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. |