CisCross

CisCross analyzes potential upstream transcription factor (TF) regulators of Arabidopsis thaliana genes using DAP-seq-derived TF binding profiles from the Plant Cistrome database.

Key Features:

• Plant Cistrome-derived TF binding profiles: Utilizes TF binding profiles generated by DAP-seq and archived in the Plant Cistrome database.
• MACS2 re-processing: Raw DAP-seq data were re-processed with the MACS2 peak caller to improve peak-calling quality metrics.
• Enhanced TF profile collection: Provides an improved collection of TF binding profiles that recovered TFs missing from earlier DAP-seq peak sets.
• Gene list enrichment and regulator ranking: Implements a gene list enrichment procedure to evaluate and rank potential upstream TF regulators.
• Flexible and precise upstream regulator evaluation: Enables refined assessment of candidate TF regulators for given gene lists.

Scientific Applications:

• Transcription factor identification for gene lists: Systematically evaluates and ranks candidate TF regulators for specified Arabidopsis thaliana gene lists.
• Plant regulatory network analysis: Supports discovery and analysis of transcriptional regulatory mechanisms in Arabidopsis thaliana for plant genomics and molecular biology studies.

Methodology:

Leverages DAP-seq TF binding profiles from the Plant Cistrome database, re-processes raw DAP-seq data with the MACS2 peak caller, and applies a gene list enrichment procedure to rank potential upstream TF regulators.