Table 4. Hierarchical clustering of DEGs in APCMin/+ proximal colonic RNA transcripts vs. control RNA samples.
| Gene name | Log2 FC | FDR | Gene name | Log2 FC | FDR |
|---|---|---|---|---|---|
| Cluster 1 | Up ↑ | Cluster 4 | Down↓ | ||
| Hoxd13 | 7.95 | 5.00E-04 | Rmrp | -3.9 | 4.00E-04 |
| Tgm3 | 9.07 | 6.00E-04 | Gm22513 | -3.97 | 8.00E-04 |
| Atp12a | 6.4 | 8.00E-04 | Gm26035 | -5.49 | 8.00E-04 |
| Ly6g | 9.39 | 8.00E-04 | Igkv5-48 | -3.23 | 0.0022 |
| Sval1 | 7.44 | 8.00E-04 | Gm24146 | -4.69 | 0.0023 |
| Fut9 | 6.44 | 0.001 | Igkv12-98 | -5.86 | 0.0023 |
| Gm8540 | 8.63 | 0.0018 | Metazoa_SRP | -3.23 | 0.0034 |
| AI854703 | 4.65 | 0.0022 | Rn7sk | -3.04 | 0.0036 |
| B3gnt7 | 5.27 | 0.0023 | Igkv3-5 | -5.88 | 0.0044 |
| Cpn2 | 4.92 | 0.0023 | Rpph1 | -2.62 | 0.0073 |
| Evx1 | 8.64 | 0.0023 | Igkv3-1 | -5.52 | 0.0224 |
| Gm15053 | 8.81 | 0.0023 | Vaultrc5 | -2.57 | 0.0267 |
| Itih2 | 5.16 | 0.0023 | Ighv1-7 | -2.54 | 0.0352 |
| Mptx1 | 5.36 | 0.0023 | Klk1b22 | -2.09 | 0.0352 |
| Myh2 | 3.28 | 0.0023 | Olfr424 | -4.87 | 0.0352 |
| Thbs4 | 4.23 | 0.0023 | Gm22179 | -3.19 | 0.0353 |
| Casp14 | 10.53 | 0.0029 | Igkv9-124 | -3.76 | 0.0445 |
| Gm16341 | 5.86 | 0.0032 | Cluster 5 | Down↓ | |
| Best4-ps | 6.75 | 0.0034 | Ighv5-15 | -6.07 | 5.00E-04 |
| Ctse | 4.5 | 0.0034 | Igkv2-109 | -5.08 | 0.0066 |
| Fxyd4 | 9.83 | 0.0034 | Cluster 6 | Down↓ | |
| Gm2539 | 10.01 | 0.0034 | Ighv9-4 | -3.72 | 0.0176 |
| Sval3 | 7.01 | 0.0034 | Igkv9-120 | -3.07 | 0.0432 |
| Klk15 | 9.86 | 0.0035 | Ighv1-80 | -3.7 | 0.0456 |
| Tmprss13 | 7.92 | 0.0035 | Cluster 7 | Down↓ | |
| Hoxb13 | 10.06 | 0.0039 | Igkv14-100 | -3.87 | 0.0388 |
| Hoxa13 | 3.92 | 0.0044 | Sel1l2 | -7.57 | 0.0444 |
| Mptx2 | 5.49 | 0.0044 | |||
| Insl5 | 4.45 | 0.0045 | |||
| Pla2g4f | 3.83 | 0.0045 | |||
| Slc28a3 | 4.12 | 0.0046 | |||
| Vsig1 | 3.39 | 0.0046 | |||
| Rims4 | 3.76 | 0.0047 | |||
| Vtcn1 | 5.41 | 0.0049 | |||
| Anxa8 | 3.61 | 0.0053 | |||
| Pdzd7 | 3.17 | 0.0053 | |||
| 4930552P12Rik | 3.66 | 0.0059 | |||
| HOXA11-AS1_5 | 4.62 | 0.0059 | |||
| Gpr83 | 4.27 | 0.006 | |||
| B3gnt5 | 2.98 | 0.0064 | |||
| Gjb5 | 3.34 | 0.0066 | |||
| Tnip3 | 2.94 | 0.0066 | |||
| Eno3 | 2.53 | 0.007 | |||
| Gjb4 | 3.84 | 0.0074 | |||
