SubcellulaRVis: a web-based tool to simplify and visualise subcellular compartment enrichment

Abstract

Cells contain intracellular compartments, including membrane-bound organelles and the nucleus, and are surrounded by a plasma membrane. Proteins are localised to one or more of these cellular compartments; the correct localisation of proteins is crucial for their correct processing and function. Moreover, proteins and the cellular processes they partake in are regulated by relocalisation in response to various cellular stimuli. High-throughput ‘omics experiments result in a list of proteins or genes of interest; one way in which their functional role can be understood is through the knowledge of their subcellular localisation, as deduced through statistical enrichment for Gene Ontology Cellular Component (GOCC) annotations or similar. We have designed a bioinformatics tool, named SubcellulaRVis, that compellingly visualises the results of GOCC enrichment for quick interpretation of the localisation of a group of proteins (rather than single proteins). We demonstrate that SubcellulaRVis precisely describes the subcellular localisation of gene lists whose locations have been previously ascertained. SubcellulaRVis can be accessed via the web (http://phenome.manchester.ac.uk/subcellular/) or as a stand-alone app (https://github.com/JoWatson2011/subcellularvis). SubcellulaRVis will be useful for experimental biologists with limited bioinformatics expertise who want to analyse data related to protein (re)localisation and location-specific modules within the intracellular protein network.

Filming space-time changes of gene expression with expressyouRcell

“…A handful of tools with alternative representation methods [11][12][13][14][15] have already been proposed, but at the time of this writing, there are no comparable alternatives to expressyouRcell. In fact, our tool addresses the data visualization problem in a different and novel approach compared to existing ones [11][12][13][14][15] .…”

“…subcellulaRVis is a web R-based application which performs and visualizes results from enrichment analysis. This tool provides the users with two graphical options: a generic cellular pictograph and a more specific visualization of the endosomal system 12 which is particularly useful to represent detailed and specific information for the endosomal compartments. The user-friendly web page interface offers the possibilities of performing enrichment analysis also to less-experienced users, and of generating easy-to-interpret graphical results.…”

“…A handful of tools with alternative representation methods [11][12][13][14][15] have already been proposed, but at the time of this writing, there are no comparable alternatives to expressyouRcell. In fact, our tool addresses the data visualization problem in a different and novel approach compared to existing ones [11][12][13][14][15] . It gives the unique possibility of creating dynamic illustrations, which can effectively support researchers in tracking the fluctuations in gene expression levels across multiple time points and reduces the complexity of biological information.…”

“…Dedicated graphical tools have been proposed as means to represent biological information through graphical approaches in the past [11][12][13][14][15] . Available web applications, such as GeneCards, UniProt or Human Protein Atlas 11,14,15 mainly consist of a user-friendly front-end for exploring gene and protein expression data obtained from experiments performed in various tissues, cell types and species.…”

“…However, this tool requires a series of advanced computational steps to handle and visualize the user’s own data 13 . Recently, an R-based application has been proposed to compute and represent results from enrichment analyses through pictographs 12 , but none of these tools reduce the biological complexity of results from sophisticated experimental designs. The lack of efficient tools for next-generation data exploitation is an urgent need in biology today.…”