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| Status |
Public on Apr 16, 2012 |
| Title |
All exon array expression data in normal colon and primary colon cancer lines [expression] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
|
| Summary |
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.
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| Overall design |
RNA from normal colon epithelial crypt controls and primary colon cancer cell lines was hybridized to Affymetrix All Exon Human ST 1.0 microarrays.
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| Contributor(s) |
Markowitz SD, Myerhoff L, Scacheri P, Saiakhova A, Akhtar-Zaidi B |
| Citation(s) |
22499810 |
| Submission date |
Mar 09, 2012 |
| Last update date |
Feb 18, 2019 |
| Contact name |
Peter Scacheri |
| E-mail(s) |
pxs183@case.edu
|
| Phone |
216-368-3458
|
| Organization name |
Case Western Reserve University
|
| Street address |
10900 Euclid Ave; BRB 647
|
| City |
Cleveland Heights |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL5175 |
[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version] |
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| Samples (14)
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| This SubSeries is part of SuperSeries: |
| GSE36401 |
Epigenomic enhancer profiling defines a signature of colon cancer |
|
| Relations |
| BioProject |
PRJNA155553 |
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