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E-GEOD-36400 - All exon array expression data in normal colon and primary colon cancer lines [expression]

Status
Released on 15 April 2012, last updated on 27 June 2012
Organism
Homo sapiens
Samples (14)
Array (1)
Protocols (7)
Description
Cancer is characterized by gene expression aberrations. Studies have largely focused on coding sequences and promoters, despite the fact that distal regulatory elements play a central role in controlling transcription patterns. Here we utilize the histone mark H3K4me1 to analyze gain and loss of enhancer activity genome wide in primary colon cancer lines relative to normal colon crypts. We identified thousands of variant enhancer loci (VELs) that comprise a signature that is robustly predictive of the in vivo colon cancer transcriptome. Furthermore, VELs are enriched in haplotype blocks containing colon cancer genetic risk variants, implicating these genomic regions in colon cancer pathogenesis. We propose that reproducible changes in the epigenome at enhancer elements drive a unique transcriptional program to promote colon carcinogenesis. We used gene expression profiles to assess correlations between the colon cancer epigenome and transcriptional activity. RNA from normal colon epithelial crypt controls and primary colon cancer cell lines was hybridized to Affymetrix All Exon Human ST 1.0 microarrays.
Experiment type
transcription profiling by array 
Contacts
Peter Scacheri <pxs183@case.edu>, Alina Saiakhova, Batool Akhtar-Zaidi, Lois Myerhoff, Sanford D Markowitz
Citation
Epigenomic enhancer profiling defines a signature of colon cancer. Akhtar-Zaidi B, Cowper-Sal-lari R, Corradin O, Saiakhova A, Bartels CF, Balasubramanian D, Myeroff L, Lutterbaugh J, Jarrar A, Kalady MF, Willis J, Moore JH, Tesar PJ, Laframboise T, Markowitz S, Lupien M, Scacheri PC. , PMID:22499810
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-36400.idf.txt
Sample and data relationshipE-GEOD-36400.sdrf.txt
Raw data (2)E-GEOD-36400.raw.1.zip, E-GEOD-36400.raw.2.zip
Processed data (1)E-GEOD-36400.processed.1.zip
Array designA-AFFY-143.adf.txt
R ExpressionSetE-GEOD-36400.eSet.r
Links