RcisTarget

RcisTarget identifies transcription factor binding motifs that are significantly over-represented near transcription start sites (TSS) in a user-defined gene list using a database of genome-wide cross-species motif rankings.

Key Features:

• Motif Identification: Detects DNA motifs significantly over-represented around transcription start sites (TSS) within a provided gene set.
• Cross-Species Analysis: Uses a database of genome-wide cross-species motif rankings to enable comparative identification of conserved regulatory motifs.
• Integration with SCENIC Framework: Supports integration with SCENIC (Single-Cell Regulatory Network Inference and Clustering) workflows and single-cell RNA-seq analyses for regulatory network inference and cell-state identification.

Scientific Applications:

• Gene Regulation Studies: Pinpoints transcription factor binding sites (TFBS) that may contribute to gene expression regulation.
• Comparative Genomics: Identifies conserved regulatory motifs across species using cross-species motif rankings.
• Transcription Factor Identification: Suggests candidate transcription factors associated with over-represented motifs near TSS in specific biological processes or disease contexts.

Methodology:

Selects DNA motifs enriched around TSS from a user-defined gene list by utilizing a specialized database of genome-wide cross-species motif rankings, performing statistical analyses to determine significant over-representation of motifs, and providing outputs that highlight key TFBS.