Table 5 List of genes differentially expressed in the indicated cell lines
From: Evolving neoantigen profiles in colorectal cancers with DNA repair defects
gene_id | Log2 fold change | p adj. |
|---|---|---|
MSS vs MSI | ||
 ABCB6 | − 1.12 | 0.01 |
 ACAD11 | 1.18 | 0.00 |
 ACOT8 | − 1.04 | 0.00 |
 AHCYL2 | 1.12 | 0.02 |
 ALDH6A1 | 1.34 | 0.00 |
 AMACR | − 1.54 | 0.01 |
 AOC1 | − 1.57 | 0.04 |
 APBB3 | 1.04 | 0.00 |
 ARHGAP18 | − 1.01 | 0.02 |
 ATOX1 | − 1.00 | 0.01 |
 ATP5E | − 1.22 | 0.00 |
 ATP9A | − 1.77 | 0.00 |
 B2M | − 1.58 | 0.00 |
 B4GALT5 | − 1.14 | 0.00 |
 BCL2L15 | − 1.73 | 0.01 |
 BCL9L | − 1.09 | 0.02 |
 BPTFP1 | 1.09 | 0.03 |
 C15orf52 | − 1.28 | 0.05 |
 C20orf24 | − 1.14 | 0.00 |
 C6orf48 | 1.05 | 0.01 |
 CAPG | − 1.30 | 0.02 |
 CCDC71L | − 1.08 | 0.02 |
 CCND3 | − 1.26 | 0.00 |
 CCPG1 | 1.16 | 0.02 |
 CD59 | − 1.01 | 0.03 |
 CD82 | − 1.37 | 0.03 |
 CDKN2A | − 3.20 | 0.00 |
 CEACAM1 | − 1.89 | 0.00 |
 CEACAM6 | − 1.71 | 0.05 |
 CGN | − 1.06 | 0.02 |
 CHKA | − 1.13 | 0.00 |
 CHMP4B | − 1.16 | 0.00 |
 CLDN1 | − 1.37 | 0.05 |
 CLDN3 | − 1.58 | 0.01 |
 COL17A1 | − 1.61 | 0.03 |
 COTL1 | − 1.61 | 0.00 |
 CPNE1 | − 1.05 | 0.00 |
 CPT1B | 1.13 | 0.00 |
 CTSA | − 1.10 | 0.00 |
 CTSD | − 1.02 | 0.03 |
 CTSH | − 1.22 | 0.03 |
 CTSS | − 2.46 | 0.00 |
 CTSV | − 1.81 | 0.00 |
 CTSZ | − 1.08 | 0.01 |
 CUEDC1 | − 1.33 | 0.02 |
 CXXC5 | − 1.24 | 0.01 |
 CYB5D1 | 1.24 | 0.00 |
 CYFIP2 | 1.37 | 0.03 |
 DAB2IP | − 1.14 | 0.00 |
 DCBLD2 | − 2.43 | 0.00 |
 DDX27 | − 1.02 | 0.00 |
 DNTTIP1 | − 1.25 | 0.00 |
 DPEP1 | − 1.88 | 0.04 |
 DYNLRB1 | − 1.04 | 0.00 |
 EDN1 | − 1.79 | 0.01 |
 EMP1 | − 1.47 | 0.03 |
 EPB41L1 | − 1.09 | 0.01 |
 EPB41L4A-AS1 | 1.04 | 0.01 |
 EPS8L1 | − 1.13 | 0.03 |
 FCGRT | − 1.69 | 0.00 |
 FECH | 1.07 | 0.00 |
 FKBP1A | − 1.02 | 0.01 |
 FZD7 | − 1.02 | 0.03 |
 GABBR1 | 1.70 | 0.01 |
 GABRE | − 1.83 | 0.00 |
 GCAT | 1.39 | 0.00 |
 GLS2 | 1.38 | 0.00 |
 GNE | − 1.13 | 0.04 |
 GSN | − 1.30 | 0.03 |
