Determining biological relevance of a list of motifs?
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5 weeks ago
Ronin ▴ 10

I have used the findMotifs.pl function in Homer to get a series of motif sites. I am curious if there is any recommended workflows or resources that might be helpful to help determine any biological relevance these motifs might have. For example, lets say that I have 8 motifs that were found to be significant in eye samples:

KLF3(Zf)/MEF-Klf3-ChIP-Seq(GSE44748)
GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)
bcd(Homeobox)/Embryo-Bcd-ChIP-Seq(GSE86966)
Otx2(Homeobox)/EpiLC-Otx2-ChIP-Seq(GSE56098)
CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)
Sox7(HMG)/ESC-Sox7-ChIP-Seq(GSE133899)
Rfx1(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)
Pax7(Paired,Homeobox),long/Myoblast-Pax7-ChIP-Seq(GSE25064)

Similar to running a GO analysis of a list of genes, I am hoping there might be a related resource available for determining what biological significance these 8 motifs might provide. I recently found Jaspar2020, though I am not sure if that will help me or not. Thank you in advance for any thoughts or suggestions you might have.

motifs HOMER • 242 views
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Can you give details on the experimental setup and what exactly you scanned for motif enrichment (and what the background was)?

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Hi, sorry for the late response, I was ill. The setup is looking at a particular tissue (eye samples) in a non-model species, and I used this command:

findMotifsGenome.pl macs2.eye_ATAC.bed /scratch/ATACseq/FASTQ_ATAC_43955/pfluv-genome/pfluv-genome.fa ./motifs/macs2/eye -p 4 -size given

So I'm taking the peaks (bed file), the genome, and then the output directory, etc. following that. After getting a motif file, I ran:

scanMotifGenomeWide.pl /scratch/ATACseq/FASTQ_ATAC_43955/sortedbams/picard/knownEyeTop5.motif /scratch/ATACseq/FASTQ_ATAC_43955/pfluv-genome/pfluv-genome.fa -bed > eye-all-motifsites.bed

If you have critiques or suggestions (perhaps this is the wrong approach), I am very curious to know how to correct these errors!

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