RNAcommender: genome-wide recommendation of RNA-protein interactions

We present RNAcommender, a recommender system capable of suggesting RNA targets to unexplored RNA binding proteins, by propagating the available interaction information taking into account the protein domain composition and the RNA predicted secondary structure. Our results show that RNAcommender is able to successfully suggest RNA interactors for RNA binding proteins using little or no interaction evidence. RNAcommender was tested on a large dataset of human RBP-RNA interactions, showing a good ranking performance (average AUC ROC of 0.75) and significant enrichment of correct recommendations for 75% of the tested RBPs. RNAcommender can be a valid tool to assist researchers in identifying potential interacting candidates for the majority of RBPs with uncharacterized binding preferences.
Availability and Implementation: The software is freely available at http://rnacommender.disi.unitn.it.
Contact: [e-mail] or [e-mail]
Supplementary information: Supplementary data are available at Bioinformatics online.

Source: Bioinformatics - November 28, 2016 Category: Bioinformatics Authors: Corrado, G., Tebaldi, T., Costa, F., Frasconi, P., Passerini, A. Tags: DATA AND TEXT MINING Source Type: research