 HELZ2 | − 1.14 | 0.01 |
 HIST1H2AC | − 1.36 | 0.01 |
 HIST1H2BD | − 1.92 | 0.00 |
 HIST1H2BK | − 1.48 | 0.00 |
 HIST2H2AA3 | − 1.13 | 0.03 |
 HIST2H4A | − 2.11 | 0.00 |
 HSPA1A | − 1.83 | 0.02 |
 HSPB1 | − 1.41 | 0.03 |
 HSPH1 | − 1.43 | 0.00 |
 IDH2 | − 1.01 | 0.04 |
 IDS | − 1.30 | 0.02 |
 IFI6 | − 1.76 | 0.03 |
 IRF1 | − 1.02 | 0.01 |
 KRT20 | − 1.73 | 0.04 |
 KRT23 | − 4.08 | 0.00 |
 LAMC2 | − 1.77 | 0.00 |
 LFNG | − 1.19 | 0.02 |
 LGALS1 | − 2.88 | 0.00 |
 LINC01089 | − 1.05 | 0.01 |
 LIPG | 1.38 | 0.00 |
 LPCAT2 | − 1.11 | 0.01 |
 LRRC75A-AS1 | 1.01 | 0.04 |
 LRRC8A | − 1.23 | 0.00 |
 LTBP3 | − 1.37 | 0.01 |
 LY6E | − 1.41 | 0.02 |
 LY75 | − 1.60 | 0.01 |
 MACF1 | − 1.23 | 0.01 |
 MALL | − 1.20 | 0.03 |
 MAP7D1 | − 1.03 | 0.02 |
 MAPRE3 | − 1.11 | 0.02 |
 MDM2 | 1.37 | 0.00 |
 MGLL | − 1.35 | 0.01 |
 MIR4435-2HG | − 1.09 | 0.05 |
 MMP14 | − 1.53 | 0.02 |
 MOCOS | 1.18 | 0.01 |
 MORC4 | 1.15 | 0.00 |
 MUC20 | − 1.64 | 0.02 |
 MYBL2 | − 1.13 | 0.01 |
 MYL5 | 1.04 | 0.01 |
 NABP1 | − 1.35 | 0.01 |
 NDUFC2 | − 1.22 | 0.00 |
 OXR1 | − 1.12 | 0.01 |
 PDP1 | − 1.01 | 0.03 |
 PEA15 | − 1.29 | 0.00 |
 PFDN4 | − 1.04 | 0.00 |
 PIGT | − 1.00 | 0.00 |
 PLA2G6 | 1.17 | 0.00 |
 PLS3 | − 1.21 | 0.03 |
 PMEPA1 | − 2.81 | 0.00 |
 PML | − 1.04 | 0.00 |
 POLE4 | − 1.01 | 0.01 |
 PPM1M | 1.46 | 0.00 |
 PPP1R14D | − 1.98 | 0.01 |
 PPP1R18 | − 1.27 | 0.01 |
 PRADC1 | − 1.19 | 0.01 |
 PRAP1 | − 1.79 | 0.04 |
 QPCT | − 1.89 | 0.02 |
 QPRT | − 2.16 | 0.00 |
 REG4 | 2.81 | 0.00 |
 ROMO1 | − 1.14 | 0.01 |
 RPL22L1 | 1.62 | 0.00 |
 RPL32P29 | 1.31 | 0.00 |
 S100A11 | − 1.62 | 0.00 |
 S100A2 | − 2.35 | 0.00 |
 S100A4 | − 2.70 | 0.00 |
 SDC4 | − 1.30 | 0.00 |
 SESN2 | 1.23 | 0.01 |
 SGK2 | − 1.40 | 0.04 |
 SLC20A2 | − 1.07 | 0.01 |
 SLC2A1 | − 1.22 | 0.04 |
 SLC39A5 | − 1.93 | 0.02 |
 SLC6A6 | − 1.40 | 0.00 |
 SNHG8 | 1.01 | 0.01 |
 SNORA73B | 1.12 | 0.02 |
 SPINK1 | − 2.25 | 0.01 |
 STAT1 | − 1.06 | 0.01 |
 SULT2B1 | − 1.78 | 0.01 |
