CRCdb

CRCdb catalogs core transcription regulatory circuitries (CRCs) driven by super enhancers (SEs) across human tissues and cells to characterize core transcription factors (TFs) and their regulatory network properties.

Key Features:

• Identification of CRCs: CRCs were identified using two distinct computational methods across large cell and tissue samples, classifying TFs as common, moderate, or specific.
• Biological Analyses: Analyses include sequence conservation, CRC activity, and genome binding affinity for the identified TFs.
• Local Module Insights: Local modules from common CRC networks were highlighted for essential functions and prognostic performance.
• Tissue-Specific Networks: Tissue-specific CRC networks related to cell identity were annotated, with core TFs reported as disease markers and as potential regulators relevant to cancer immunotherapy.
• Comprehensive Data: Detailed data include identified CRCs and core TFs, the most representative CRCs, TF frequency, and network metrics such as indegree and outdegree.

Scientific Applications:

• Gene expression regulation: Characterizes TF-driven regulation mediated by SEs to study transcriptional control.
• Cell identity and differentiation: Supports analysis of tissue-specific CRC networks that define cell identity.
• Disease mechanisms and oncology: Facilitates investigation of TFs and CRCs implicated in disease progression and cancer-related regulatory programs.
• Biomarker and therapeutic target discovery: Aids identification of core TFs as disease markers and potential targets for cancer immunotherapy and personalized treatment strategies.

Methodology:

CRCs were identified using two distinct methods, followed by analyses integrating sequence conservation, CRC activity, genome binding affinity, and network metrics such as TF frequency and indegree/outdegree.