Intervene: a tool for intersection and visualization of multiple gene or genomic region sets

Aziz Khan,Anthony Mathelier

doi:10.1186/s12859-017-1708-7

Aziz Khan, Anthony Mathelier

Open Access

https://doi.org/10.1186/s12859-017-1708-7

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Journal: BMC Bioinformatics	Publication Date: May 31, 2017
Citations: 379	License type: open-access

Affiliation: University of Oslo, Oslo University Hospital

Abstract

BackgroundA common task for scientists relies on comparing lists of genes or genomic regions derived from high-throughput sequencing experiments. While several tools exist to intersect and visualize sets of genes, similar tools dedicated to the visualization of genomic region sets are currently limited.ResultsTo address this gap, we have developed the Intervene tool, which provides an easy and automated interface for the effective intersection and visualization of genomic region or list sets, thus facilitating their analysis and interpretation. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. Intervene, and its interactive web ShinyApp companion, generate publication-quality figures for the interpretation of genomic region and list sets.ConclusionsIntervene and its web application companion provide an easy command line and an interactive web interface to compute intersections of multiple genomic and list sets. They have the capacity to plot intersections using easy-to-interpret visual approaches. Intervene is developed and designed to meet the needs of both computer scientists and biologists. The source code is freely available at https://bitbucket.org/CBGR/intervene, with the web application available at https://asntech.shinyapps.io/intervene.

Highlights

A common task for scientists relies on comparing lists of genes or genomic regions derived from high-throughput sequencing experiments
We developed Intervene, an easyto-use command line tool to compute and visualize intersections of genomic regions with Venn diagrams, UpSet plots, or clustered heat maps
Intervene produces results as text files, which can be imported to the web application for interactive visualization and customization of plots

Summary

Introduction

A common task for scientists relies on comparing lists of genes or genomic regions derived from high-throughput sequencing experiments. Most of the data sets generated by such assays are lists of genes or variants, and genomic region sets. The intersection or overlap between different sets, such as gene lists, is represented by Venn diagrams [1] or Edwards-Venn [2]. The UpSet plots, was introduced to depict the intersection of more than three sets [3]. With a large number of sets, UpSet plots become an ineffective way of illustrating set intersections. To visualize a large number of sets, one can represent pairwise intersections using a clustered heat map as suggested in [4]

Results

Discussion

Conclusion