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| 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
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| 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.
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| Overall design |
Exon level expression on 176 HapMap cell lines.
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| 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, 26714498, 20975837, 21304891 |
| Submission date |
Nov 27, 2007 |
| Last update date |
Aug 28, 2019 |
| Contact name |
Eileen Dolan |
| E-mail(s) |
edolan@medicine.bsd.uchicago.edu
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| Phone |
773-702-4441
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| Fax |
773-702-0963
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| Organization name |
University of Chicago
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| Department |
Medicine
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| Lab |
Dolan Lab
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| Street address |
5841 S. Maryland
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60657 |
| Country |
USA |
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| Platforms (1) |
| GPL5188 |
[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [probe set (exon) version] |
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| Samples (176)
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| Relations |
| BioProject |
PRJNA103609 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE9703_RAW.tar |
6.5 Gb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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