Transcription factor for regulon doesnt appear to be a transcription factor

[satkins1]

Hi

I have run the SCENIC pipeline in accordance with the tutorial on a 10X dataset. This has given me some interesting results most of which make sense in the biological context of the experiment. One of the most interesting results is that it has identified a regulon which has been assigned to the transcription factor TFF3. On further reading however it appears that TFF3 is not actually a transcription factor. However the output identifies TFF3 as a TF and gives the motif tfdimers__MD00424 as bestMotif for highConfAnnot. I cant find any information on how this annotation has been made.

If I have misunderstood the output I would be grateful for clarification otherwise are you able to offer any input on the interpretation or underlying data for ascribing the annotation?

Happy to provide any additional information as needed.

Thanks

Steve

[steinaerts]

Hi Steve, This sometimes happens due to orthology mappings when transferring PWMs from other species to human. The easiest might be to re-analyse that particular TFF3 module (or the regulon) in the Cytoscape plugin iRegulon. The motif enrichment that you’ll get provides more details about the original PWM, and the TF it was linked to, in which other species. In the future we have to think about ways to maintain the motif2TF info as metadata in the cisTarget databases. Stein