BED file from GSEA gene set

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2.5 years ago

2138493o ▴ 20

Hi all!

Sorry if this is a very simple question but I was wondering what is the easiest way to create a BED file of genes of interest from a GSEA gene set? For context, I would like to use computeMatrix (followed by plotHeatmap) of the deeptools toolkit to plot ChIP-seq signal within the region of genes within a specific GSEA gene set. Thank you in advance everyone!

BED ChIP-seq deeptools GSEA • 878 views

ADD COMMENT • link updated 23 months ago by Ram 44k • written 2.5 years ago by 2138493o ▴ 20

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What exactly is the question? Do you need code to make a BED file, and if so based on what? Gene symbols, coordinates of peaks? Please add details.

ADD REPLY • link 2.5 years ago by ATpoint 85k

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I would like to use deeptoolsMatrix to plot ChIP signal within the TSS of my genes of interest; my genes of interest being PRC2 targets. So if I have a set of genes from GSEA (e.g. https://www.gsea-msigdb.org/gsea/msigdb/cards/BENPORATH_PRC2_TARGETS) which provides a list of all the genes and their gene symbols and Entrez ID's, is there anyway I can quickly use this information to create a BED file containing all the genes and their coordinates?

ADD REPLY • link 2.5 years ago by 2138493o ▴ 20

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Download an annotation file (.gff3 file type, for example) and merge the two data frames by column in R, for example performing an inner_join.

ADD REPLY • link 2.5 years ago by Marco Pannone ▴ 810

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