remap-database

What problem does it solve?

This Skill allows you to query the ReMap 2022 database to find transcription factor (TF) binding sites from ChIP-seq experiments, enabling detailed analysis of gene regulation.

Core Features & Use Cases

• Genomic Region Overlap: Find all TF binding peaks that overlap a specific genomic region.
• Gene-Centric Queries: Retrieve TF peaks located near a gene's transcription start site (TSS).
• TF-Specific Peak Retrieval: Get all binding peaks for a particular TF across different cell types.
• Biotype Filtering: Filter peaks based on their regulatory annotation (e.g., promoter, enhancer).
• Data Download: Download peak data in BED format for offline analysis.
• Use Case: Identify which TFs bind near a specific gene of interest to understand its regulatory network, or find all TFs binding at a GWAS locus to prioritize candidate genes.

Quick Start

Use the remap-database skill to find all TF binding peaks overlapping the genomic region chr17:7670000-7690000 in the hg38 assembly.