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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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difference between "TF" regulon and "TF_extended" regulon? #72

Closed WeiCSong closed 5 years ago

WeiCSong commented 5 years ago

Hi everyone, i'm currently using SCENIC step2&3 for my research, and i'm puzzled about "extended" regulon. I guess that one regulon is a subset of its "_extended" regulon, and has a higher threshold of determination of regulation. Shall i choose the "_extended" regulon to study one TF? How shall i explain to the reviewer why i choose it? I don't quite understand the biological meanings of their difference. Wish to learn from you. Thanks!

mellyS commented 5 years ago

I have the same question . Could you please explain us the difference between the two outputs ? Thanks !

s-aibar commented 5 years ago

Dear @WeiCSong and @mellyS ,

The "extended" regulons include motifs that have been linked to the TF by lower confidence annotations (e.g. inferred by motif similarity).

You can find the full explanation in the detailed vignette detailedStep_2_createRegulons.Rmd :

1.2 Annotate motifs to TFs ... The annotations provided by the cisTarget databases can be divided into high-confidence or low-confidence, depending on the annotation source (annotated in the original database, inferred by orthology, or inferred by motif similarity). The main regulons only use the “high confidence” annotations, which by default are “direct annotation” and “inferred by orthology”. The sufix _extended in the regulon name indicates lower confidence annotations (by default “inferred by motif similarity”) are also used.

Sorry that is is not more clear in the main vignette. To avoid overcrowding it, I have just created a FAQ that includes this question.

Thank you for your feedback! Sara