 SUPT4H1 | 1.22 | 0.00 |
 SYT7 | − 1.82 | 0.00 |
 TCF7 | − 1.03 | 0.04 |
 TFF1 | 2.17 | 0.02 |
 TGFBI | − 2.43 | 0.00 |
 TIMP2 | − 2.16 | 0.01 |
 TM4SF1 | − 1.70 | 0.01 |
 TMEM52 | 1.08 | 0.03 |
 TMPRSS4 | − 1.35 | 0.04 |
 TNFSF9 | 2.01 | 0.00 |
 TRIM7 | 1.24 | 0.05 |
 TSPAN6 | − 1.49 | 0.00 |
 TUBA4A | − 1.11 | 0.00 |
 TUBE1 | 1.12 | 0.01 |
 TXNDC9 | − 1.04 | 0.00 |
 UCA1 | − 1.79 | 0.03 |
 UCP2 | − 1.38 | 0.03 |
 UNC13D | − 1.81 | 0.01 |
 VAMP8 | − 1.09 | 0.00 |
 VOPP1 | − 1.13 | 0.01 |
 ZMYND8 | − 1.11 | 0.00 |
 ZNFX1 | − 1.08 | 0.00 |
Hypermutated vs non-hypermutated | ||
 ABHD12 | − 1.10 | 0.00 |
 ACOT8 | − 1.09 | 0.00 |
 AHCYL2 | 1.00 | 0.01 |
 AKR1C3 | − 1.52 | 0.02 |
 ALDH6A1 | 1.30 | 0.00 |
 AMN | 1.06 | 0.04 |
 ANXA6 | − 1.94 | 0.00 |
 AOC1 | − 1.96 | 0.00 |
 ARHGEF10 | 1.15 | 0.04 |
 ARL4C | − 1.56 | 0.01 |
 ATOX1 | − 1.12 | 0.00 |
 ATP5E | − 1.31 | 0.00 |
 ATP8B1 | 1.09 | 0.00 |
 ATP9A | − 1.77 | 0.00 |
 B2M | − 1.82 | 0.00 |
 BCAS4 | − 1.06 | 0.00 |
 BCL2L1 | − 1.02 | 0.00 |
 BNIP3 | 1.31 | 0.02 |
 C15orf52 | − 1.10 | 0.04 |
 C20orf24 | − 1.21 | 0.00 |
 C2orf54 | − 2.00 | 0.00 |
 C7orf50 | − 1.20 | 0.00 |
 CAPG | − 1.02 | 0.03 |
 CCDC71L | − 1.00 | 0.01 |
 CD59 | − 1.13 | 0.00 |
 CD82 | − 1.31 | 0.01 |
 CDKN2A | − 1.43 | 0.03 |
 CEACAM1 | − 1.42 | 0.00 |
 CFD | 1.65 | 0.00 |
 CHKA | − 1.17 | 0.00 |
 CHMP4B | − 1.25 | 0.00 |
 CLDN3 | − 1.45 | 0.00 |
 COL17A1 | − 1.33 | 0.03 |
 COTL1 | − 1.67 | 0.00 |
 CPNE1 | − 1.09 | 0.00 |
 CST3 | − 1.29 | 0.00 |
 CTSA | − 1.01 | 0.00 |
 CTSD | − 1.27 | 0.00 |
 CTSH | − 1.31 | 0.00 |
 CTSS | − 2.26 | 0.00 |
 CTSV | − 2.11 | 0.00 |
 CTSZ | − 1.05 | 0.00 |
 CUEDC1 | − 1.59 | 0.00 |
 CXXC5 | − 1.01 | 0.01 |
 CYB5D1 | 1.17 | 0.00 |
 CYTOR | − 1.42 | 0.00 |
 DBNDD2 | − 1.06 | 0.00 |
 DCBLD2 | − 2.20 | 0.00 |
 DGAT2 | − 1.04 | 0.01 |
 DHRS3 | − 1.09 | 0.01 |
 DNTTIP1 | − 1.23 | 0.00 |
 DYNLRB1 | − 1.25 | 0.00 |
 EDN1 | − 1.27 | 0.03 |
 EHD1 | − 1.01 | 0.00 |
