interpreting FIMO results - p value and q value
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Entering edit mode
6.2 years ago
Affan ▴ 290

I used FIMO to scan promoter regions (defined as 10,000 upstream from TSS) only on chromosome 1 of mm9. The results can be viewed here: http://nbcr-222.ucsd.edu/opal-jobs/appFIMO_4.10.01429210665330517302090/fimo.html

I have a couple of questions:

1) For each gene ('sequence name'), it finds a hit on both the positive and negative strand. What does this mean? Can I get rid of one of them and only consider the positive strand? Even the start and end coordinates are the same.

2) Could someone explain to me the p value (and the corresponding q value)? Since the results are sorted by p value and the first result has a p value of 1.64e-6 .. doesn't that mean that that hit is deemed to be a true positive? Why then is the q value so high? Why are my q values so high regardless?

3) I have a control data set. Its a chip seq experiment on the transcription factor of interest. Can I just go through the results from FIMO and determine which results lie within the peaks of the chipseq experiment and as that information to create sensitivity analysis?

motif position weight matrix • 3.0k views
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1
Entering edit mode
6.2 years ago
Ram 33k
  1. If the motif you're looking for is its own reverse complement, you'll definitely find hits on both strands between the same co-ordinates.

    EDIT: Just checked your motif (CTATATATAG - this is its own reverse complement, so your results are expected)

  2. Not sure about this. Maybe the q-value is low only for really long or really specific/rigid motifs. Maybe your motif matrix is a bit lenient.

  3. You could definitely do that. Correlating an analysis of the p-values would also give you a weighted measure of sensitivity.

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