Table 1. Differentially methylated candidate genes with 5′CpG Islands identified with MSRF.
| Clone | Pr1 | Pr2 | Hyper-methylation | Chr Band | Gene homology | Location | CGI at 5′ end | Gene Ontology |
| A1 | 20 | 21 | Low PAH | 8q24.3 | NIK and IKKbetta-binding protein | INTRON15 | NF-kappaB-inducing kinase acitivity | |
| A2 | 20 | 21 | High PAH | 6p25.1 | cDNA clone IMAGE:4825327 | 5′ END | ||
| A3 | 20 | 21 | High PAH | 1q41 | N/A | |||
| A4 | 20 | 21 | High PAH | 19p13.3 | cDNA clone FLJ14311 | INTRON2 | ||
| A5 | 20 | 21 | High PAH | 10q26.3 | N/A | |||
| A6 | 20 | 21 | High PAH | 11q12.1 | N/A | |||
| A7 | 20 | 21 | High PAH | 8q24.11 | Protein in DNA double-strand break repair, RAD21 | 5′ END | <1 kb | Double strand break repair |
| A8 | 20 | 21 | High PAH | 6p25.3 | Dual specificity phosphatase 22, DUSP22 | INTRON1 | <1 kb | Stress kinase involved in MAPK pathway |
| A9 | 20 | 21 | High PAH | 8p23.1 | Beta-defensin 107, DEFB107 | 3′ END | Defense response | |
| B1 | 22 | 23 | High PAH | 1q32.2 | mRNA for KIAA0463 protein, partial cds | INTRON4 | ||
| B2 | 22 | 23 | High PAH | 2p24.2 | N/A | |||
| B3 | 22 | 23 | High PAH | 3q24 | WIAF-4002-STS Human THudson EST STS cDNA | INTRON1 | ||
| B4 | 22 | 23 | High PAH | 1q41 | N/A | |||
| D1 | 22 | 23 | Low PAH | 2p24.2 | N/A | |||
| D2 | 22 | 23 | Low PAH | 1q32.1 | N/A | |||
| D4 | 22 | 23 | Low PAH | 15q22.2 | Vacuolar protein sorting-associated protein 13C, VPS13C | EXON7 | Trans-Golgi to endosome transport | |
| D5 | 22 | 23 | Low PAH | 1q41 | N/A | |||
| D6 | 22 | 23 | High PAH | 19p13.2 | N/A | |||
| D7 | 22 | 23 | High PAH | 2q36.1 | Acyl-CoA synthetase long-chain family member 3, ACSL3 | INTRON1 | <1 kb | Fatty acid metabolism |
| D8 | 22 | 23 | Low PAH | 11q25 | cDNA clone DKFZp686H1949 | INTRON1 | ||
| D9 | 22 | 23 | Low PAH | 1p32.3 | Clone BNGH42007037, similar to zinc finger protein GLI1 | INTRON1 | ||
| D10 | 22 | 23 | Low PAH | 14q21.1 | CTAGE-5B protein mRNA, complete cds, alternatively spliced | INTRON1 | ||
| E1 | 7 | 11 | High PAH | 4q21.22 | Stearoyl-CoA desaturase 5, SCD5 | INTRON1 | <1 kb | Fatty acid metabolism |
| E2 | 7 | 11 | High PAH | 16p13.11 | N/A | |||
| E3 | 7 | 11 | High PAH | 16q24.2 | Junctophilin 3, JPH3 | INTRON3 | Integral to membrane | |
| E4 | 7 | 11 | High PAH | Xq13.1 | Ribosomal protein S4, X-linked | INTRON8 | Translation | |
| F1 | 10 | 11 | High PAH | 11q23.1 | N/A | |||
| F3 | 10 | 11 | High PAH | 10p14 | Scm-like with four mbt domains 2, SFMBT2 | INTRON1 | <2 kb | Gene transcription |
| F4 | 10 | 11 | High PAH | 16q13 | Small inducible cytokine A17 precursor, CCL17 | INTRON2 | Chemokine activity | |
| G1 | 22 | 11 | Low PAH | 13q32.3 | N/A | |||
| G2 | 22 | 11 | Low PAH | 16q23.1 | WW domain-containing oxidoreductase isoform , WWOX | INTRON1 | <1 kb | Gene transcription |
Note: Sequences were identified based on BLAT (UCSC genome center database) and RefSeq (NCBI database) search.
Abbreviation: NA, not available.