How to select a few TF binding site using JASPAR on UCSC

Question

[rb56]

I'm trying to find Transcription factor binding sites using JASPAR on UCSC. The area of thee genome I am interested in ends up having a lot of TF binding site, is there a way to customize JASPAR to include only few interesting TF and their binding sites?

Thank you

[Hamid Ghaedi]

I have doubt that the Biostarts is the right place for posting such questions. However still you are not clear, what do you mean exactly by "...only few interesting TF and their binding sites" ! Yo have such results because of the fact that: several TF are binding to a regulatory region in the genome. There are tissue-specific TFs, that may tend to attach to a regulatory region of the genome in different tissue. Add to this that even the stage of development and cell cycle could be detrimental for TF binding even in the same tissue or cell. These could contibute to what you get!

[rb56]

I meant out of all the TFs, is there a way to visualize only a few, instead of having them all together at once.

Answer 1

[Luis Nassar]

Hello,

We just recently made JASPAR a native track for both hg38 and hg19. These tracks include a few filtering options. If you click into the track (or right click it on the image to configure) you will see options to filter by score (1-1000) or you can filter by specific TF name.

Here is an example with a score filter of 600 applied, you will see that the label says 20,863 items are currently filtered out: http://genome.ucsc.edu/s/Lou/jasparHg38

If you have any follow up questions, our public help desk can always be reached at [e-mail]. You may also send questions to [e-mail] if they contain sensitive data. For any Genome Browser questions on Biostars, the UCSC tag is the best way to ensure visibility by the team.

[Alex Reynolds]

Hi Luis, is the score range (1-1000) a UCSC-transformed one for convenience, or does that range correspond to TF site p-values?

[Luis Nassar]

Hello Alex,

They are scales 1-1000. This was done directly by the JASPAR group who originally created the track, some more info here: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=jaspar

The shading of the boxes indicates the p-value of the profile's match to that position (scaled between 0-1000 scores, where 0 corresponds to a p-value of 1 and 1000 to a p-value ≤ 10-10)