 EMP1 | − 1.60 | 0.00 |
 EPB41L1 | − 1.06 | 0.00 |
 EPS8L1 | − 1.20 | 0.00 |
 FAH | − 1.28 | 0.00 |
 FAM84B | − 1.10 | 0.02 |
 FCGRT | − 1.60 | 0.00 |
 FECH | 1.27 | 0.00 |
 FKBP10 | − 1.41 | 0.04 |
 FKBP1A | − 1.16 | 0.00 |
 FUNDC2 | − 1.04 | 0.00 |
 FUNDC2P1 | − 1.08 | 0.00 |
 FZD7 | − 1.19 | 0.00 |
 GABARAPL1 | − 1.35 | 0.01 |
 GABRE | − 1.53 | 0.00 |
 GCAT | 1.01 | 0.01 |
 GNE | − 1.03 | 0.02 |
 GPC1 | − 1.01 | 0.05 |
 GSN | − 1.75 | 0.00 |
 HELZ2 | − 1.02 | 0.01 |
 HIST1H2BD | − 1.04 | 0.01 |
 HIST2H4A | − 1.38 | 0.00 |
 HSD11B2 | − 1.11 | 0.03 |
 HSPB1 | − 1.20 | 0.02 |
 IDS | − 1.60 | 0.00 |
 IFI27 | − 1.48 | 0.03 |
 IFI27L2 | − 1.03 | 0.03 |
 IFI6 | − 1.86 | 0.00 |
 IGFBP4 | − 1.15 | 0.02 |
 IL33 | 1.58 | 0.04 |
 IRF1 | − 1.28 | 0.00 |
 ISG15 | − 1.13 | 0.04 |
 ITGA3 | − 1.23 | 0.01 |
 ITGB5 | − 1.09 | 0.00 |
 KIFC3 | − 1.20 | 0.04 |
 KLK6 | − 2.00 | 0.00 |
 KRT20 | − 1.56 | 0.02 |
 KRT23 | − 3.88 | 0.00 |
 KRT80 | − 1.58 | 0.00 |
 LAMC2 | − 1.57 | 0.00 |
 LFNG | − 1.23 | 0.00 |
 LGALS1 | − 2.44 | 0.00 |
 LIPG | 1.38 | 0.00 |
 LITAF | − 1.20 | 0.01 |
 LTBP3 | − 1.63 | 0.00 |
 LTBP4 | 1.17 | 0.00 |
 LY6E | − 1.74 | 0.00 |
 LY6G6D | − 2.03 | 0.01 |
 LY75 | − 1.60 | 0.00 |
 MAPRE3 | − 1.23 | 0.00 |
 MBOAT2 | − 1.03 | 0.02 |
 MCRIP1 | − 1.02 | 0.00 |
 MDK | − 1.36 | 0.01 |
 MDM2 | 1.09 | 0.00 |
 MELTF | − 1.18 | 0.01 |
 MGLL | − 1.20 | 0.00 |
 MIR4435-2HG | − 1.47 | 0.00 |
 MMP14 | − 1.64 | 0.00 |
 MOCOS | 1.13 | 0.00 |
 MOSPD1 | − 1.01 | 0.00 |
 MUC20 | − 1.58 | 0.00 |
 MYBL2 | − 1.06 | 0.00 |
 NABP1 | − 1.05 | 0.01 |
 NDUFC2 | − 1.11 | 0.00 |
 PDP1 | − 1.16 | 0.00 |
 PEA15 | − 1.30 | 0.00 |
 PFDN4 | − 1.20 | 0.00 |
 PHLDB1 | − 1.05 | 0.05 |
 PLAUR | − 1.18 | 0.00 |
 PLTP | − 1.53 | 0.03 |
 PMEPA1 | − 2.92 | 0.00 |
 PML | − 1.03 | 0.00 |
 POLD4 | − 1.06 | 0.00 |
 PPP1R14D | − 2.05 | 0.00 |
 PRDX5 | − 1.09 | 0.00 |
 PRR15 | − 1.06 | 0.03 |
 PRSS23 | − 1.09 | 0.02 |
 PSMA7 | − 1.00 | 0.00 |
 PSMB10 | − 1.27 | 0.00 |
