<p>For chip-seq data, I had analyzed the samples until motif discovery using both cluster profiler and Homer for each histone mark. I was wondering what is the efficient method to determine if each GO term or identified motifs has a biological meaning or not or if there is any way to filter out the genes/motifs for only specific cell types such as PBMCs, how to prioritize genes? I know random matches might even surpass the biologically relevant matches but right now I am not sure how to narrow down the motifs/genes? Your help would be greatly appreciated.</p>

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2021-02-25T23:58:38.977Z
To add more detail I have extracted PBMCs from infectious patients with Anthrax. I performed chip-seq for 3 histone marks: (H3K27ac, H3K4me3, H3K27me3).I'd like to know if the bacteria is affecting the epigenetic signature of PBMCs? 
After peak calling and annotation for each marks, I have more than 2000 genes for each mark and more than 500 motifs called by Homer. I am trying to narrow the genes to those which I expect to see in PBMCs cells and those which have biological meaning. Right now I am struggling to find a way to filter out meaningful genes.
Mariam
<chip-seq><gene-ontology><motifs><homer><clusterprofiler>
How to identify specific motif for chip-seq data
# How to identify specific motif for chip-seq data

(Asked by: username_0 on 2021-02-24)

For chip-seq data, I had analyzed the samples until motif discovery using both cluster profiler and Homer for each histone mark. I was wondering what is the efficient method to determine if each GO term or identified motifs has a biological meaning or not or if there is any way to filter out the genes/motifs for only specific cell types such as PBMCs, how to prioritize genes? I know random matches might even surpass the biologically relevant matches but right now I am not sure how to narrow down the motifs/genes? Your help would be greatly appreciated.

**Tags:** chip-seq, gene-ontology, motifs, homer, clusterprofiler
> **Comments:**
> **username_0**: To add more detail I have extracted PBMCs from infectious patients with Anthrax. I performed chip-seq for 3 histone marks: (H3K27ac, H3K4me3, H3K27me3).I'd like to know if the bacteria is affecting the epigenetic signature of PBMCs?  After peak calling and annotation for each marks, I have more than 2000 genes for each mark and more than 500 motifs called by Homer. I am trying to narrow the genes to those which I expect to see in PBMCs cells and those which have biological meaning. Right now I am struggling to find a way to filter out meaningful genes.  

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