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Series GSE9703 Query DataSets for GSE9703
Status Public on Mar 23, 2009
Title Identification of Common Genetic Variants that Account for Transcript Isoform Variation between Human Populations
Organism Homo sapiens
Experiment type Expression profiling by array
Summary In addition to the differences between populations in transcriptional and translational regulation of genes, alternative pre-mRNA splicing (AS) is also likely to play an important role in regulating gene expression and generating variation in mRNA and protein isoforms. Recently, the genetic contribution to transcript isoform variation has been reported in individuals of recent European descent. We report here results of an investigation of the differences in AS patterns between human populations. AS patterns in 176 HapMap lymphoblastoid cell lines derived from individuals of European and African ancestry were evaluated using the Affymetrix GeneChip Human Exon 1.0 ST Array. A variety of biological processes such as immune response and mRNA metabolic process were found to be enriched among the differentially spliced genes. The differentially spliced genes also include some involved in human diseases that have different prevalence or susceptibility between populations. The genetic contribution to the population differences in transcript isoform variation was then evaluated by a genome-wide association using the HapMap genotypic data on single nucleotide polymorphisms (SNPs). The results suggest that local and distant genetic variants account for a substantial fraction of the observed transcript isoform variation between human populations.
 
Overall design Exon level expression on 176 HapMap cell lines.
 
Contributor(s) Zhang W, Duan S, Bleibel WK, Wisel SA, Wu X, Huang RS, He L, Roe CA, Clark TA, Chen TX, Schweitzer AC, Blume JE, Dolan ME, Cox NJ
Citation(s) 19052777, 19925429, 25818895
Submission date Nov 27, 2007
Last update date Apr 02, 2015
Contact name Eileen Dolan
E-mail edolan@medicine.bsd.uchicago.edu
Phone 773-702-4441
Fax 773-702-0963
Organization name University of Chicago
Department Medicine
Lab Dolan Lab
Street address 5841 S. Maryland
City Chicago
State/province IL
ZIP/Postal code 60657
Country USA
 
Platforms (1)
GPL5188 [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [probe set (exon) version]
Samples (176)
GSM245496 GM06985
GSM245497 GM07048
GSM245498 GM18521
Relations
BioProject PRJNA103609

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
GSE9703_RAW.tar 6.5 Gb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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