 QPCT | − 2.23 | 0.00 |
 QPRT | − 1.32 | 0.05 |
 RASL11A | − 1.19 | 0.04 |
 REG4 | 2.99 | 0.00 |
 RGCC | − 2.97 | 0.00 |
 RGMB | 1.49 | 0.00 |
 RHOD | − 1.22 | 0.01 |
 ROMO1 | − 1.28 | 0.00 |
 RPL22L1 | 1.12 | 0.01 |
 RTFDC1 | − 1.04 | 0.00 |
 S100A11 | − 1.65 | 0.00 |
 S100A2 | − 2.87 | 0.00 |
 S100A4 | − 1.55 | 0.02 |
 SDC4 | − 1.30 | 0.00 |
 SLC20A2 | − 1.01 | 0.00 |
 SLC2A1 | − 1.42 | 0.00 |
 SLC2A4RG | − 1.04 | 0.00 |
 SLC2A8 | − 1.04 | 0.00 |
 SLC39A5 | − 1.70 | 0.01 |
 SLCO1B3 | 1.46 | 0.05 |
 SMAD3 | − 1.08 | 0.00 |
 SMIM22 | − 1.19 | 0.01 |
 SNORA73B | 1.00 | 0.01 |
 SPINK1 | − 2.72 | 0.00 |
 SULT2B1 | − 1.60 | 0.00 |
 SYT7 | − 1.55 | 0.00 |
 TACSTD2 | − 2.32 | 0.00 |
 TCF7 | − 1.18 | 0.00 |
 TGFBI | − 2.28 | 0.00 |
 TIMP2 | − 2.59 | 0.00 |
 TM4SF1 | − 1.78 | 0.00 |
 TMEM176A | − 2.16 | 0.00 |
 TMEM176B | − 1.85 | 0.01 |
 TMEM185A | − 1.07 | 0.00 |
 TMPRSS4 | − 1.35 | 0.01 |
 TNFRSF14-AS1 | 1.19 | 0.02 |
 TNFRSF1B | − 1.44 | 0.00 |
 TRIB1 | − 1.11 | 0.02 |
 TRIM7 | 1.08 | 0.04 |
 TSC22D1 | − 1.01 | 0.01 |
 TUBA4A | − 1.01 | 0.00 |
 TUBB2A | − 1.49 | 0.00 |
 TUBE1 | 1.12 | 0.00 |
 UCA1 | − 1.49 | 0.03 |
 UCP2 | − 1.16 | 0.02 |
 VAMP8 | − 1.10 | 0.00 |
 VEGFB | − 1.25 | 0.00 |
 VOPP1 | − 1.27 | 0.00 |
 VSIR | − 1.68 | 0.00 |
 ZFP90 | 1.13 | 0.00 |
 ZMYND8 | − 1.07 | 0.00 |
EVOLVING-CRC vs STABLE-CRC | ||
 ABCB6 | − 1.00 | 0.04 |
 AHI1 | 1.04 | 0.02 |
 ANXA6 | − 1.83 | 0.02 |
 ATOX1 | − 1.07 | 0.01 |
 B2M | − 1.57 | 0.00 |
 CPNE1 | − 1.12 | 0.00 |
 FAT1 | 1.09 | 0.04 |
 GTF3A | − 1.09 | 0.03 |
 IGFBP6 | − 2.01 | 0.02 |
 IRF1 | − 1.05 | 0.02 |
 LGALS1 | − 2.45 | 0.00 |
 LY6E | − 1.47 | 0.02 |
 PAM | − 1.27 | 0.03 |
 PEA15 | − 1.12 | 0.01 |
 PLA2G2A | 2.56 | 0.01 |
 PSMB10 | − 1.05 | 0.02 |
 S100A2 | − 1.96 | 0.00 |
 SDC4 | − 1.04 | 0.05 |
 SLC7A11 | 1.63 | 0.01 |
 TGFBI | − 1.50 | 0.04 |
 TIMP2 | − 1.82 | 0.03 |
 TUBA1A | − 1.71 | 0.05 |
 TUBB2A | − 1.55 | 0.03 |
 TUBE1 | 1.27 | 0.01 |
 VEGFA | 1.08 | 0.05 |