Analysis of gene expression variation in the HapMap samples using genome-wide expression arrays.
We have produced a dataset of gene expression data from EBV-transformed lymphoblastoid cell lines from all 270 HapMap individuals used in the phase I and phase II of the project (populations: CEU, CHB, JPT and YRI).
This is a collaborative effort that involves the groups of:
Our groups aim at performing various types of global analysis in this dataset such as:
These data are being released freely to the scientific community and can be considered a community resource. However, the data generators reserve the right to be the first to publish on the bulk data as indicated by the Fort Lauderdale meeting report (see data release policy below).
A pilot effort of this study with a small set of genes has been published in:
| Genome-wide associations of gene expression variation in humans. Stranger BE, Forrest MS, Clark AG, Minichiello MJ, Deutsch S, Lyle R, Hunt S, Kahl B, Antonarakis SE, Tavaré S, Deloukas P, Dermitzakis ET PLoS Genet. 2005;1;e78. PMID: 16362079 DOI: 10.1371/journal.pgen.0010078 |
| Relative impact of nucleotide and copy number variation on gene expression phenotypes. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, Tyler-Smith C, Carter N, Scherer SW, Tavaré S, Deloukas P, Hurles ME, Dermitzakis ET Science. 2007;315;848-53. PMID: 17289997 DOI: 10.1126/science.1136678 |
| Population genomics of human gene expression. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, Beazley C, Ingle CE, Dunning M, Flicek P, Koller D, Montgomery S, Tavaré S, Deloukas P, Dermitzakis ET Nat Genet. 2007;39;1217-24. PMID: 17873874 DOI: 10.1038/ng2142 |
For any questions regarding the data and the data release policy please contact:
Manolis Dermitzakis (md4@sanger.ac.uk)
Barbara Stranger (bes@sanger.ac.uk)
The data was generated using illumina genome-wide expression arrays (wg GEX human 6). Each individual has 4 replicate hybridizations.
NEWS
DATA DOWNLOAD
Raw and normalized data sets as well as a file with transcript information can be downloaded here.
The files of the normalized data are now available.
ACKNOWLEGDMENTS
Stranger B. E., Forrest M. S. , Dunning M. , Ingle C., Minichiello M. J., Kahl B., Clark A. G., Tavare S., Deloukas P., Dermitzakis E. T.
Funding was provided by the Wellcome Trust.
DATA RELEASE POLICY
The release of pre-publication data from large resource-generating scientific projects was the subject of a meeting held in January 2003, the "Fort Lauderdale meeting", sponsored by the Wellcome Trust, one of the Project funders. The report from that meeting can be viewed here.
The recommendations of the Fort Lauderdale meeting address the roles and responsibilities of data producers, data users, and funders of "community resource projects", with the aim of establishing and maintaining an appropriate balance between the interests of data users in rapid access to data and the needs of data producers to receive recognition for their work. The conclusion of the attendees at the meeting was that responsible use of the data is necessary to ensure that first-rate data producers will continue to participate in such projects and produce and quickly release valuable large-scale data sets. "Responsible use" was defined as allowing the data producers to have the opportunity to publish the initial global analyses of the data, as articulated at the outset of the project. Doing so also will ensure that the data generated are fully described.
