"Familial profile #" in UCSC browser

[Laura Farr]

Hi,

I'm a big fan of using the UCSC browser for aligning TFs within my gene, but it seems I can no longer search by TF name.   All of the TFs are now "familial profile #" in the alignment (https://virginia.box.com/s/r8ckz4mxemaz6legvslcaqz70a8drmcv), which is a less than ideal way to find my TFs of interest.  I did not have this issue in the 2020 version (https://virginia.box.com/s/honwm7zjp0d4xbf6tv8cnxfijzpg0lad), which makes me think it's an update issue.  Is there any way to change these names back?  Or at least find out the corresponding Jaspar IDs for each familial profile #?

Thanks.

[anthony....@gmail.com]

Hi Laura,

Thanks for raising this. If you use the native JASPAR tracks in UCSC, you should still be able to filter based on TFs (https://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=286937382_5q5ViZo8aroEeIXOYNhEeoACAZI9&db=hg38&c=chrX&g=jaspar). Let me know if it does not work.

[Wojciech Rosikiewicz]

Hi,

However, when i downloaded the entire familial profiles collection for human hg19 (52GB big *.bb file) i only have the access to the "familial profile IDs". E.g., when displayed in IGV, e.g.:

Is it possible to somewhere get the list of profile IDs and their matched Transcription factors? I was unable to find in anywhere in the download section of your page (https://jaspar.genereg.net/downloads/), nor in the newest manuscript (https://academic.oup.com/nar/article/50/D1/D165/6446529).

This kind of list would be amazing to have, the work you have done is of an enormous value and its awesome that you provide the possibility of utilizing the pre-identified sites from these *bb files. To me the only missing part there is this ability to match the profiles with TF names / PFM IDs or TF families etc. That would allow to filter the *bb files with in-house scripts and accelerate research and the numbers of citations of your database :D

All the best and thank you!

Wojciech

[anthony....@gmail.com]

Dear Wojciech,

You have a good point here. We provide the mapping but in a non-parsable way, which is not great at all. We will generate such mapping in the coming days and will keep you posted.

In the meantime, you can find the .bb files from the TFBSs derived from all matrices, without familial binding profiles, at http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/2022/. Please note though that we found a few bugs and we are working on updating these files as well.

Sorry about that.