CREPE

CREPE identifies, catalogues, and annotates transcription factors to support analysis of gene regulatory networks and comparative transcription factor repertoires.

Key Features:

• Transcription factor identification: Detects transcription factors from input datasets for downstream cataloguing and annotation.
• Cataloguing: Generates structured catalogues of transcription factors for organism-specific and cross-species analyses.
• Annotation: Assigns annotation information to transcription factors to facilitate functional and comparative studies.
• Benchmarking: Validates identification and annotation results by benchmarking against curated human TF datasets.
• Comparative repertoire analysis: Enables comparison of transcription factor repertoires across species to support evolutionary and comparative genomics investigations.
• Support for gene regulatory network analysis: Produces TF-centric outputs usable for investigation of gene regulatory networks.

Scientific Applications:

• Gene regulatory network analysis: Provides TF annotations and catalogues for building and interpreting gene regulatory networks.
• Comparative TF repertoire studies: Facilitates analysis of transcription factor repertoires in species such as Heliconius erato and Heliconius melpomene.
• Annotation validation: Supports validation of TF annotations through benchmarking with curated human TF datasets.
• Evolutionary and functional genomics: Applies to studies in evolutionary biology, genetics, and systems biology that require TF identification and comparison.

Methodology:

Computational operations explicitly include identification, cataloguing and annotation of transcription factors, benchmarking against curated human TF datasets, and comparative analysis of transcription factor repertoires in Heliconius erato and Heliconius melpomene.