{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T08:09:46Z","timestamp":1770970186460,"version":"3.50.1"},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,3,4]],"date-time":"2024-03-04T00:00:00Z","timestamp":1709510400000},"content-version":"vor","delay-in-days":42,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Spanish Ministry of Economy and Competitiveness","award":["PID2019-108096RB-C21"],"award-info":[{"award-number":["PID2019-108096RB-C21"]}]},{"name":"Spanish Ministry of Economy and Competitiveness","award":["PID2022-140047OB-C21"],"award-info":[{"award-number":["PID2022-140047OB-C21"]}]},{"DOI":"10.13039\/501100004587","name":"Institute of Health Carlos III","doi-asserted-by":"publisher","award":["IMP\/00019"],"award-info":[{"award-number":["IMP\/00019"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"name":"EURAS","award":["101080580"],"award-info":[{"award-number":["101080580"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>A wide range of approaches can be used to detect micro RNA (miRNA)\u2013target gene pairs (mTPs) from expression data, differing in the ways the gene and miRNA expression profiles are calculated, combined and correlated. However, there is no clear consensus on which is the best approach across all datasets. Here, we have implemented multiple strategies and applied them to three distinct rare disease datasets that comprise smallRNA-Seq and RNA-Seq data obtained from the same samples, obtaining mTPs related to the disease pathology. All datasets were preprocessed using a standardized, freely available computational workflow, DEG_workflow. This workflow includes coRmiT, a method to compare multiple strategies for mTP detection. We used it to investigate the overlap of the detected mTPs with predicted and validated mTPs from 11 different databases. Results show that there is no clear best strategy for mTP detection applicable to all situations. We therefore propose the integration of the results of the different strategies by selecting the one with the highest odds ratio for each miRNA, as the optimal way to integrate the results. We applied this selection-integration method to the datasets and showed it to be robust to changes in the predicted and validated mTP databases. Our findings have important implications for miRNA analysis. coRmiT is implemented as part of the ExpHunterSuite Bioconductor package available from https:\/\/bioconductor.org\/packages\/ExpHunterSuite.<\/jats:p>","DOI":"10.1093\/bib\/bbae060","type":"journal-article","created":{"date-parts":[[2024,3,4]],"date-time":"2024-03-04T13:43:36Z","timestamp":1709559816000},"source":"Crossref","is-referenced-by-count":4,"title":["Exploring miRNA\u2013target gene pair detection in disease with coRmiT"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1821-5742","authenticated-orcid":false,"given":"Jose","family":"Cordoba-Caballero","sequence":"first","affiliation":[{"name":"Departamento de Biolog\u00eda Molecular y Bioqu\u00edmica , Facultad de Ciencias, , Bulevar Louis Pasteur, 31, M\u00e1laga, 29010 , Spain"},{"name":"Universidad de M\u00e1laga , Facultad de Ciencias, , Bulevar Louis Pasteur, 31, M\u00e1laga, 29010 , Spain"},{"name":"Research Unit , Biomedical Research and Innovation Institute of C\u00e1diz (INiBICA), , C\u00e1diz , Spain"},{"name":"Puerta del Mar University Hospital , Biomedical Research and Innovation Institute of C\u00e1diz (INiBICA), , C\u00e1diz , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4108-096X","authenticated-orcid":false,"given":"James R","family":"Perkins","sequence":"additional","affiliation":[{"name":"Departamento de Biolog\u00eda Molecular y Bioqu\u00edmica , Facultad de Ciencias, , Bulevar Louis Pasteur, 31, M\u00e1laga, 29010 , Spain"},{"name":"Universidad de M\u00e1laga , Facultad de Ciencias, , Bulevar Louis Pasteur, 31, M\u00e1laga, 29010 , Spain"},{"name":"Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND) , C\/ Severo Ochoa, 35, Parque Tecnol\u00f3gico de Andaluc\u00eda (PTA), Campanillas, M\u00e1laga, 29590 , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5123-8348","authenticated-orcid":false,"given":"Federico","family":"Garc\u00eda-Criado","sequence":"additional","affiliation":[{"name":"Departamento de Biolog\u00eda Molecular y Bioqu\u00edmica , Facultad de