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Front. Genet. | doi: 10.3389/fgene.2019.00421

DiVenn: An Interactive and Integrated Web-based Visualization Tool for Comparing Gene Lists

  • 1Noble Research Institute, LLC, United States
  • 2Noble Research Institute, LLC, United States
  • 3Agricultural University of Hebei, China

Gene expression data generated from multiple biological samples (mutant, double mutant and wild-type) are often compared via Venn diagram tools. It is of great interest to know the expression pattern between overlapping genes and their associated gene pathways or gene ontology (GO) terms. We developed DiVenn (Dive into the Venn diagram and create a force directed graph) — a novel web-based tool that compares gene lists from multiple RNA-Seq experiments in a force-directed graph, which shows the gene regulation levels for each gene and integrated KEGG pathway and gene ontology knowledge for the data visualization. DiVenn has four key features: (i) informative force-directed graph with gene expression levels to compare multiple data sets; (ii) interactive visualization with biological annotations and integrated pathway and GO databases, which can be used to subset or highlight gene nodes to pathway or GO terms of interest in the graph; (iii) Pathway and GO enrichment analysis of all or selected genes in the graph; and (iv) high resolution image and gene-associated information export. DiVenn is freely available at http://divenn.noble.org/.

Keywords: Venn diagram, visualization, Transcriptome data, KEGG, gene ontology, pathogen infection

Received: 01 Feb 2019; Accepted: 17 Apr 2019.

Edited by:

Alfredo Pulvirenti, Università degli Studi di Catania, Italy

Reviewed by:

Andreas Dräger, University of Tübingen, Germany
Fuliang Xie, Qiagen (United States), United States  

Copyright: © 2019 Sun, Dong, Ge, Fonseca, Robinson, Mysore and Mehta. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Liang Sun, Noble Research Institute, LLC, Ardmore, United States, lsun@noble.org