KBase: RNA-Seq Expression Analysis Made Easy Using the Narrative Interface

The U.S Department of Energy Systems Biology Knowledgebase (KBase, http://kbase.us) provides an open, web-accessible system for systems biology research focused on microbes, plants and their communities. It offers access to a range of integrated biological data types and a variety of analysis tools that include modeling, simulation methods and visualizations.

KBase allows users to integrate new analysis tools and data, and supports a rich set of computational methods and curated datasets for gene expression analysis based on RNA-seq. This includes a selection of preprocessed high-quality reference genomes and a wide variety of algorithms for short-read mapping, identification of splice junctions, differential expression analysis, and visualization. More specifically, KBase supports the original and new Tuxedo suite of tools, including Bowtie2, TopHat2, HISAT2, Cufflinks, StringTie, Cuffdiff, and CummeRbund.

KBase also provides services that are compatible with gene expression profiles to do downstream analysis including clustering of expression profiles using different clustering algorithms. The RNA-seq analysis services are available from within a highly interactive user interface called the Narrative Interface that supports the creation of dynamic workflow documents called Narratives. Within a Narrative, short reads from an RNA-seq experiment can be uploaded into KBase to perform gene expression analysis and the results can be shared such that the research can be reproduced and extended by others in the KBase community. We demonstrate the utility of Narratives by performing a point-and-click, yet detailed analysis of public RNA-seq data from several species and tissue types, including experiments in A. thaliana, P. trichocarpa, and E. coli.