[BUG] Non-transcription factor gene “Fgf15” found in mm_mgi_tfs.txt

[Ashone1992]

Bug Report: Incorrect inclusion of "Fgf15" in mm_mgi_tfs.txt

Dear pySCENIC team,

I have identified a potential issue in the mm_mgi_tfs.txt file provided in the resources folder of the repository. Specifically, the gene Fgf15 is included in the list of mouse transcription factors at line 1227 (see attached screenshot for reference).

Problem Details

• File: resources/mm_mgi_tfs.txt
• Line: 1227
• Issue: Fgf15 is not recognized as a transcription factor in the literature or commonly used databases. Fgf15 is known to function as a member of the fibroblast growth factor family and is primarily involved in signaling pathways rather than transcriptional regulation.

Evidence

• Supporting databases (e.g., MGI, UniProt) and relevant literature classify Fgf15 as a signaling molecule, not a transcription factor.
• Fgf15's role as a fibroblast growth factor does not align with the definition of transcription factors, which directly regulate gene expression by binding to DNA.

Expected Behavior

The file should only include genes that are validated as transcription factors. It is likely that Fgf15 was added in error and should be removed after confirmation.

Steps to Reproduce

1. Clone the pySCENIC repository.
2. Navigate to the resources folder.
3. Open the mm_mgi_tfs.txt file and search for "Fgf15".

Suggested Actions

1. Verify the inclusion of Fgf15 in this list and remove it if confirmed to be a mistake.
2. Additionally, it might be helpful to conduct a thorough review of the mm_mgi_tfs.txt file to identify and correct any similar errors, ensuring the integrity of the transcription factor list.

Thank you for maintaining such an important tool for the community. I hope this report helps improve its accuracy and reliability!

Best regards,

Tianxiang Tang