For the pilot project we want to recreate the results obtained in Shen, 2007 paper. To do that I need to identify IDs of the CpGs that they used in their analyses. Here is the list:
Classical CIMP markers: MINT1, MINT2, MINT27, MINT12, MINT31, MINT17
Type C genes (methylated only in cancer): p14 (9p21), MLH1 (2p22), THBS1 (15q14), THBS2 (6q), MGMT (10q26), COX2 (1q25.2), Megalin (1q21.1), RIZ1 (1p36), p16 (9p21), RASSF1A (I remember from my PhD work that this was my very good positive control for methylation in cancer cell lines; 3p21.31), DAPK (9p34.1), TIMP3 (22q12.1), hTERT (5p15.33), Neurog1 (5q31.1), SOCS1 (16p13.13), RUNX3 (1p36.11)
Type A genes (methylated in normal and cancer): ER alpha (6q25.1), MyoD1 (11p15.4), N33 (8p22), SFRP1 (8p12), HPP1 (2q32.3)
They provided the sequences for some of the markers and indicated the publications from which they got the sequence for the other markers for the methylation assays. Use them to map the CpG regions they assays. Map them to hg19:
| Gene/marker | Entrez ID | Selected CpG | CpG location |
|---|---|---|---|
| p14/CDKN2D | 1029 | cg13601799 | chr9:21974704 |