| Nxpe4 | 3.51 | 0.0074 | |||
| Spink3 | 3.63 | 0.0083 | |||
| Trpv3 | 3.11 | 0.0091 | |||
| Hoxa11os | 3.58 | 0.0098 | |||
| 2310079G19Rik | 8.03 | 0.01 | |||
| Gm11535 | 7.68 | 0.01 | |||
| Cyp2f2 | 3.9 | 0.0112 | |||
| HOXA11-AS1_4 | 3.93 | 0.0112 | |||
| Muc1 | 3.11 | 0.0112 | |||
| St8sia5 | 7.08 | 0.0126 | |||
| HOXB13-AS1_2 | 7.9 | 0.015 | |||
| Cyp2a12 | 6.98 | 0.0156 | |||
| Ttr | 2.01 | 0.0172 | |||
| Nccrp1 | 3.85 | 0.0173 | |||
| Evx2 | 7.43 | 0.0187 | |||
| Slc46a1 | 2.38 | 0.0187 | |||
| Csta | 4.42 | 0.0188 | |||
| Gm16556 | 3.57 | 0.0191 | |||
| Sycn | 2.76 | 0.0191 | |||
| Slc15a1 | 3.24 | 0.0204 | |||
| Grin2b | 3.81 | 0.022 | |||
| Cyp2d12 | 3.51 | 0.0223 | |||
| Gm11830 | 3.09 | 0.0236 | |||
| HOTTIP_2 | 7.46 | 0.0236 | |||
| HOXB13-AS1_1 | 6.11 | 0.0236 | |||
| Psg17 | 3.46 | 0.0236 | |||
| Cela1 | 2.1 | 0.0258 | |||
| Iqch | 3.58 | 0.0258 | |||
| Foxq1 | 2.17 | 0.0259 | |||
| Ms4a10 | 1.48 | 0.0259 | |||
| Nt5c1a | 3.4 | 0.026 | |||
| Il18 | 1.6 | 0.0264 | |||
| Myo16 | 2.71 | 0.0264 | |||
| Hoxd12 | 5.36 | 0.0271 | |||
| Brinp2 | 2.7 | 0.0291 | |||
| Ankdd1b | 2.84 | 0.0292 | |||
| Defb45 | 4.97 | 0.0292 | |||
| Gp6 | 3.93 | 0.0328 | |||
| Ggh | 2.36 | 0.0336 | |||
| Gm15401 | 1.69 | 0.0336 | |||
| A930011G23Rik | 1.78 | 0.035 | |||
| Rdh16 | 1.75 | 0.035 | |||
| Hrg | 4.05 | 0.0369 | |||
| 1700042G15Rik | 5.12 | 0.0411 | |||
| Wnt8b | 3.96 | 0.0413 | |||
| Ctgf | 1.44 | 0.0432 | |||
| Slc36a1 | 2.23 | 0.0432 | |||
| Nt5e | 1.75 | 0.0434 | |||
| Sh3d21 | 1.87 | 0.0461 | |||
| Slc16a12 | 1.93 | 0.0466 | |||
| Gm16557 | 5.58 | 0.0469 | |||
| Ano4 | 2.8 | 0.0477 | |||
| Pla2g5 | 1.87 | 0.0477 | |||
| Gpr137b | 2.36 | 0.0483 | |||
| Cd207 | 6.32 | 0.0493 | |||
| Gm17384 | 6.35 | 0.0494 | |||
| Cluster 2 | Up ↑ | ||||
| Gm10800 | 10 | 0.0023 | |||
| Gm10801 | 9.72 | 0.0034 | |||
| Gm21738 | 9.54 | 0.0035 | |||
| Gm26870 | 7.7 | 0.0191 | |||
| Gm10718 | 7.06 | 0.0236 | |||
| Cluster 3 | Up↑ | ||||
| Apon | 2.18 | 0.0419 |
One hundred thirty DEGs were selected by edgeR analysis of RNA sequence data (see Methods) and grouped into seven clusters by hierarchical clustering. Shown on the left are the three upregulated clusters (1–3), and shown on the right are the four dowregulated clusters (4–7).