catRAPID omics: a web server for large-scale prediction of protein-RNA interactions

Abstract

Summary: Here we introduce catRAPID omics, a server for large-scale calculations of protein-RNA interactions. Our web server allows (i) predictions at proteomic and transcriptomic level; (ii) use of protein and RNA sequences without size restriction; (iii) analysis of nucleic acid binding regions in proteins; and (iv) detection of RNA motifs involved in protein recognition.

Results: We developed a web server to allow fast calculation of ribonucleoprotein associations in Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae and Xenopus tropicalis (custom libraries can be also generated). The catRAPID omics was benchmarked on the recently published RNA interactomes of Serine/arginine-rich splicing factor 1 (SRSF1), Histone-lysine N-methyltransferase EZH2 (EZH2), TAR DNA-binding protein 43 (TDP43) and RNA-binding protein FUS (FUS) as well as on the protein interactomes of U1/U2 small nucleolar RNAs, X inactive specific transcript (Xist) repeat A region (RepA) and Crumbs homolog 3 (CRB3) 3'-untranslated region RNAs. Our predictions are highly significant (P < 0.05) and will help the experimentalist to identify candidates for further validation.

Availability: catRAPID omics can be freely accessed on the Web at http://s.tartaglialab.com/catrapid/omics. Documentation, tutorial and FAQs are available at http://s.tartaglialab.com/page/catrapid_group.

Fig. 1.

catRAPID omics features and performances. (A) Example of the output table showing Z-score (interaction propensity normalized with respect to experimental cases), discriminative power (with respect to training sets), interaction strength (enrichment with respect to random interactions) and presence of RNA binding domains as well as RNA motifs. Interaction scores are ranked according to a ‘star rating system’ ranging from 0 to 3 (http://service.tartaglialab.com/static_files/shared/faqs.html). A click on the text redirects to reference pages. Performances on (B) full-length proteins and (C) RNA binding protein domains. Gray is used to highlight transcriptomic studies (i.e. RNA sequencing) and red indicates proteomic analyses (i.e. mass spectrometry). The significance of our predictions was assessed using Fisher’s exact test (the dashed line corresponds to P = 0.05)