README.md

Reprogramming Recovery

This git repo contains code and data and the website supporting the paper "Ranking Reprogramming Factors for Directed Differentiation."

Citation

Ranking Reprogramming Factors for Directed Differentiation
Jennifer Hammelman, Tulsi Patel, Michael Closser, Hynek Wichterle, David Gifford
bioRxiv 2021.05.14.444080; doi: https://doi.org/10.1101/2021.05.14.444080

cluster_consensus_motifs

Folder contains methods for generating a consensus transcription factor motif data base of 107 consensus motifs representing 356 motifs in the HOCOMOCOv11 core mouse database using the script 00_cluster_motifs.sh.

perform_motif_enrichment

Folder contains scripts for performing motif enrichment using DREME, AME, HOMER, and KMAC.

data

consensus_HOCOMOCOv11_core_MOUSE-affinityprop-handannotated.meme

consensus database of 107 motifs representing TF families in meme format

consensus_HOCOMOCOv11_core_MOUSE-affinityprop-handannotated.motifs

consensus database of 107 motifs representing TF families in chan PWM format

consensus_HOCOMOCOv11_core_MOUSE-affinityprop-mapping.txt

mapping of 356 transcription factors to 107 motif consensus families

mouse_ensemble_tfs_from_lambertetal_isyes.unique.txt

list of ensemble mouse gene names of 1,374 transcription factors curated in Lambert et al., 2018.