CLIPreg: constructing translational regulatory networks from CLIP-, Ribo- and RNA-seq

Abstract

Abstract Motivation The creation and analysis of gene regulatory networks have been the focus of bioinformatics research and underpins much of what is known about gene regulation. However, as a result of a bias in the availability of data types that are collected, the vast majority of gene regulatory network resources and tools have focused on either transcriptional regulation or protein–protein interactions. This has left other areas of regulation, for instance, translational regulation, vastly underrepresented despite them having been shown to play a critical role in both health and disease. Results In order to address this, we have developed CLIPreg, a package that integrates RNA, Ribo and CLIP- sequencing data in order to construct translational regulatory networks coordinated by RNA-binding proteins and micro-RNAs. This is the first tool of its type to be created, allowing for detailed investigation into a previously unseen layer of regulation. Availability and implementation CLIPreg is available at https://github.com/SGDDNB/CLIPreg. Supplementary information Supplementary data are available at Bioinformatics online.