Question: Trascription factor binding sites prediction using FIMO
gravatar for Eisuan
17 months ago by
Vita-Salute San Raffaele University (Milan - Italy)
Eisuan0 wrote:

Hello everyone!

In these days I was performing TF binding sites prediction using FIMO (MEME Suite). I am trying to check if there are TF binding sites for TF related to biological processes at the promoter level of the gene in my interest.

I am performing the analysis using;

  • Proximal promoter sequence (-800 / +200 from TSS)
  • promoter sequence region annotated in the ENSEMBL regulatory feature (-1600 / +1800 from TSS)
  • JASPAR 2018 PWM

In some cases I have obtained results with very high q values (like 0,50; but this was not always the case) and, in general, I know that this kind of predictions may result in many false positives. However, by contextualizing the position of the predicted binding sites (and others that are known to be near to each other) I got results that make sense.

I was wondering if there are other computational methods for increasing prediction reliability. By trying to visualize ChIP-seq experiment peaks I have seen that there were correspondences in predictions regions and peaks. The same thing for checking identity with the promoter of the orthologous gene in mouse. However, I have to admit that my approach in doing that was very naive and I am not sure it is correct.

Thank you for your support! Daniele

promoter gene • 844 views
ADD COMMENTlink modified 16 months ago by Biostar ♦♦ 20 • written 17 months ago by Eisuan0

Is this human? If so you can intersect your promoter region with the ReMap database to see if there is experimental (ChIP-seq) evidence for binding at the promoter.

ADD REPLYlink written 17 months ago by ATpoint44k

Thank you for this suggestion. I've just tried using that tool but unfortunately, it doesn't reveal any TF in the region of interest neither using the ENSEMBL gene ID (and modifying upstream/downstream analysis settings).

PS. Yes, it's a human gene and I am using hg38 reference genome.

ADD REPLYlink written 17 months ago by Eisuan0

That is unfortunate. You can always try to see if there is published ChIP-seq data towards the TFs whose motifs you found. ReMap is extensive but not comprehensive as far as I understand things. Beyond that it will probably come down to experments doing ChIP-(seq) on the factors you think that bind there.

ADD REPLYlink written 17 months ago by ATpoint44k

It is funny because all the time I try to apply some tools that search matches in a database using this promoter region I find few / no results. I had the same experience using AME (Meme Suite) for this region.

I am pretty sure there are no problems with the promoter sequence I am using.

ADD REPLYlink modified 17 months ago • written 17 months ago by Eisuan0

If you reproducibly get no results this may be because there are none?

ADD REPLYlink written 17 months ago by ATpoint44k

Sounds like you've been pretty thorough to me.

ADD REPLYlink written 17 months ago by i.sudbery10k
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