Transcription Factor Functions

Question

[axolotl]

I have been wondering if there is a database that contains information about whether a transcription factor has a repressive or an activating or a context-dependent function.

Answer 1

[Alex Reynolds]

If you performed a whole-genome FIMO scan, selecting those hits that match your TF of interest, you might perform set operations on those hits against datasets like epilogos, which calculate functional annotations for different sets of biosamples from their respective chromatin state patterns.

Tabix files are available from that site for local queries (click on the arrow button in the top-right corner of the browser and select "Data"), or the Python tool can be run locally for custom analyses.

As an example, biosamples for female human will have greater transcriptional activity over regions in chrX like FIRRE (OMIM), as compared with male biosamples. These and other functional differences would be expected along this sex chromosome. Set ops over the paired biosample tabix would give differential scores useful for inspecting regions and doing further analysis.

Given regions of differential function, one could use MEME to look for de novo motifs over their sequences, or use FIMO to get all hits and then do a bedmap-style operation over said regions-of-interest.