W-ChIPeaks

W-ChIPeaks identifies peaks in ChIP-chip and ChIP-seq data and annotates transcription factor binding sites to support studies of transcriptional regulation.

Key Features:

• Support for ChIP-chip and ChIP-seq: Processes data from ChIP-chip (hybridization with spotted or tiling microarrays) and ChIP-seq (paired-end tag sequencing and massively parallel sequencing).
• Probe-based/Bin-based enrichment threshold: Uses probe-based or bin-based enrichment thresholds to define peaks in ChIP data.
• PELT module for ChIP-chip: Applies PELT optimized for array hybridization data from spotted or tiling microarrays.
• BELT module for ChIP-seq: Applies BELT for paired-end tag sequencing and massively parallel sequencing data.
• Statistical FDR control: Implements statistical methods to control the false discovery rate of identified peaks.
• Output formats: Exports peak and signal data in GFF, BED, bedGraph, and .wig formats.
• Gene annotation: Associates identified peaks with related genes for downstream interpretation.
• Validation on published datasets: Methods have been tested using previously published experimental datasets.

Scientific Applications:

• Transcription factor profiling: Identification and annotation of transcription factor binding sites from ChIP-chip and ChIP-seq experiments.
• Transcriptional regulation studies: Support for analyses aimed at elucidating transcriptional regulation mechanisms in living cells.
• Gene regulatory network analysis: Enabling inference of regulatory interactions by linking peaks to genes.
• Downstream integrative analyses: Generation of GFF, BED, bedGraph, and .wig outputs for integration with genome browsers and other computational workflows.

Methodology:

Peak calling using probe-based or bin-based enrichment thresholds; PELT for ChIP-chip (spotted/tiling microarrays) and BELT for ChIP-seq (paired-end tag and massively parallel sequencing); statistical methods to control FDR; export to GFF, BED, bedGraph, and .wig; peak-to-gene annotation; validation on published datasets.