Coordinates for Transcription Start Site (TSS)

Question

[ResearchR]

Dear all,

I am working with the gene annotation hg19 (ensembl release 74). I would like to get the TSS for each gene. For the most recent release of hg19, Ensembl provides the transcription start site, but not for release 74. Do you know, where I can get this information from? Using the first base of each transcript does not seem (at least to me) right way to go.

Thanks guys and best wishes,

Chris

Answer 1

[Kristoffer Vitting-Seerup]

The problem is there is no good definition of which TSS to use from a specific gene - I'm guessing for release 74 Ensemble simply reported the most upstream - but our research shows that is not a good proxy for the most used (only in ~50% of cases).

I think you might be better of with using the FANTOM5 TSS which are derived from high-thoughput experiments (CAGE) - you can read more about it here. In column2 (short description) the data derived TSS I linked to the TSS are annotated as pX@geneName. Here p1@geneName will correspond to the TSS most highly expressed across all F5 datasets - and might therefore be what you want.

Hope this helps.

Cheers Kristoffer

[ResearchR]

Let's see if it helps, thanks for the idea!

Answer 2

[mollitz]

Also there is a published reference annotation data set (refTSS) here:

https://www.sciencedirect.com/science/article/pii/S0022283619302530 http://reftss.clst.riken.jp/

Answer 3

[BioinfGuru]

Ensembl Biomart does provide this here

Under attributes select chromosome name and transcript start

Then click "results" and download the TSV file

[ResearchR]

Do you assume that the transcription start site is the same as the transcript start (= first nucleotide of the transcript)?

[BioinfGuru]

yes...in later bioimart archives they call it transcription start site instead but you can email them...they are very quick to reply