Is there gene expression and/or functional annotation available for the samples?

Functional annotation

As part of our phase 1 analysis we performed functional annotation of our phase 1 variants with respect to both coding and non-coding annotation from GENCODE and the ENCODE project respectively.

This functional annotation can be found in our phase 1 analysis results directory. We present both the annotation we compared the variants to and VCF files which contain the functional consequences for each variant.

Gene expresssion

The most important available existing expression datasets involving 1000 Genomes individuals are probably the following:

Pre-publication RNA-sequencing data from the Geuvadis project is available

http://www.ebi.ac.uk/arrayexpress/experiments/E-GEUV-1/samples.html
http://www.ebi.ac.uk/arrayexpress/experiments/E-GEUV-2/samples.html

http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-197

http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-198
http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-264

http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-19480

References

  1. Reference:Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature. 2010 Apr 1;464(7289):773-7. Epub 2010 Mar 10.
  2. Reference: Stranger,B.E S.B. Montgomery, A.S. Dimas, L. Parts, O. Stegle, C.E. Ingle, M. Sekowska, G. Davey Smith, D. Evans, M. Gutierrez-Arcelus, A. Price, T. Raj J. Nisbett, A.C. Nica, C. Beazley, R. Durbin, P. Deloukas, E.T. Dermitzakis. Patterns of cis regulatory variation in diverse human populations. PLoS Genetics in press
  3. Reference: Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature. 2010 Apr 1;464(7289):768-72. Epub 2010 Mar 10.

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