tooluniverse-gene-regulatory-networks

• SKILL.mdcore · 11,357 bytes

# Gene Regulatory Network Analysis

**GRN inference starts with: which TF regulates which gene?** Direct evidence (ChIP-seq binding) is stronger than indirect (co-expression correlation). A TF binding near a gene doesn't prove regulation — check if expression changes when the TF is perturbed. JASPAR provides binding motifs but motif presence in a promoter is only computational evidence (T3); ENCODE ChIP-seq data that places the TF at the locus in the relevant cell type is stronger (T1). eQTLs from GTEx show which variants affect expression but don't identify the upstream regulator — combine with TF motif disruption analysis for mechanistic insight.

**LOOK UP DON'T GUESS**: never assume JASPAR matrix IDs, Enrichr library names, or GTEx tissue identifiers — always search JASPAR by TF name and verify library names before calling enrichr.

## When to Use

Activate this skill when the user asks about:
- Transcription factor (TF) binding sites, motifs, or target genes
- Gene regulatory networks or transcriptional regulation
- Chromatin state and histone modifications in regulatory context
- TF-target relationships and co-regulation
- eQTL effects on gene regulation