Question: Tissue specific major transcript expressed?
2
gravatar for Rm
4.1 years ago by
Rm7.8k
Danville, PA
Rm7.8k wrote:

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

ADD COMMENTlink modified 4.1 years ago by mark.ziemann1.2k • written 4.1 years ago by Rm7.8k

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.

ADD REPLYlink written 4.1 years ago by RamRS21k
0
gravatar for mark.ziemann
4.1 years ago by
mark.ziemann1.2k
Australia/Mebourne/Geelong/Deakin
mark.ziemann1.2k wrote:

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.

ADD COMMENTlink written 4.1 years ago by mark.ziemann1.2k
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