What problem does it solve?
Determining what regulates a gene or whether a non-coding variant is functionally important requires combining motif databases, experimental ChIP-seq data, chromatin annotations, and variant scoring — evidence scattered across JASPAR, ENCODE, UCSC, and RegulomeDB that is tedious to query and integrate manually.
Core Features & Use Cases
- TF motif and binding-site discovery: Retrieve TF binding motifs from JASPAR and curated direct TF-DNA binding sites from UniBind, then cross-reference with ENCODE ChIP-seq experiments.
- Regulatory element annotation: Map cCREs (promoters, enhancers, CTCF sites) around any genomic region via UCSC and ENCODE annotations, ChromHMM states, and ATAC-seq/DNase-seq data.
- Variant impact assessment: Score regulatory variants with RegulomeDB rankings, and predict quantitative effects of non-coding variants from raw sequence using AlphaGenome, Enformer, Borzoi, ChromBPNet, or Evo 2.
- Use Case: Given a GWAS hit like rs1234567, score its regulatory impact with RegulomeDB, check whether it overlaps a cCRE, find which TF motifs it disrupts, and predict its effect size on expression with a sequence-based model.
Quick Start
Ask the agent to determine whether a specific SNP overlaps a regulatory element and predict its effect on gene expression using ENCODE, RegulomeDB, and sequence-based models.
