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Identify predicted TF targets by binding motif

Hello,

I am using Chromvar on single nuclei multiome data to identify possible transcription factors acting in my cell clusters of interest. This tends to work very well as I get an output of over represented motifs in the clusters, based on the accessibility around genes that each clusters shows.

My question is, how can I identify from the dataset which genes within my cluster of interest it’s picking up specifically as being accessible.

For example, a TF like SOX2 comes back as a potential regulator in stem cells. How would I go about finding which genes in the Stem cells SOX2 is predicted to bind to.

Thanks

atac-seq multiome chromatin seurat
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written by V V

Do you get any information about the motif enrichment and which genes are associated with that motif in a cluster ? If not, you may want to do an MSA in MEME with the promoters of all the genes in the cluster and check against the custom motifs you found using Chromvar.

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written by pixie@bioinfo pixie@bioinfo

I get information about which motif is enriched in the cluster (and which TF binds to it), but I cant see which genes have that motif. But I will look in MEME. Thank you!

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written by V V

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