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

Kerouanton, Baptiste, Schäfer, Sebastian, Ho, Lena, Chothani, Sonia and Rackham, Owen J.L. , Ponty, Yann (ed.) (2022) CLIPreg: constructing translational regulatory networks from CLIP-, Ribo- and RNA-seq. Bioinformatics, 38 (14), 3651-3653. (doi:10.1093/bioinformatics/btac363).

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 CLIPsequencing 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.

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Contributors

Author: Owen J.L. Rackham

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