RNAct: Protein-RNA interaction predictions for model organisms with supporting experimental data

Nucleic Acids Res. 2019 Jan 8;47(D1):D601-D606. doi: 10.1093/nar/gky967.

Abstract

Protein-RNA interactions are implicated in a number of physiological roles as well as diseases, with molecular mechanisms ranging from defects in RNA splicing, localization and translation to the formation of aggregates. Currently, ∼1400 human proteins have experimental evidence of RNA-binding activity. However, only ∼250 of these proteins currently have experimental data on their target RNAs from various sequencing-based methods such as eCLIP. To bridge this gap, we used an established, computationally expensive protein-RNA interaction prediction method, catRAPID, to populate a large database, RNAct. RNAct allows easy lookup of known and predicted interactions and enables global views of the human, mouse and yeast protein-RNA interactomes, expanding them in a genome-wide manner far beyond experimental data (http://rnact.crg.eu).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Databases, Genetic
  • Genomics / methods*
  • Humans
  • Mice
  • Protein Binding
  • Protein Interaction Mapping / methods*
  • Protein Interaction Maps
  • RNA / chemistry
  • RNA / metabolism*
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / metabolism*
  • Software*
  • Yeasts

Substances

  • RNA-Binding Proteins
  • RNA