NetAn: A Python Toolbox Leveraging Network Topology for Comprehensive Gene Annotation Enrichments

Abstract

Summary: Gene annotation enrichment analysis is the gold standard for studying the biological context of a set of genes, but available tools often overlook important network properties of the underlying gene regulatory system. This paper introduces the NETwork ANnotation enrichment package, NetAn, which augments annotation analysis with approaches such as the inference of closely related genes to include local neighbors in the analysis, and the separation of over-representation analyses based on network clustering, cliques, and the extraction of separate components. By using NetAn, an example of how such approaches enhance the identification of pertinent annotations in human gene sets is demonstrated. Availability and Implementation: The software is implemented in Python under a GNU GENERAL PUBLIC LICENSE V3, and can be downloaded from https://github.com/rasma774/netan. Contact: rasmus.magnusson@his.se Supplementary Information: The code relevant to this article is available in the doc/article_material folder of the NetAn repository.