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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.

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  • $\begingroup$ There is no easy answer to this without knowing what you are exactly doing and which question you want to answer. In general ChIP-seq is a good support experiment to answer a scientific question you have, deriving a question from it is hard. Please add some details, even though I am tempted to vote for closing as this is very unspecific and open-ended, but lets see the details first. $\endgroup$
    – ATpoint
    Feb 25 at 9:26
  • $\begingroup$ 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. $\endgroup$
    – Mariam
    Feb 25 at 23:58

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