PLANAtools - an interactive gene expression repository for the planarian Schmidtea mediterranea

Abstract

MotivationPlanarians are a widespread model for studying regeneration. Major efforts for studying gene function in planarian regeneration produced massive datasets, including transcriptome-wide gene expression analyses from hundreds of conditions. However, the accessibility of gene expression datasets to investigators is limited because of the need for expertise in gene expression analysis in this model, the requirement for computational resources, and the lack of a curated planarian gene expression metadata resource associating samples and their controls. ResultsWe implemented a computational resource, PLANAtools, that is available online and provides a portal to the analysis of over 160 gene expression analyses. Planarian gene expression datasets from the last decade were processed using a standardized pipeline based on curated planarian metadata. PLANAtools generates plots, annotations, and analyses of gene expression data, based on user parameters. AvailabilityPLANAtools is implemented using the R/Shiny framework and is accessible from https://wurtzellab.org/planatools