Question: Confusion of TF-gene interactions database
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gravatar for Batu
3 months ago by
Batu110
Batu110 wrote:

I'm looking for a database that includes the list of TF-gene interactions which are found experimentally (not predicted). There are some posts about this here, but I wanted to ask again, because I had some confusion as I told below.

I will use the list in DREM 2.0. It already includes a such list, but we would like to use the list that includes:

  • more TFs (127 is much less, human genome includes ~2000 TFs),
  • currently updated (even it shouldn't be that current enough, 2011 is really outdated),
  • includes much interactions (like the list in DREM).

According to the posts I found here, tftargers/github seems nice to include some databases. Additionally, I found Harmonizome (filtered by "transcription factor"), this also seems useful. I wanted to check JASPAR, but I could only find PWM lists, not TF-gene interactions list.

And interestingly, I compared the list in DREM 2.0 (and retrieved from ENCODE, includes 127 TFs) with the Marbach2016 list (found in tftargers/github, includes 643 TFs) and found out that only 64 TFs are common between two lists. And expectedly, DREM results for an expression matrix resulted much different between two. Why is there a such difference between different TF lists?

According to these, do you have any suggestion about which one can be used, or for which points we should be careful? Thanks...

ADD COMMENTlink modified 3 months ago by biostart290 • written 3 months ago by Batu110
0
gravatar for biostart
3 months ago by
biostart290
Germany
biostart290 wrote:

You can try http://chip-atlas.org/

ADD COMMENTlink written 3 months ago by biostart290

That website is not suitable for me, I cannot extract TF-gene interaction list from there. But it seems like an interesting website, thanks...

ADD REPLYlink written 12 weeks ago by Batu110
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