Tissue specific major transcript expressed?

Question

[Rm]

I am exploring Gtex, Atlas, Humanbody map 2 and others, I get expression patterns across tissues at gene level. Is there a database or collection/analysis done which would catalog major transcript expressed in each of the tissues.

Example: for TTN and PCSK9 genes: I would like to know major transcript expressed in heart tissues and muscle

Thanks

[Ram]

This is a concern in my project as well. I'd appreciate if we could get a solution to this problem for use in high throughput analysis of gene panels where literature search per transcript becomes a huge pain.

Answer 1

[mark.ziemann]

If you are looking for genes that are biomarkers of a tissue, ie selectively expressed in a tissue compared to the others, then try this.Generate a matrix of counts or intensities for expression of each gene in each sample. Then normalise the scores (this depends on the data RNA-seq or array). Calculate the average expression level for each gene over all of the tissues. Then for each gene in each tissue, calculate the ratio (tissue expression / average expression). A high score means that the gene is selectively expressed in that tissue. You can then sort that column and identify the genes that have selective expression in that tissue. I describe this procedure in a blog post from a while back.