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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