STANDARD_NAME WEBER_METHYLATED_IN_COLON_CANCER SYSTEMATIC_NAME M14473 COLLECTION C2:CGP MSIGDB_URL https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/WEBER_METHYLATED_IN_COLON_CANCER NAMESPACE HUMAN_SEQ_ACCESSION DESCRIPTION_BRIEF Genes identified as hypermethylated in SW48 cells (colon cancer). DESCRIPTION_FULL Cytosine methylation is required for mammalian development and is often perturbed in human cancer. To determine how this epigenetic modification is distributed in the genomes of primary and transformed cells, we used an immunocapturing approach followed by DNA microarray analysis to generate methylation profiles of all human chromosomes at 80-kb resolution and for a large set of CpG islands. In primary cells we identified broad genomic regions of differential methylation with higher levels in gene-rich neighborhoods. Female and male cells had indistinguishable profiles for autosomes but differences on the X chromosome. The inactive X chromosome (Xi) was hypermethylated at only a subset of gene-rich regions and, unexpectedly, overall hypomethylated relative to its active counterpart. The chromosomal methylation profile of transformed cells was similar to that of primary cells. Nevertheless, we detected large genomic segments with hypomethylation in the transformed cell residing in gene-poor areas. Furthermore, analysis of 6,000 CpG islands showed that only a small set of promoters was methylated differentially, suggesting that aberrant methylation of CpG island promoters in malignancy might be less frequent than previously hypothesized. PMID 16007088 GEOID GSE2653,GSE2664 AUTHORS Weber M,Davies JJ,Wittig D,Oakeley EJ,Haase M,Lam WL,Schübeler D CONTRIBUTOR John Newman CONTRIBUTOR_ORG University of Washington EXACT_SOURCE Table 1 FILTERED_BY_SIMILARITY EXTERNAL_NAMES_FOR_SIMILAR_TERMS EXTERNAL_DETAILS_URL SOURCE_MEMBERS BC038214,NM_000193,NM_000280,NM_001002295,NM_001451,NM_003238,NM_003474,NM_004394,NM_014653,NM_015472,NM_015920,NM_021926,NM_032838,NM_144725,NM_152562,NM_182609,NM_198849,NM_206827 GENE_SYMBOLS C1orf53,SHH,PAX6,GATA3,FOXF1,TGFB2,ADAM12,DAP,WSCD2,WWTR1,RPS27L,ALX4,ZNF566,TTC23L,CDCA2,ZNF677,SIAH3,RASL11A FOUNDER_NAMES