search

stephens999 / gtex-viz

repo for code to visualize results of gtex project
1 stars 0 forks source link

looking at expression patterns according to eQTL type. #8

Open stephens999 opened 9 years ago

stephens999 commented 9 years ago

one issue I'd like to know is do "tissue-specific" eQTLs tend to be for genes that show tissue specific expression patterns. One way to do this would be an Rqtlchart where the top panel shows expression across the 44 genes and the bottom panels show clusters of different types of eQTLs (as in issues

3 and #4) so we can highlight tissue-specific eQTLs in bottom panel and see what their

expression looks like across tissues in top panel.

The top panel could also show both the expression and eQTL effect data (ie a row of 88 numbers in stead of 44). Not the best way to do this, but the easiest given the current capabilities of Rqtlchart.

kkdey commented 9 years ago

Looked at the expression pattern of Testis for the gene snp pairs that were tissue specific to testis. Did not show much structure in the gene expression, which is what we had seen previously also that gene expression does not reflect the tissue specific nature.The link to the plot: https://github.com/stephens999/gtex-viz/blob/master/gtex.Kushal/plots/cis.gene.expr.analysis.html

kkdey commented 9 years ago

A file of the average read counts for the 16407 genes across 53 tissues is on Github: https://github.com/stephens999/gtex-viz/blob/master/gtex.Kushal/data/cis_gene_expression_per_tissue.txt

The bigger dataset for 16407 genes and 8555 samples is on : /project/mstephens/gtex/analysis/june2014/reads_expression/cis_gene_expression_all_samples.txt