Gene expression and SNPs…very neat stuff

microarray_nhgri_publicA question on the blog last week got me going through my old posts, because I was sure that I had done one on a database of SNP effects on gene expression.  But it turned out that was in my memory, but still in the draft posts for the blog….

I had come across the work on Genomeweb here:

Duke Team Finds Variants Linked to Tissue-Specific Gene Expression, Splicing

A team of Duke University researchers used a genome-wide screen to find interactions between genetic variants, gene expression, and alternative splicing in blood and brain tissue. In doing so, they found extensive between-tissue differences in SNP effects — only about half of the polymorphisms had common effects in both tissues tested. The team is starting to catalogue the data on the effects that specific genetic variants have on gene expression and splicing in various tissues.

So of course I went looking for the paper and the catalog….

Tissue-Specific Genetic Control of Splicing: Implications for the Study of Complex Traits by Heinzen et al.  The paper is from PLoS Biology last December, and they introduce some QTLs that were new to me–eQTLs, for expression quantitative trait loci, and sQTLs for splicing ones.  They interrogate exon-based microarrays and look for possible effects of nearby SNPs.  I think this approach has some limitations that they concede (you can’t tell exactly which transcript may be affected, just that there is likely an effect on that gene’s expression).  I also think that known exons do not represent the alternative splicing world completely yet.  I think there are a lot of rare temporal and spatial transcription events that aren’t captured in the public databases yet, and won’t be represented in the tissue types selected.  But I think it was a nice attempt to ask the question, and I’m sure  more tissues will be explored over time.

The resource you can explore that has this data is called SNPExpress, and the introduction states:

SNPExpress is a database and its user interface that we developed to permit interrogation of the effects of common SNPs on exon and transcript level expression, in two different human tissues: brain and PBMC ( Peripheral Blood Mononuclear Cell ).

So if this type of data is of interest to you, please check out their paper and their database.  They also have a related tool attached to SNPExpress that is a WGA viewer that might be of interest.

Specific links from post:

GenomeWeb article http://www.genomeweb.com/issues/news/151467-1.html

SNPExpress: http://people.genome.duke.edu/~dg48/SNPExpress/

WGA viewer: http://people.genome.duke.edu/~dg48/WGAViewer/

SNPs in splicing paper: http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.1000001&ct=1

Heinzen, E., Ge, D., Cronin, K., Maia, J., Shianna, K., Gabriel, W., Welsh-Bohmer, K., Hulette, C., Denny, T., & Goldstein, D. (2008). Tissue-Specific Genetic Control of Splicing: Implications for the Study of Complex Traits PLoS Biology, 6 (12) DOI: 10.1371/journal.pbio.1000001

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UPDATE: (6/13/2012) I just noticed that the links to this software weren’t working, so I checked with the team. The new link for SNPExpress is: http://compute1.lsrc.duke.edu/softwares/SNPExpress/

WGAViewer is http://compute1.lsrc.duke.edu/softwares/WGAViewer/