Question: How to find list of gene name from HOMER motif output
0
gravatar for Mike
2.5 years ago by
Mike1.6k
UK
Mike1.6k wrote:

Hi all,

I am using "findMotifs.pl" script from HOMER to find motifs from a list. I used following command..

perl findMotifs.pl    genelist.txt   human   motifoutputdir  -len 25

I got following output list,

simple text file:

Motif Name  Consensus   P-value Log P-value q-value (Benjamini) # of Target Sequences with Motif(of 18) % of Target Sequences with Motif    # of Background Sequences with Motif(of 38431)  % of Background Sequences with Motif

BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer    GNCACGTG    1e-3    -6.938e+00  0.2560  10.0     55.56% 7740.1  20.14%

and graphical output..

graphical output

Output result file give me number of genes having particular motif, But I want to find list of gene name from column "# of Target Sequences with Motif(of 18)".

Could you please help me, how to find name of genes having particular motif ?

Thanks

motif homer • 1.8k views
ADD COMMENTlink modified 2.5 years ago by mcjmigdal10 • written 2.5 years ago by Mike1.6k

I am trying to do something similar but I am getting an error as it can not find the <promoter set="">. I want to find motifs in promoters from the given list. Can I ask how did you manage to install and specify your promoter set? I have tried with "data/genomes/hg19/hg19.tss", and followed the suggestions from the error, but anything has worked so far... Thanks!

ADD REPLYlink modified 5 months ago • written 5 months ago by CL0
0
gravatar for mcjmigdal
2.5 years ago by
mcjmigdal10
mcjmigdal10 wrote:

Hi,

what findMotifs.pl does is actually to search for motifs near the TSS of the genes from the list you have provided (genelist.txt). According to homer documentation the default settings for the near TSS region are -300 upstream and 50 downstream. So the most straightforward solution to your problem that I can think of, would be to:

  1. Take the motifs you are interested in (like BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer) and save them somewhere
  2. Extract the -300, 50 region around your genes of interest TSS
  3. Scan those regions with selected motifs; preferably using one of homer utilities designed for this purpose as they should work with homer formatted motifs files out of the box

Hope it helps, if there is a simpler solution I would really benefit from learning it too :)

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by mcjmigdal10

I am trying to do something similar but I am getting an error as it can not find the <promoter set="">. I want to find motifs in promoters from the given list. Can I ask how did you manage to install and specify your promoter set? I have tried with "data/genomes/hg19/hg19.tss", and followed the suggestions from the error, but anything has worked so far... Thanks!

ADD REPLYlink written 5 months ago by CL0
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