Protocol to identify transcription factor target genes using TargetOrtho2
TargetOrtho2 uses transcription factor binding site information to predict transcription factor targets in C. elegans, based on an in silico phylogenetic footprinting approach. Here, we present a protocol to identify transcription factor target genes using a new version of TargetOrtho2. We provide instructions for installing TargetOrtho2 and its required suite of programs, for predicting transcription factor target genes, and for updating and adding new genomes to TargetOrtho2.
Authors
- Jonathan D. Rumley (ORCID: https://orcid.org/0000-0002-5962-7575)
- Oliver Hobert (ORCID: https://orcid.org/0000-0002-7634-2854)
- J. Kim (ORCID: https://orcid.org/0000-0003-0304-3738)
Institutions
- Howard Hughes Medical Institute (US)
- Columbia University (US)
Publication Details
- Journal
- STAR Protocols
- Published
- 2025-03-01
- DOI
- https://doi.org/10.1016/j.xpro.2025.103680
- Citations
- 2
- Primary Topic
- Genomics and Chromatin Dynamics
- Type
- article
- Field-Weighted Citation Impact
- 1.61
Funders
- Howard Hughes Medical Institute
- Bio-oriented Technology Research Advancement Institution
- National Institute of General Medical Sciences
- National Institute of Neurological Disorders and Stroke