Factor Binding Sites cTFBS Using GalaxyUCSC Table Browser

Conserved matches to binding sites for transcription factors with weight matrices in TRANSFAC (20) can be obtained via the UCSC Table Browser and retrieved into Galaxy. The software used is an update of the tffind program (24).

1. From the Galaxy Portal page, take the link to the UCSC Table Browser, where the user should select the group "Expression and Regulation" and the track "TFBS Conserved." Under region, select position and enter the chromosome name and coordinates of interest. Otherwise, select "genome."

2. To restrict the search to a single binding site, you should filter by name. Next to "filter," click on "create." This brings up a new page, on which you should select "does" match, next to "name." The name of the binding site matrix should be entered after "match." For instance, using the term "V$GATA*" will return conserved matches to a set of weight matrices for GATA-1 and GATA-3 binding sites (see Note 13).

3. Press "submit" to upload the filter to the Table Browser query page, and then click on "get output." Results will appear on the Galaxy history page.

0 0

Post a comment