ANANASTRA

ANANASTRA annotates regulatory single-nucleotide polymorphisms (SNPs) by identifying allele-specific binding (ASB) events from ChIP-Seq data and testing their enrichment to assess functional regulatory effects.

Key Features:

• Input Flexibility: Accepts dbSNP IDs or Variant Call Format (VCF) files as input.
• Allele-Specific Binding Analysis: Identifies ASB sites for specific transcription factors across various cell types by detecting allelic imbalances in ChIP-Seq data.
• Enrichment Testing: Performs enrichment tests by comparing ASBs in the query SNP list to background SNP sets derived from the same ChIP-Seq experiments lacking significant allelic imbalance.
• Systematic Approach: Builds on a systematic analysis of allelic imbalances observed in ChIP-Seq experiments to nominate regulatory SNPs.

Scientific Applications:

• GWAS follow-up: Prioritizes SNPs with allele-specific binding to formulate functional hypotheses for variants identified in genome-wide association studies.
• Experimental prioritization: Guides selection of candidate regulatory variants for downstream experimental validation based on ASB evidence and enrichment results.

Methodology:

Analyzes ChIP-Seq data to detect allelic imbalances indicative of allele-specific binding and compares SNPs with significant ASBs to background SNP sets from the same experiments for enrichment testing.