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aertslab / SCENIC

SCENIC is an R package to infer 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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Mis-labelled motifs - SCENIC+ #442

Closed JaanaB1 closed 5 months ago

JaanaB1 commented 5 months ago

Hi Team,

Thank you for generating this package! I have a slight issue in regards to the motif nomenclature. I understand that the Motif library has been generated from multiple databases (and redundancies have been removed to make this more concise). However, I have an issue in that the motif which one of my regulons has been based on does not seem to belong to the regulon protein.

Here I have a regulon named as the Irf8 regulon which was based from the following motif;

metacluster_167.7 metacluster_167 7

The software calls this an Irf8 motif however looking at the Jaspar database the Irf8 motif is as follows;

image MA0652.1 - Irf8 motif (Jaspar)

The above motif is not the same as the metacluster 167.7 motif, in fact the motif called is the motif for the Spi1 protein: image

I understand that as these two proteins interact there might be merged motifs however how does the software assign the motif (and regulon) itself to one protein or the other? Is this a case of the Irf8 motif being mis-labelled in the curated dataset?

Additionally, instead of using this curated database, is there an option by which we could feed SCENIC+ with only one database (for example JASPAR).

Many thanks in advance!

JaanaB1 commented 5 months ago

Apologies - this is a question for SCENIC+