC Medical Genomics 2012 5:46   doi:10.1186/1755-8794-5-46

Open Data