RESTRING: A SOFTWARE TO MANAGE FUNCTIONAL ENRICHMENT OF COMPLEX EXPERIMENTAL DESIGNS

Background and Aims : Functional enrichment analysis is an analytical method popularized by the ever-growing application of high-throughput techniques to provide biological insights. It tackles the problem of putting overall analyte abundance changes into a broader biological context which represents a daunting task for the average wet-biology researcher. To enable all researchers to explore more easily their data sets, we developed reString, a cross-platform software. Methods: reString (https://github.com/Stemanz/restring), is an opensource software that seamlessly retrieves from STRING functional enrichments from multiple user-supplied gene sets, without any need for specific bioinformatics skills. With a few clicks, it aggregates multiple findings into human-readable table summaries, and user-customizable, publication-grade clustermaps and bubble plots. Everything is managed through reString’s straightforward graphical user interface in just a few clicks and seconds of processing times. The software is backed with a comprehensive online documentation, YouTube installation tutorials, sample input files, online support, and a Scientific Reports publication. Results: To demonstrate reString features, we profiled RNAseq data from aorta samples of double knockout Apoe/Apoa1 (DKO) mice, and DKO expressing human APOA1. Eight-weeks old mice were fed with normal laboratory diet (NLD) or WD for either 6 or 22 weeks. All possible diet, genotype and time comparisons were processed with reString. Conclusions: We developed reString, a cross-platform software with a graphical user interface, written in Python, to enable all researchers the possibility of broadening the exploration of their RNAseq or highthroughput proteomics datasets, effortlessly automating a series of tasks that would be otherwise daunting if performed by hand.