Human Gene Set: ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN


Standard name ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN
Systematic name M11156
Brief description Genes down-regulated in normal tissue adjacent to liver tumor, compared to the normal liver samples.
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
      CGP: Chemical and Genetic Perturbations
Source publication Pubmed 18413731   Authors: Acevedo LG,Bieda M,Green R,Farnham PJ
Exact source Table 17S
Related gene sets (show 10 additional gene sets from the source publication)
External links
Filtered by similarity ?
Source species Homo sapiens
Contributed by Jessica Robertson (MSigDB Team)
Source platform or
identifier namespace		 Human_NCBI_Gene_ID
Dataset references (show 1 datasets)
Download gene set format: grp | gmt | xml | json | TSV metadata
Compute overlaps ? (show collections to investigate for overlap with this gene set)
Compendia expression profiles ? NG-CHM interactive heatmaps
(Please note that clustering takes a few seconds)
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)

Legacy heatmaps (PNG)
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)
Advanced query Further investigate these 354 genes
Gene families ? Categorize these 354 genes by gene family
Show members (show 354 source identifiers mapped to 354 genes)
Version history 3.0: First introduced

See MSigDB license terms here. Please note that certain gene sets have special access terms.