Supplementary material Gut Supplementary Table 3. Marker genes in each malignant epithelial cells cluster Gene Log(Fold-change) Pct.1 Pct.2 Adj p- value Cluster LEFTY1 2.690865644 0.899 0.067 0.00E+00 C1 TFF2 2.186713379 0.855 0.36 0.00E+00 C1 CCT2 1.701377329 0.801 0.283 0.00E+00 C1 SPINK4 1.663911876 0.654 0.128 0.00E+00 C1 TFF3 1.632604627 0.882 0.43 0.00E+00 C1 CXCL17 1.616238928 0.659 0.079 0.00E+00 C1 LDHB 1.407263152 0.711 0.137 0.00E+00 C1 CLDN18 1.398880496 0.825 0.278 0.00E+00 C1 TESC 1.382790712 0.79 0.212 0.00E+00 C1 PDIA6 1.295630983 0.789 0.404 0.00E+00 C1 PSCA 1.263596359 0.922 0.241 0.00E+00 C1 SRD5A3 1.246561606 0.586 0.098 0.00E+00 C1 PDIA4 1.180717046 0.849 0.419 0.00E+00 C1 DPCR1 1.175754587 0.506 0.06 0.00E+00 C1 WBP5 1.163957541 0.734 0.106 0.00E+00 C1 LYZ 1.141614179 0.969 0.727 0.00E+00 C1 RAP1B 1.125989315 0.68 0.255 0.00E+00 C1 S100P 1.055862172 0.962 0.758 0.00E+00 C1 OS9 1.05478066 0.787 0.338 0.00E+00 C1 R3HDM2 1.031695733 0.742 0.167 0.00E+00 C1 B3GNT7 1.031632795 0.549 0.088 0.00E+00 C1 MORF4L1 1.023176967 0.768 0.409 0.00E+00 C1 TMEM165 0.999912261 0.649 0.196 0.00E+00 C1 GALNT3 0.995165397 0.705 0.254 0.00E+00 C1 TFF1 0.962929536 0.96 0.591 0.00E+00 C1 LY6D 0.94328396 0.484 0.007 0.00E+00 C1 MIA 0.895355862 0.623 0.103 0.00E+00 C1 MDM2 0.864864363 0.615 0.089 0.00E+00 C1 YEATS4 0.864197638 0.585 0.128 0.00E+00 C1 CPM 0.831257805 0.511 0.026 0.00E+00 C1 NGFRAP1 0.776686405 0.552 0.027 0.00E+00 C1 TCEAL8 0.747773737 0.549 0.064 0.00E+00 C1 SFTA2 0.710176136 0.52 0.066 0.00E+00 C1 FKBP10 0.567908872 0.427 0.007 0.00E+00 C1 HOXB2 0.52009395 0.466 0.03 0.00E+00 C1 ALDH1L1 0.478075328 0.386 0.009 0.00E+00 C1 BCAR4 0.405445074 0.384 0 0.00E+00 C1 YWHAE 0.941441648 0.797 0.453 6.63E-301 C1 MUC5B 0.749504079 0.441 0.032 9.41E-296 C1 PKM 1.024781554 0.835 0.518 4.67E-293 C1 ATP1B1 1.094054311 0.838 0.514 5.73E-290 C1 PRKCDBP 0.521875888 0.445 0.04 1.78E-288 C1 PTP4A2 1.006611051 0.74 0.358 1.11E-281 C1 RAB34 0.379470725 0.394 0.022 1.26E-279 C1 C1QBP 1.055652495 0.699 0.29 1.74E-277 C1 AGR2 1.043123785 0.967 0.832 7.02E-277 C1 Zhang M, et al. Gut 2020;0:1–12. doi: 10.1136/gutjnl-2019-320368 Supplementary material Gut VSIG1 0.728079807 0.537 0.093 8.17E-275 C1 NUP107 0.744204709 0.569 0.123 2.00E-274 C1 REG4 1.083913316 0.905 0.499 1.30E-270 C1 RP11-10A14.5 0.297216094 0.321 0 2.05E-269 C1 PTPLAD1 0.947636123 0.666 0.255 8.18E-269 C1 KRT17 0.903244887 0.401 0.03 1.67E-268 C1 DSTN 0.854726665 0.853 0.613 3.41E-268 C1 GALNT7 0.709216869 0.631 0.165 7.55E-268 C1 TFPI 0.753551093 0.647 0.186 1.34E-262 C1 HSP90AB1 0.844714478 0.922 0.665 7.40E-262 C1 SRSF9 0.978838275 0.658 0.282 6.15E-261 C1 GPR110 0.792021592 0.397 0.033 1.05E-256 C1 YWHAQ 0.917645011 0.684 0.318 3.66E-256 C1 SCGB2A1 0.350719764 0.323 0.005 1.20E-255 C1 DCTN2 0.855691592 0.617 0.219 2.39E-255 C1 CDK4 0.96724454 0.603 0.204 5.51E-255 C1 BEX2 0.312185722 0.323 0.006 1.10E-252 C1 ZFAND6 0.859643177 0.62 0.228 7.87E-251 C1 HSP90B1 0.894697739 0.881 0.592 7.89E-251 C1 RP11-2E17.1 0.333995995 0.3 0 1.03E-250 C1 CSTB 1.133047426 0.85 0.649 1.19E-248 C1 ULBP2 0.349850496 0.325 0.009 4.54E-247 C1 PUM1 0.730101664 0.655 0.226 1.47E-245 C1 CLIC1 1.06446547 0.835 0.65 1.46E-244 