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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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how to prepare motif2tf file for `path_to_motif_annotations` in plant #434

Closed xuzhougeng closed 3 months ago

xuzhougeng commented 4 months ago

Hi, I'm trying to use SECNICPLUS in my plant species recently, but I'm having problems.

Referred to https://scenicplus.readthedocs.io/en/latest/human_cerebellum_ctx_db.html, I create a motif database for my species, but I encountered a problem at this step (https://scenicplus.readthedocs.io/en/latest/human_cerebellum.html ), as I don't have the corresponding file for path_to_motif_annotations which is path to the motif-to-TF annotaiton

You have provided motif matrices collected and organized in multiple databases, and provide files of motif2tf for some of the species, like chiken, flybase, human and mouse. For animals like pigs, dogs, and zebrafish, it might be possible to perform conversions based on homologous genes

However, the plants may be evolutionarily distant from all the species mentioned above and may not be directly usable. So, without being able to use homologous gene conversion, how can I find the corresponding tf in the plants I'm studying based on the motif collection you provided?

I would greatly appreciate your response and thank you sincerely.

SeppeDeWinter commented 3 months ago

Hi @xuzhougeng

Without being able to use orthology it is very difficult to map the motif-to-TF annotations. Your best way forward would be to use another motif collection, with motifs that do have annotations in the plants you are studying.

Best,

Seppe

xuzhougeng commented 3 months ago

Thank you for your thoughtful response