Haystack

Haystack identifies hotspots of epigenetic variability and cell-type-specific cis-regulatory elements and associates them with transcription factor motifs to elucidate gene expression regulation and cell identity.

Key Features:

• Epigenetic Variability Analysis: Pinpoints hotspots of epigenetic variability among different cell types.
• Cis-Regulatory Element Identification: Identifies cell-type-specific cis-regulatory elements and regulatory DNA sequences across multiple cell types.
• Transcription Factor Association: Associates identified regulatory sequences with relevant transcription factors and motifs.
• Applicability to Various Epigenetic Marks: Applies to any epigenetic mark for analysis across diverse datasets.
• Precomputed Tracks for Functional Annotation: Provides precomputed tracks for functional annotation of the human genome.

Scientific Applications:

• Investigating Epigenetic Switches: Enables exploration of mechanisms underlying epigenetic switches during development by mapping variable epigenetic regions.
• Functional Genomics Research: Supports identification of regulatory elements and their transcription factors to dissect gene regulation networks.
• Cell Identity Studies: Facilitates analysis of cell-type-specific regulatory sequences to study cellular identity and differentiation.

Methodology:

Haystack employs a systematic computational approach that integrates public-domain genomic and epigenomic datasets and is implemented as an open-source Python package.