How to find list of gene name from HOMER motif output

Question

[Mike]

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..

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

[CL]

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!

[bekereindra]

I extracted promoter coordinates (-400; +100 bp from TSS in my case) using biomaRt in R from my gene list and then used the coordinates with homer annotatePeaks.pl

Answer 1

[mcjmigdal]

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 :)

[CL]

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!