Question: Good Strategies To Strengthen The Validity Of The Data Used While Searching For Tfbss
1
gravatar for Anima Mundi
6.6 years ago by
Anima Mundi2.3k
Italy
Anima Mundi2.3k wrote:

Hello,

this is potentially a very broad (and maybe a bit subjective) question, if you want I agree to treat it as a community-wiky. I am searching for TFBSs on a list of putative regulatory sequences from the Xenopus genome. I am using MEME Suite's FIMO. The problem is that, despite the strong support from the presence of the TFBS arising from our wet-lab experience, I am not able to obtain FIMO q-values under the desired threshold (0.05).

In general, what are good strategies to strengthen the validity of the data used in such experiments?

What comes to my mind is:

a) use data with a robust biological background;

b) use as short as possible strings;

c) carefully mask undesired signals;

d) use a PSWM as robust as possible;

e) set the algorithm's parameters properly.

binding pssm transcription • 1.3k views
ADD COMMENTlink modified 6.5 years ago by Lars Juhl Jensen11k • written 6.6 years ago by Anima Mundi2.3k

Are you doing a de novo search for the motifs (i.e. are you trying to define the motifs using the sequences) or are you scanning for binding sites using a pre-defined set of motifs?

ADD REPLYlink written 6.6 years ago by Qdjm1.9k

FIMO scans for binding sites using a pre-defined set of motifs.

ADD REPLYlink written 6.6 years ago by Anima Mundi2.3k

I suspect the specific software used to perform the search and/or derive the motifs would also have an effect here.

I'm not sure if any of the JASPAR (http://jaspar.genereg.net/) or TransFac (http://www.biobase-international.com/product/transcription-factor-binding-sites) folks are on BioStar, I suspect they will have suggestions relating to this. So you may want to consider contacting them asking for advise (and mention this question of course).

ADD REPLYlink written 6.6 years ago by Hamish3.0k

Thank you, I will try to get in contact with some of them mentioning this question. If I find some useful information, I will report it here.

ADD REPLYlink written 6.6 years ago by Anima Mundi2.3k
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