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Series GSE31151 Query DataSets for GSE31151
Status Public on Aug 17, 2012
Title Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Genome-wide association studies (GWASs) have identified thousands of single nucleotide polymorphisms (SNPs) associated with human traits and diseases. But because the vast majority of these SNPs are located in the noncoding regions of the genome their risk promoting mechanisms are elusive. Employing a new methodology combining cistromics, epigenomics and genotype imputation we annotate the noncoding regions of the genome in breast cancer cells and systematically identify the functional nature of SNPs associated with breast cancer risk. Our results demonstrate that breast cancer risk-associated SNPs are enriched in the cistromes of FOXA1 and ESR1 and the epigenome of H3K4me1 in a cancer and cell-type-specific manner. Furthermore, the majority of these risk-associated SNPs modulate the affinity of chromatin for FOXA1 at distal regulatory elements, which results in allele-specific gene expression, exemplified by the effect of the rs4784227 SNP on the TOX3 gene found within the 16q12.1 risk locus.
 
Overall design Examination of histone modification H3K4me2 in untreated and E2 treated cells
 
Contributor(s) Zhang X
Citation(s) 23001124
Submission date Aug 02, 2011
Last update date May 15, 2019
Contact name xiaoyang zhang
E-mail(s) xiaoyang.zhang@dartmouth.edu
Organization name Dartmouth Medical School
Street address 1 Medical Center Driver
City Lebanon
ZIP/Postal code 03756
Country USA
 
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (2)
GSM771028 untreated MCF7 H3K4me2 ChIP-Seq
GSM771029 E2 treated MCF7 H3K4me2 ChIP-Seq
Relations
SRA SRP007653
BioProject PRJNA144815

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE31151_RAW.tar 1.2 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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