As you may know, we’ve been doing these video tips-of-the-week for FOUR years now. We have completed around 200 little tidbit introductions to various resources from last year, 2011 (yep, it’s 2012 now). At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.
SNPexp is a nice simple tool that uses PLINK to calculate the correlation (p-value) between SNPs in a given range of locations in the genome, or alternatively a list of specific SNP rsIDs, and the expression of a gene of interest. It combines the data from these two datasets: the HapMap project and GENEVAR*. It provides a simple web-based interface to allow you to make those calculations and to either download the results in a series of files, or to view the results as a custom track in the UCSC Genome Browser. Today’s tip gives you a quick introduction to using the tool.
*GENEVAR is both a database of “analysis of gene expression variation in the HapMap samples using genome-wide expression arrays (47294 transcripts) from EBV-transformed lymphoblastoid cell lines from the same 270 HapMap individuals AND a downloadable software tool to allow you to “perform analysis and visualization of associations between sequence variation and gene expression in eQTL studies.” It’s an additional tool that might be of interest and providing for more in-depth analysis.