Good Strategies To Strengthen The Validity Of The Data Used While Searching For Tfbss
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12.7 years ago
Anima Mundi ★ 2.9k

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.

transcription binding pssm • 2.5k views
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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?

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

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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 or TransFac 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).

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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.

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