31.7: Tools and Resources
- Page ID
- 41239
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- The Costapas Lab distributes code to calculate CPMA from GWAS association p-values which can be found here: www.cotsapaslab.info/index.php/software/cpma/
- The Pritchard lab has several resources (found here: http://eqtl.uchicago.edu/Home.html) for eQTL research and gene regulation including:
– DNase-seq data from 70 YRI lymphoblastoid cell lines
– Downloading positions of transcription factor binding sites inferred in the HapMap lymphoblastoid
cell lines by CENTIPEDE
– Raw and mapped RNA-Seq data from Pickrell et al.
– Assorted scripts for identifying sequencing reads covering genes, polyadenylation sites and exon- exon junctions
– Data and meQTL results for Illumina27K methylation data in HapMap lymphoblastoid cell lines.
– Files to ignore areas of the genome that are prone to causing false positives in ChIP-seq and other
sequencing based functional assays
– Browser for eQTLs identified in recent studies in multiple tissues
- The Wellcome Trust Sanger Institute has developed packaged database and web services (Genevar) that are designed to help integrative analysis and visualization of SNP-gene associations in eQTL studies. This information can be found here: www.sanger.ac.uk/resources/software/genevar/
- The Wellcome Trust Sanger Institute has also developed databases that contain information relevant to eQTL studies such as finding and identifying all functional elements in the human genome sequence and maintaining automatic annotation on selected eukaryotic genomes. This information can be found here: http://www.sanger.ac.uk/resources/databases/.
- Finally, the NIH is progressing on the Genotype-Tissue Expansion Projext (GTEx). Currently, the project stands at 35 tissues from 50 donors; the aim is to acquire and analyze 20,000 tissues from 900 donors, with the hope of gathering even more data for further genetic analyses, especially for eQTL and trans-eQTL analyses that require larger sample sizes.