I have a list of genes that differential expressed in RNA-seq and would like to filter only transcription factors. Do we have any tools or good way to do this? Thank you so much!
What have you tried? Have you looked at GO annotations?
Yes, I do GO and GSEA to get pathway. I download the background gene at https://www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp#C3 The things I am quite confuse is there are many different pathway when I use GO, GSEA or using different database such as KEGG or others, so not sure which pathway I should focus on. I found there are many functions that perform pathway analysis such as fgsea(), gseGO(), gseKEGG(), enrichGO()
This database has been the best I've found.
Curious how redundant these TFs are. Jeff Vierstra has done some analysis on this to simplify model sets: https://www.vierstra.org/resources/motif_clustering
That's a nice resource. Motif redundancy is by far the most frustrating aspect of motif analyses, in my experience. To a degree, we address it by filtering via expression, but it still results in imperfect results.
Thank you so much!
Definitely the best resource.
Was also going to recommend this one.
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