Explanation of SCENIC+ output and columns

[Xieeeee]

Hi,
Thanks for this great tool! I am browsing around the tutorial, issue and discussion but I cannot find myself a detailed explanation of the output file and its information generated by scenic+ (for example, what each column in direct_e_regulon_metadata means). Would you mind kindly pointing me to some source? Thanks a lot!!

Best,
Y

[SeppeDeWinter]

Hi

See below for an explanation

Region: predicted target region
Gene: predicted target gene
importance_R2G: importance score of region-to-gene link (from GRNBoost)
rho_R2G: correlation coefficient of region-to-gene link
importance_x_rho: the product of the previous two columns
importance_x_abs_rho: the product of the previous two columns, but the absolute value of rho_R2G is taken
TF: TF name
is_extended: wether the motif-to-TF annotation is from direct evidence or not (i.e. orthology or similarity based)
eRegulon_name: regulon name
Gene_signature_name: gene signature name
Region_signature_name: region signature name
importance_TF2G: TF-to-gene importance score (grn boost)
regulation: wether the interaction is activating or repressive
rho_TF2G: TF-to-gene correlation coefficient
triplet_rank: Triplet rank score (see paper for detailed explanation)

I hope this helps?

All the best,

Seppe

[Xieeeee]

This is definitely helpful! Thank you so much.

Best,
Yang