ShinyBioHEAT: an interactive shiny app to identify phenotype driver genes in E.coli and B.subtilis

• Published in: Bioinformatics (Oxford, England) Vol. 39; no. 8
• Main Authors: Wang, Chen, Govindarajan, Harikumar, Katsonis, Panagiotis, Lichtarge, Olivier
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.08.2023
• Subjects: Applications Note; Data Interpretation, Statistical; Escherichia coli - genetics; Mobile Applications; Mutation; Mutation Rate; Software
• DOI: 10.1093/bioinformatics/btad467
• ISSN: 1367-4811; 1367-4803

Abstract Summary In any population under selective pressure, a central challenge is to distinguish the genes that drive adaptation from others which, subject to population variation, harbor many neutral mutations de novo. We recently showed that such genes could be identified by supplementing information on mutational frequency with an evolutionary analysis of the likely functional impact of coding variants. This approach improved the discovery of driver genes in both lab-evolved and environmental Escherichia coli strains. To facilitate general adoption, we now developed ShinyBioHEAT, an R Shiny web-based application that enables identification of phenotype driving gene in two commonly used model bacteria, E.coli and Bacillus subtilis, with no specific computational skill requirements. ShinyBioHEAT not only supports transparent and interactive analysis of lab evolution data in E.coli and B.subtilis, but it also creates dynamic visualizations of mutational impact on protein structures, which add orthogonal checks on predicted drivers. Availability and implementation Code for ShinyBioHEAT is available at https://github.com/LichtargeLab/ShinyBioHEAT. The Shiny application is additionally hosted at http://bioheat.lichtargelab.org/.