cat RAPID omics: a web server for large-scale prediction of protein–RNA interactions
Open accessAbstract
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. Contact: gian.tartaglia@crg.eu
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catRAPID predicts the binding affinity of protein-RNA pairs.
“catRAPID, an algorithm designed to predict the binding affinity of protein–RNA pairs”
From The mitochondrial long non-coding RNA lncMtloop regulates mitochondrial transcription and suppresses Alzheimer’s disease (2024) · cites this paper as Agostini et al, 2013
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The Pfam protein families database
Finn, R. D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J. E., Gavin, O. L., Gunasekaran, P., Ceric, G., Forslund, K., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp985 · Cited by 2,694 · see citing works
A compendium of RNA-binding motifs for decoding gene regulation
Ray, D., Kazan, H., Cook, K. B., Weirauch, M. T., Najafabadi, H. S., Li, X., Gueroussov, S., Albu, M., Zheng, H., Yang, A., et al. (2013) · Nature · doi:10.1038/nature12311 · Cited by 1,480 · cited 2× · see citing works
“Here we introduce catRAPID omics to perform high-throughput predictions of protein–RNA interactions using the information on protein and RNA domains involved in macromolecular recognition.”
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- Agostini F X-inactivation: quantitative predictions of protein interactions in the Xist network Nucleic Acids Res. 2013 41 e31 23093590 PMC3592426
- Bellucci M Predicting protein associations with long noncoding RNAs Nat. Methods 2011 8 444 445 21623348
- Castello A Insights into RNA biology from an atlas of mammalian mRNA-binding proteins Cell 2012 149 1393 1406 22658674
- Cirillo D Neurodegenerative diseases: quantitative predictions of protein–RNA interactions RNA 2013a 19 129 140 23264567 PMC3543085
- Cirillo D Predictions of protein–RNA interactions Wiley Interdiscip. Rev. Comput. Mol. Sci. 2013b 3 161 175
- Cook KB RBPDB: a database of RNA-binding specificities Nucleic Acids Res. 2011 39 D301 D308 21036867 PMC3013675
- Cvitkovic I Jurica MS Spliceosome database: a tool for tracking components of the spliceosome Nucleic Acids Res. 2012 41 D132 D141 23118483 PMC3531166
- Finn RD HMMER web server: interactive sequence similarity searching Nucleic Acids Res. 2011 39 W29 W37 21593126 PMC3125773
- Giulietti M SpliceAid-F: a database of human splicing factors and their RNA-binding sites Nucleic Acids Res. 2013 41 D125 D131 23118479 PMC3531144
- Han TW Cell-free formation of RNA granules: bound RNAs identify features and components of cellular assemblies Cell 2012 149 768 779 22579282
- Iioka H Efficient detection of RNA-protein interactions using tethered RNAs Nucleic Acids Res. 2011 39 e53 21300640 PMC3082893
- Johnson R Neurodegeneration as an RNA disorder Prog. Neurobiol. 2012 99 293 315 23063563 PMC7116994
- Kazan H RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins PLoS Comput. Biol. 2010 6 e1000832 20617199 PMC2895634
- Khalil AM Rinn JL RNA-protein interactions in human health and disease Semin. Cell Dev. Biol. 2011 22 359 365 21333748 PMC3184770
- Maenner S 2-D structure of the A Region of Xist RNA and its implication for PRC2 association PLoS Biol. 2010 8 e1000276 20052282 PMC2796953
- Muppirala UK Predicting RNA-protein interactions using only sequence information BMC Bioinformatics 2011 12 489 22192482 PMC3322362
- Royce-Tolland ME The A-repeat links ASF/SF2-dependent Xist RNA processing with random choice during X inactivation Nat. Struct. Mol. Biol. 2010 17 948 954 20657585 PMC4336797
- Sanford JR Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts Genome Res. 2009 19 381 394 19116412 PMC2661799
- Sephton CF Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes J. Biol. Chem. 2011 286 1204 1215 21051541 PMC3020728
- Zanzoni A Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein Nucleic Acids Res. 2013 [Epub ahead of print, doi: 10.1093/nar/gkt794, September 3, 2013] PMC3905859 24003031 · DOI
- Zhao J Genome-wide identification of polycomb-associated RNAs by RIP-seq Mol. Cell 2010 40 939 953 21172659 PMC3021903
Cited by
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Xiong, W., Xu, K., Sun, J. K.-L., Liu, S., Zhao, B., Shi, J., Herrup, K., Chow, H.-M., Lu, L., & Li, J. (2024) · The EMBO Journal · doi:10.1038/s44318-024-00270-7 · Cited by 17 · see citing works
“With all existing and known mtDNA transcription factors, prediction using the catRAPID algorithm was performed for potential lncMtDloop interactions based on the physical-chemical properties between the binding partners (Agostini et al, 2013; Bellucci et al, 2011; Livi et al, 2016).”
- Authors
- Agostini, F., Zanzoni, A., Klus, P., Marchese, D., Cirillo, D., & Tartaglia, G. G.
- Affiliations
- Universitat Pompeu Fabra (ES)
- 1 Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Corresponding author
- Tartaglia, Gian Gaetano
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-08-23
- Volume
- 29
- Issue
- 22
- Pages
- 2928-2930
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC3810848
- OpenAlex
- W2108575282
- Cited by
- 313
- References
- 2
- Citations by year
- 2026: 10 · 2025: 16 · 2024: 26 · 2023: 44 · 2022: 28 · 2021: 58 · 2020: 28 · 2019: 22 · 2018: 25 · 2017: 9 · 2016: 16 · 2015: 21 · 2014: 8 · 2013: 1
- FWCI
- 6.87
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Bioinformatics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (publishedVersion, cc-by)
- IRIS Research product catalog (Sapienza University of Rome) (submittedVersion, cc-by)
- RECERCAT (Consorci de Serveis Universitaris de Catalunya) (submittedVersion, cc-by)
- Funders
- Ministerio de Economía y Competitividad
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- RNA-protein interactions, web server, RNA-binding proteins, RNA motifs, RNA interactome, protein-protein interaction network, small nucleolar RNA, XIST, CRB3, SRSF1, EZH2, TDP-43, FUS, Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae, Xenopus tropicalis, mice, rats
- MeSH terms
- Algorithms, Animals, Humans, RNA, Software, RNA-Binding Proteins, Caenorhabditis elegans, Sequence Analysis, RNA, Protein Structure, Tertiary, Internet, 3' Untranslated Regions, Sequence Analysis, Protein, Gene Expression Profiling, Proteomics, Mice, Rats, Nucleotide Motifs
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