Some targets contain their TF of the regulon.

[xinghansun]

Hello,

I used pySCENIC cli to run grn and ctx with loom file as input; all database were downloaded from pyscenic website: allTFs_hg38.txt, ["hg38_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather",
"hg38_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather"], motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl.

In the ctx output, some of the regulons' targets also include the TF of the regulon, and that kind of target gene will always have a 1.0 weight.

For instance, a regulon with EOMES as TF:

• Normal regulon - without the regulon TF in targetGenes:
  EOMES,taipale_tf_pairs__ETV5_EOMES_RNGTGNNNNNNNNNNNNNRCRCCGGAWSN_CAP,0.2581240768094535,3.1320751755985827,0.0,1.0,gene is directly annotated,"frozenset({'hg38_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings', 'top50', 'activating'})","[('CCSER1', 188.0), ('ST6GAL2', 190.0), ('AKT3', 171.0), ('ZBTB20', 179.0), ('CACNA2D1', 179.0), ('MARCH1', 173.0), ('EGFEM1P', 172.0), ('FNBP1L', 167.0), ('SEMA6D', 171.0), ('SLC22A23', 169.0), ('SYNE2', 173.0), ('MAP2', 171.0), ('GRIA2', 178.0), ('IGF1R', 177.0), ('KMT2C', 167.0), ('FBXO11', 171.0), ('CEP170', 167.0), ('CDK14', 174.0)]",935

• Weired regulon - with the regulon TF in targetGenes:
  EOMES,taipale_tf_pairs__HOXB13_EOMES_NNMRTAAANTMACACNN_CAP_repr,0.1338237737730177,3.2429313528141797,0.0,1.0,gene is directly annotated,"frozenset({'activating', 'top50', 'hg38_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings'})","[('ZFHX4', 181.0), ('CXXC5', 178.0), ('TNIK', 183.0), ('EOMES', 1.0), ('TMEM108', 192.0), ('MAST2', 180.0), ('ZBTB20', 181.0), ('GRIA2', 183.0), ('SNCAIP', 181.0), ('CBLB', 179.0), ('HDAC9', 181.0)]",1037

Based on my understanding, the geneTargets are derived from co-expression and thus shouldn't include the TF itself. Although it doesn't affect a lot when other genes' weights are large, but there are indeed regulons whose target genes' weights are less than 1; in this case I guess it can affect the result?

Has anyone got similar result?

Thank you.