Table 1 Integrated catalog of candidate genes combined from targeted bisulfite sequencing, RNA-seq, and ATAC-seq analysis
Genomic location | Gene | Targeted bisulfite sequencing | RNA-seq (TCGA) | RNA-seq (GSE162515) | ATAC-seq (GSE162515) | ||
|---|---|---|---|---|---|---|---|
Met diff (T1 - T2) | LFC | Padj | LFC | Padj | LFC | ||
chr11:65352231-65353134 | EHBP1L1 | 34.28 | 0.70 | 4.4E-20 | 1.28 | 5.5E-03 | 0.44 |
chr11:65359292-65360328 | EHBP1L1 | 29.75 | 0.70 | 4.4E-20 | 1.28 | 5.5E-03 | 0.27 |
chr12:58132478-58132734 | AGAP2 | 29.19 | 1.43 | 1.4E-36 | 2.74 | 1.6E-06 | 1.60 |
chr4:81109887-81110460 | PRDM8 | 28.44 | 1.81 | 1.8E-47 | 2.29 | 2.1E-04 | 0.48 |
chr5:10649367-10650352 | ANKRD33B | 27.73 | 0.91 | 3.1E-12 | 2.20 | 1.2E-04 | 0.39 |
chr14:93153278-93154759 | RIN3 | 26.37 | 0.82 | 2.6E-28 | 1.89 | 3.4E-05 | 0.39 |
chr12:58130870-58132047 | AGAP2 | 24.94 | 1.43 | 1.4E-36 | 2.74 | 1.6E-06 | 0.58 |
chr12:58119909-58121551 | AGAP2 | 24.36 | 1.43 | 1.4E-36 | 2.74 | 1.6E-06 | 0.36 |
chr16:67686860-67687674 | CARMIL2 | 24.28 | 2.92 | 1.7E-77 | 4.30 | 3.4E-06 | 0.25 |
chr15:40583093-40583526 | PLCB2 | 23.26 | 1.61 | 2.1E-47 | 2.62 | 3.4E-05 | 0.28 |
chr19:49841187-49841628 | CD37 | 22.72 | 2.19 | 5.2E-57 | 3.85 | 4.0E-06 | 0.98 |
chr19:17877468-17877777 | FCHO1 | 22.70 | 0.77 | 2.0E-06 | 2.47 | 3.1E-03 | 0.28 |
chr5:43037259-43037520 | ANXA2R | 22.32 | 1.24 | 1.1E-27 | 2.06 | 7.4E-05 | 1.99 |
chr2:11774310-11774521 | GREB1 | 22.24 | -0.87 | 4.7E-05 | −2.15 | 2.0E-02 | 0.72 |
chr19:15563869-15564223 | RASAL3 | 21.03 | 1.76 | 5.7E-57 | 3.01 | 3.2E-06 | 0.32 |
chr19:15568027-15569227 | RASAL3 | 20.10 | 1.76 | 5.7E-57 | 3.01 | 3.2E-06 | 0.87 |
chr21:45789090-45789373 | TRPM2 | 20.00 | 1.38 | 2.0E-36 | 1.95 | 3.1E-04 | 0.63 |
chr4:81128229-81128691 | PRDM8 | 19.74 | 1.81 | 1.8E-47 | 2.29 | 2.1E-04 | 0.29 |
chr16:67681975-67683924 | CARMIL2 | 18.68 | 2.92 | 1.7E-77 | 4.30 | 3.4E-06 | 0.76 |
chr2:198029068-198029438 | ANKRD44 | 17.22 | 1.08 | 8.1E-35 | 2.75 | 5.1E-07 | 0.34 |
chr12:54764065-54764510 | GPR84 | 16.72 | 1.48 | 8.2E-33 | 1.90 | 1.4E-02 | 0.30 |
chr17:3847999-3848570 | ATP2A3 | 16.40 | 1.27 | 6.8E-32 | 2.84 | 3.4E-06 | 1.47 |
chr17:14201726-14202052 | HS3ST3B1 | 15.68 | 1.29 | 8.7E-28 | 3.00 | 3.0E-07 | 1.88 |
chr19:49842654-49843628 | CD37 | 15.67 | 2.19 | 5.2E-57 | 3.85 | 4.0E-06 | 0.64 |
chr19:1070985-1071812 | ARHGAP45 | 15.06 | 1.09 | 5.4E-33 | 2.61 | 3.4E-05 | 0.52 |
chr7:5336513-5336894 | SLC29A4 | -16.26 | -0.90 | 5.2E-06 | −2.22 | 9.6E-03 | 2.48 |
chr22:50483350-50483579 | IL17REL | -16.26 | 2.55 | 1.1E-29 | 5.48 | 1.9E-03 | 0.32 |
chr16:29675845-29676120 | SPN | -17.67 | 1.77 | 2.5E-44 | 2.64 | 6.5E-04 | 2.61 |
chr11:65408344-65408631 | SIPA1 | -18.32 | 0.62 | 3.8E-14 | 1.72 | 5.4E-05 | 2.42 |
chr19:13207375-13207621 | LYL1 | -19.67 | 0.94 | 1.0E-16 | 2.40 | 1.1E-05 | 1.84 |
chr11:67176945-67177169 | TBC1D10C | -21.63 | 0.79 | 9.2E-15 | 1.91 | 1.5E-04 | 2.71 |
chr17:72347924-72348322 | BTBD17 | -21.72 | −1.76 | 1.1E-05 | -3.49 | 3.5E-02 | 0.70 |
chr19:3178741-3179986 | S1PR4 | -24.25 | 1.71 | 2.0E-45 | 3.32 | 4.7E-07 | 2.61 |
chr12:6664425-6665336 | IFFO1 | -27.25 | 1.07 | 3.0E-37 | 1.46 | 4.1E-04 | 2.66 |
chr11:63974829-63975048 | FERMT3 | -37.59 | 1.83 | 2.4E-54 | 2.68 | 1.0E-05 | 2.47 |
