How can I couple transcript IDs with tissue type?

[Mathijs]

Hi,

I would like to investigate tissue specific lncRNAs. To do so, I obtained the assembly GTF from your website. (could not find tissue/cancer specific assemblies) Now I want to filter out tissue type, but can´t find any information about tissue type/study ID or a cohort ID encoded in the GTF. Also the library_info.txt file did not really help me.

My question is, am I looking wrong? is the tissue type somehow encoded in e.g. the transcript_ID? Or is there another file that allows me to couple transcript_ids with tissue/study/cohort information?

Thanks in advance,

Mathijs

[Yashar Niknafs]

Hello Mathijs,

So to answer your question, there isn't a hard and fast "tissue type" for the genes. We performed differential expression testing to determine the degree of lineage specificity for the genes. Many analyses were done for the different tissue types, etc. But ultimately there is not a hard and fast "tissue type" assigned to the genes. 

Hope this help,

Yashar