GPSmatch

GPSmatch compares ChIP-Seq genomic-binding profiles to quantify similarity among transcriptional regulators and support identification of shared regulatory interactions.

Key Features:

• Jaccard Index Calculation: Employs the Jaccard index to quantify overlap between ChIP-Seq peaks from different experiments.
• Customizable Database Integration: Accepts a user-supplied customizable database of experimental ChIP-Seq peak sets for comparison against a target dataset.
• Statistical Significance Evaluation: Assesses significance of Jaccard indices using a nonparametric Monte Carlo procedure.
• Ranking and Identification: Identifies and ranks transcriptional regulators by similarity of genomic-binding profiles based on similarity indices and significance.
• Implementation: Distributed as an R package for computational analysis of genomic-binding profile similarity.

Scientific Applications:

• Transcriptional Regulation Analysis: Enables analysis of how transcriptional regulators coordinate or compete by sharing genomic-binding sites derived from ChIP-Seq experiments.
• Data Integration Across Studies: Facilitates meta-analysis by integrating ChIP-Seq datasets from multiple studies to consolidate findings about transcriptional regulation.

Methodology:

Calculates the Jaccard index between ChIP-Seq peaks from a target experiment and entries in a user-defined database, then applies a nonparametric Monte Carlo procedure to assess significance and rank regulators by similarity.