GPSmatch: An R Package for Comparing Genomic-binding Profile Similarity among Transcriptional Regulators using Customizable Databases.

SUMMARY: Eukaryotic gene expression requires coordination among hundreds of transcriptional regulators. To characterize a specific transcriptional regulator, identifying how it shares genomic-binding profiles with others can generate important insights into its action. As genomic data such as ChIP-Seq are being rapidly generated from individual labs, there is a demand for timely integration and analysis of these new data. We have developed an R package, GPSmatch (Genomic-binding Profile Similarity match), for calculating the Jaccard index to compare ChIP-Seq peaks from one experiment to the peaks of other ChIP-Seq experiments stored in a user-supplied customizable database. GPSmatch also evaluates the statistical significance of the calculated Jaccard index using a nonparametric Monte Carlo procedure. We show that GPSmatch is suitable for identifying transcriptional regulators that share similar genomic-binding profiles, which may unravel potential mechanistic actions of gene regulation. AVAILABILITY: The software is freely available at https://github.com/Bao-Lab/GPSmatch.