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aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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[question] hg19 tf list #541

Open colin893 opened 4 months ago

colin893 commented 4 months ago

Describe the bug

Hi, first thanks for the tool. I am not really facing a bug, but I can't find the transcription factor list for hg19 genome, I've look in the different folders of "https://resources.aertslab.org/cistarget/" as well as in "old" ones but can't have it. I wonder if it is still suitable to launch analyses with such version? It was aligned long time ago.

Thanks in advance for your time,

ghuls commented 3 months ago

You will have to check your gene expression matrix to see which gene symbols are used and if they don't match the current HGNC symbols.

Theoretically you can use the hg38 TFs with hg19 gene expression data assuming that the latter is using a relatively recent gene annotation (so most gene symbols are the same):

https://resources.aertslab.org/cistarget/tf_lists/allTFs_hg38.txt

https://ncbiinsights.ncbi.nlm.nih.gov/2020/11/12/human-grch37-hg19-refseq-annotation-update/

You could try: https://www.genenames.org/ => BioMart => Gene to map your hg19 gene symbols to current gene symbols.

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