C1 BACE2 0.776146486 0.629 0.21 1.42E-242 C1 ANXA5 0.701165432 0.568 0.159 9.35E-239 C1 ZFC3H1 0.677887382 0.611 0.17 8.10E-234 C1 MAL2 0.952741646 0.742 0.397 1.27E-233 C1 MBD6 0.504246192 0.497 0.097 3.90E-231 C1 RBM47 0.886709293 0.705 0.357 5.12E-229 C1 TUBB 0.948856295 0.719 0.338 1.85E-228 C1 RAB3IP 0.740840685 0.566 0.161 5.86E-226 C1 SMC5 0.620713614 0.591 0.179 4.29E-224 C1 PIP4K2C 0.444414038 0.423 0.064 6.67E-223 C1 SLC35E3 0.422166937 0.392 0.05 3.86E-221 C1 ARL14 1.302472547 0.738 0.367 1.90E-220 C1 ANXA10 0.781303497 0.751 0.311 4.97E-220 C1 FRS2 0.36581964 0.368 0.039 5.55E-219 C1 SERINC2 0.751146496 0.785 0.471 1.10E-218 C1 HMGA1 0.836465129 0.781 0.485 1.33E-218 C1 C8orf4 0.869162861 0.726 0.288 7.08E-215 C1 RP11-519G16.5 0.275871768 0.278 0.005 2.19E-214 C1 FDFT1 0.88076215 0.625 0.257 6.92E-212 C1 TMED2 0.851218937 0.676 0.347 6.88E-210 C1 KRT19 0.82881006 0.969 0.874 4.18E-209 C1 CHMP1B 0.767154492 0.692 0.311 8.40E-209 C1 MTDH 0.719515427 0.792 0.488 4.07E-208 C1 RAB32 0.275438262 0.344 0.032 1.08E-204 C1 Zhang M, et al. Gut 2020;0:1–12. doi: 10.1136/gutjnl-2019-320368 Supplementary material Gut RAB21 0.481720994 0.478 0.11 8.39E-204 C1 CAP1 0.845841827 0.641 0.316 3.80E-203 C1 MYL12A 0.947954026 0.817 0.649 7.09E-203 C1 SDCBP 0.777669854 0.685 0.346 1.33E-202 C1 STARD10 0.733799598 0.854 0.536 1.36E-202 C1 SRP9 0.782786299 0.677 0.355 4.62E-202 C1 AHR 0.538273196 0.573 0.167 5.71E-202 C1 AKIRIN1 0.47764806 0.499 0.126 1.29E-201 C1 PDIA3 0.795061975 0.766 0.484 2.87E-197 C1 AKAP13 0.749638262 0.693 0.319 4.44E-197 C1 DST 0.680727101 0.706 0.282 5.07E-197 C1 TSPAN31 0.445008926 0.459 0.103 4.70E-196 C1 ANXA1 0.990611597 0.623 0.236 2.26E-195 C1 ANXA2 0.923005092 0.867 0.733 1.09E-194 C1 TFPT 0.433556663 0.492 0.12 3.67E-194 C1 SYNE4 0.276709421 0.295 0.018 5.91E-194 C1 PABPC1 0.58828564 0.933 0.752 9.95E-194 C1 MGST1 0.72142683 0.648 0.274 3.87E-193 C1 HIST1H2BK 0.845917465 0.665 0.342 6.48E-193 C1 MAGED1 0.397100639 0.427 0.082 1.45E-192 C1 CRK 0.526217931 0.559 0.178 2.04E-192 C1 TSPAN3 0.754095483 0.776 0.493 1.67E-191 C1 AGAP2 0.324034798 0.251 0.005 1.72E-191 C1 ARMCX3 0.393037375 0.435 0.087 9.19E-191 C1 MARS 0.507454194 0.464 0.107 1.66E-190 C1 RAN 0.831480759 0.747 0.465 1.81E-190 C1 ECI2 0.572148619 0.455 0.112 3.03E-190 C1 RHBDL2 0.416071426 0.456 0.102 9.05E-190 C1 HSPA5 0.813668975 0.775 0.442 5.45E-189 C1 ICAM2 0.282680792 0.283 0.017 1.47E-188 C1 CTSE 0.630732705 0.717 0.316 1.78E-187 C1 ZNF430 0.427332087 0.379 0.063 2.47E-187 C1 TM4SF1 1.0672273 0.705 0.377 4.05E-187 C1 VAPA 0.771645976 0.65 0.343 1.27E-186 C1 RCAN1 0.635068931 0.409 0.077 5.09E-186 C1 FRMD4B 0.610702297 0.43 0.092 1.65E-185 C1 DDIT3 0.796008573 0.606 0.219 1.93E-185 C1 PRPF4B 0.740129307 0.815 0.408 7.56E-184 C1 ABCF1 0.663423185 0.722 0.338 8.01E-184 C1 LDLR 0.774135152 0.71 0.337 2.04E-183 C1 TSPAN13 0.69173611 0.603 0.26 3.34E-183 C1 ACTR2 0.644131887 0.651 0.298 1.18E-182 C1 RAB11FIP1 0.797810148 0.766 0.437 3.38E-181 C1 NDUFV2 0.780467632 0.671 0.38 5.18E-180 C1 KRT7 0.686045312 0.698 0.306 1.03E-179 C1 NMB 0.452105539 0.428 0.099 1.55E-179 C1 SQLE 0.820767424 0.628 0.258 1.61E-179 C1 ADAM17 0.421792244 0.455 0.111 2.05E-178 C1 Zhang M, et al.