Table 1 Overrepresented KEGG pathways of differentially expressed genes in virus-infected versus uninfected primary NSCLC specimens
From: Impact of viral presence in tumor on gene expression in non-small cell lung cancer
KEGG ID | Name | Count | Pop.Hits | Fold Enrichment | FDR | Genes | Total list | |
|---|---|---|---|---|---|---|---|---|
Over-expressed genes in Virus-infected primary NSCLC tumors | hsa04110 | Cell cycle | 23 | 124 | 4.121 | 0.000 | E2F2, CDC6, FZR1, E2F4, RBL1, SKP2, PKMYT1, CHEK1, CDC20, PTTG1, MCM2, CDK4, CDC25B, MCM6, CCNE1, CDC45, CCNB2, CCND2, TFDP2, BUB1, BUB1B, CCNA2, STAG1 | 311 |
hsa03050 | Proteasome | 10 | 44 | 5.050 | 0.001 | PSMF1, PSMC4, PSMC3, PSMD11, PSME2, PSMB3, PSMB2, PSMD2, PSMD3, PSME3 | 311 | |
hsa04115 | p53 signaling pathway | 12 | 67 | 3.979 | 0.002 | CCNE1, CCNB2, CCND2, SERPINB5, RRM2, BAX, CHEK1, PMAIP1, PERP, CDK4, GTSE1, SESN3 | 311 | |
hsa05203 | Viral carcinogenesis | 22 | 205 | 2.384 | 0.004 | HRAS, RBL1, UBR4, SKP2, ACTN1, CHEK1, CDC20, PMAIP1, MAPKAPK2, CDK4, SRF, PKM, CDC42, CCNE1, MAPK1, GTF2A1, CCND2, BAX, RANBP1, CCNA2, CHD4, DLG1 | 311 | |
hsa04120 | Ubiquitin mediated proteolysis | 16 | 137 | 2.595 | 0.015 | FZR1, UBE2A, SOCS1, CBL, UBE4B, SKP2, UBE2J1, SAE1, CDC20, KEAP1, UBE2L3, BRCA1, FANCL, PIAS2, PIAS1, UBE2S | 311 | |
hsa03015 | mRNA surveillance pathway | 12 | 91 | 2.930 | 0.030 | NXT1, NCBP2, SYMPK, FIP1L1, ALYREF, HBS1L, SRRM1, MSI2, SMG1, ETF1, PPP2R2B, PPP2R3C | 311 | |
hsa05166 | HTLV-I infection | 23 | 256 | 1.996 | 0.031 | DVL3, E2F2, IL6, HRAS, TLN2, SLC25A5, ELK1, CHEK1, CDC20, PTTG1, CD40, MYBL2, CDK4, SRF, MSX2, POLE2, ELK4, CCND2, BAX, SLC2A1, BUB1B, RANBP1, DLG1 | 311 | |
hsa03040 | Spliceosome | 13 | 133 | 2.172 | 0.187 | NCBP2, DHX8, SNRPA1, TRA2B, LSM6, U2SURP, ALYREF, SF3B3, CTNNBL1, SRSF4, TCERG1, SNRNP40, SNRPF | 311 | |
Under-expressed genes in Virus-infected primary NSCLC tumors | hsa04024 | cAMP signaling pathway | 18 | 198 | 2.804 | 0.003 | ACOX1, ATP1B1, ROCK1, ROCK2, ADCY6, PDE4D, PDE4C, ATP1A2, PPP1CB, PLCE1, GRIA1, ABCC4, RAP1A, HHIP, HCN4, ADCY10, CACNA1D, HCAR1 | 224 |
hsa04270 | Vascular smooth muscle contraction | 13 | 119 | 3.370 | 0.005 | ROCK1, PLA2G10, ROCK2, PPP1R12B, ADCY6, NPR2, ARHGEF12, PPP1CB, GNAQ, PLA2G12A, PLA2G12B, CACNA1D, PPP1R14A | 224 | |
hsa01100 | Metabolic pathways | 59 | 1228 | 1.482 | 0.015 | ACOX2, ACOX1, CYP3A5, COX11, SGMS2, AMT, ALG2, ADH1A, PPOX, GPAT2, HIBADH, ASAH1, PDHB, ASAH2, ASPA, PIGM, NDUFS8, BPNT1, AGPAT2, NDUFS1, COX15, IDUA, NMNAT2, C1GALT1C1, HMGCLL1, SUCLG2, COX4I2, LPIN2, CDS1, TAT, ALDH3B1, ATP6V1C1, PLCE1, ALOX15B, MGAT5, AOC1, PRODH, ME3, LOC102724788, ALDOB, CTPS2, PLA2G12A, PLCH1, B3GNT6, PLA2G12B, BDH2, HSD17B7, ACSL5, PLA2G10, B3GALT2, KL, MAOA, NAT1, ACSM3, DBT, PON2, AHCYL2, ABO, PON3 | 224 | |
hsa04390 | Hippo signaling pathway | 12 | 151 | 2.452 | 0.114 | BMP4, PARD6B, BMP2, TP53BP2, WTIP, FZD5, PPP1CB, BMP5, LLGL2, BMPR1A, CTNNB1, PPP2R2A | 224 | |
hsa04972 | Pancreatic secretion | 9 | 93 | 2.985 | 0.121 | ATP1B1, SLC12A2, GNAQ, PLA2G10, PLA2G12A, PLA2G12B, ADCY6, RAP1A, ATP1A2 | 224 | |
hsa00564 | Glycerophospholipid metabolism | 9 | 95 | 2.922 | 0.135 | GPD1L, LPGAT1, PLA2G10, PLA2G12A, PLA2G12B, LPIN2, GPAT2, CDS1, AGPAT2 | 224 | |
hsa04961 | Endocrine and other factor-regulated calcium reabsorption | 6 | 45 | 4.113 | 0.168 | ATP1B1, GNAQ, KL, PTH1R, ADCY6, ATP1A2 | 224 | |
hsa04510 | Focal adhesion | 14 | 206 | 2.096 | 0.182 | COL4A4, COL4A3, ROCK1, PAK3, ROCK2, FLT4, PPP1R12B, ITGA8, ITGA1, ITGA10, RAP1A, ACTN2, PPP1CB, CTNNB1 | 224 | |
hsa04146 | Peroxisome | 8 | 83 | 2.973 | 0.199 | ACOX2, ACOX1, HMGCLL1, NUDT12, PEX1, ABCD3, PEX13, ACSL5 | 224 |