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Simona P, Panneerselvam K, Porras P, Duesbury M, Perfetto L, Licata L, Hermjakob H, Orchard S. The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study. Database (Oxford) 2023; 2023:baad066. [PMID: 37819683 PMCID: PMC10566539 DOI: 10.1093/database/baad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/29/2023] [Accepted: 09/15/2023] [Indexed: 10/13/2023]
Abstract
In recent years, a huge amount of data on ncRNA interactions has been described in scientific papers and databases. Although considerable effort has been made to annotate the available knowledge in public repositories, there are still significant discrepancies in how different resources capture and interpret data on ncRNA functional and physical associations. In the present paper, we present a collection of microRNA-mRNA interactions annotated from the scientific literature following recognized standard criteria and focused on microRNAs, which regulate genes associated with rare diseases as a case study. The list of protein-coding genes with a known role in specific rare diseases was retrieved from the Genome England PanelApp, and associated microRNA-mRNA interactions were annotated in the IntAct database and compared with other datasets. RNAcentral identifiers were used for unambiguous, stable identification of ncRNAs. The information about the interaction was enhanced by a detailed description of the cell types and experimental conditions, providing a computer-interpretable summary of the published data, integrated with the huge amount of protein interactions already gathered in the database. Furthermore, for each interaction, the binding sites of the microRNA are precisely mapped on a well-defined mRNA transcript of the target gene. This information is crucial to conceive and design optimal microRNA mimics or inhibitors to interfere in vivo with a deregulated process. As these approaches become more feasible, high-quality, reliable networks of microRNA interactions are needed to help, for instance, in the selection of the best target to be inhibited and to predict potential secondary off-target effects. Database URL https://www.ebi.ac.uk/intact.
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Affiliation(s)
- Panni Simona
- Dipartimento di Biologia Ecologia e Scienze della Terra, Università della Calabria, Rende 87036, Italy
| | - Kalpana Panneerselvam
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus Hinxton, Cambridge CB10 1SD, UK
| | - Pablo Porras
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus Hinxton, Cambridge CB10 1SD, UK
- Astra Zeneca, Data Office, Data Science and AI, UK Academy House, 136 Hills Road, Cambridge CB2 8PA, UK
| | - Margaret Duesbury
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus Hinxton, Cambridge CB10 1SD, UK
| | - Livia Perfetto
- Department of Biology and Biotechnologies “Charles Darwin”, La Sapienza University, Rome, Italy
| | - Luana Licata
- Department of Biology, University of Tor Vergata, Rome, Italy
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus Hinxton, Cambridge CB10 1SD, UK
| | - Sandra Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus Hinxton, Cambridge CB10 1SD, UK
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Mazzuero A, Simona P, Minacci V, Candusso MG, Tommasi SCA, Lupi A. P423Use of short leads for the implantation of dual-chamber pacemakers. Europace 2017. [DOI: 10.1093/ehjci/eux141.147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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