Gene Set: ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN

Standard name ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN
Systematic name M16009
Brief description Genes whose DNA is hypo-methylated in hepatocellular carcinoma (HCC) compared to normal liver.
Full description or abstract There is widespread interest in efficient characterization of differences between tumor and normal samples. Here, we show an effective methodology for genome-scale characterization of tumors. Using matched normal and tumor samples from liver cancer patients, as well as non-cancer-related normal liver tissue, we first determined changes in gene expression as monitored on RNA expression arrays. We identified several hundred mRNAs that were consistently changed in the tumor samples. To characterize the mechanisms responsible for creation of the tumor-specific transcriptome, we performed chromatin immunoprecipitation on microarray experiments to assay binding of RNA polymerase II, H3me3K27, and H3me3K9 and DNA methylation in 25,000 promoter regions. These experiments identified changes in active and silenced regions of the genome in the tumor cells. Finally, we used a virtual comparative genomic hybridization method to identify copy number alterations in the tumor samples. Through comparison of RNA polymerase II binding, chromatin structure, DNA methylation, and copy number changes, we suggest that the major contributor to creation of the liver tumor transcriptome was changes in gene copy number.
Collection C2: curated gene sets
      CGP: chemical and genetic perturbations
Source publication Pubmed 18413731   Authors: Acevedo LG,Bieda M,Green R,Farnham PJ
Exact source Table 26S: lower 5-MeC in tumor
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Organism Homo sapiens
Contributed by Jessica Robertson (MSigDB Team)
Source platform HUMAN_SEQ_ACCESSION
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