Ciencias, , Bulevar Louis Pasteur, 31, M\u00e1laga, 29010 , Spain"},{"name":"Universidad de M\u00e1laga , Facultad de Ciencias, , Bulevar Louis Pasteur, 31, M\u00e1laga, 29010 , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3866-7316","authenticated-orcid":false,"given":"Diana","family":"Gallego","sequence":"additional","affiliation":[{"name":"CIBER de Enfermedades Raras (CIBERER) , Avda. Monforte de Lemos, 3-5, Pabell\u00f3n 11, Planta 0, Madrid, 28029 , Spain"},{"name":"Centro de Diagn\u00f3stico de Enfermedades Moleculares, Centro de Biolog\u00eda Molecular-SO UAM-CSIC, Universidad Aut\u00f3noma de Madrid , Campus de Cantoblanco, Madrid , Spain"},{"name":"Instituto de Investigaci\u00f3n Sanitaria IdiPaZ , Madrid , Spain"}]},{"given":"Alicia","family":"Navarro-S\u00e1nchez","sequence":"additional","affiliation":[{"name":"CIBER de Enfermedades Raras (CIBERER) , Avda. Monforte de Lemos, 3-5, Pabell\u00f3n 11, Planta 0, Madrid, 28029 , Spain"},{"name":"Departament de Fisiologia , Facultat de Medicina i Odontologia, , Av. Blasco Ib\u00e1\u00f1ez 15, 46010, Val\u00e8ncia , Spain"},{"name":"Universitat de Val\u00e8ncia , Facultat de Medicina i Odontologia, , Av. Blasco Ib\u00e1\u00f1ez 15, 46010, Val\u00e8ncia , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8759-8794","authenticated-orcid":false,"given":"Mireia","family":"Moreno-Estell\u00e9s","sequence":"additional","affiliation":[{"name":"CIBER de Enfermedades Raras (CIBERER) , Avda. Monforte de Lemos, 3-5, Pabell\u00f3n 11, Planta 0, Madrid, 28029 , Spain"},{"name":"Consejo Superior de Investigaciones Cient\u00edficas, Instituto de Biomedicina de Valencia , Jaime Roig 11, 46010, Valencia , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9903-511X","authenticated-orcid":false,"given":"Concepci\u00f3n","family":"Garc\u00e9s","sequence":"additional","affiliation":[{"name":"CIBER de Enfermedades Raras (CIBERER) , Avda. Monforte de Lemos, 3-5, Pabell\u00f3n 11, Planta 0, Madrid, 28029 , Spain"},{"name":"Departament de Fisiologia , Facultat de Medicina i Odontologia, , Av. Blasco Ib\u00e1\u00f1ez 15, 46010, Val\u00e8ncia , Spain"},{"name":"Universitat de Val\u00e8ncia , Facultat de Medicina i Odontologia, , Av. Blasco Ib\u00e1\u00f1ez 15, 46010, Val\u00e8ncia , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9855-8173","authenticated-orcid":false,"given":"Fernando","family":"Bonet","sequence":"additional","affiliation":[{"name":"Research Unit , Biomedical Research and Innovation Institute of C\u00e1diz (INiBICA), , C\u00e1diz , Spain"},{"name":"Puerta del Mar University Hospital , Biomedical Research and Innovation Institute of C\u00e1diz (INiBICA), , C\u00e1diz , Spain"},{"name":"Medicine Department , School of Medicine, , C\u00e1diz , Spain"},{"name":"University of C\u00e1diz , School of Medicine, , C\u00e1diz , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7981-7157","authenticated-orcid":false,"given":"Carlos","family":"Rom\u00e1-Mateo","sequence":"additional","affiliation":[{"name":"CIBER de Enfermedades Raras (CIBERER) , Avda. Monforte de Lemos, 3-5, Pabell\u00f3n 11, Planta 0, Madrid, 28029 , Spain"},{"name":"Departament de Fisiologia , Facultat de Medicina i Odontologia, , Av. Blasco Ib\u00e1\u00f1ez 15, 46010, Val\u00e8ncia , Spain"},{"name":"Universitat de Val\u00e8ncia , Facultat de Medicina i Odontologia, , Av. Blasco Ib\u00e1\u00f1ez 15, 46010, Val\u00e8ncia , Spain"},{"name":"Incliva Biomedical Research Institute , 46010, Val\u00e8ncia , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3136-1776","authenticated-orcid":false,"given":"Rocio","family":"Toro","sequence":"additional","affiliation":[{"name":"Research Unit , Biomedical Research and Innovation Institute of C\u00e1diz (INiBICA), , C\u00e1diz , Spain"},{"name":"Puerta del Mar University Hospital , Biomedical Research and Innovation Institute of C\u00e1diz (INiBICA), , C\u00e1diz , Spain"},{"name":"Medicine Department , School of Medicine, , C\u00e1diz , Spain"},{"name":"University of C\u00e1diz , School of Medicine, , C\u00e1diz , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3190-1958","authenticated-orcid":false,"given":"Bel\u00e9n","family":"Perez","sequence":"additional","affiliation":[{"name":"CIBER de Enfermedades Raras (CIBERER) , Avda. Monforte de Lemos, 3-5, Pabell\u00f3n 11, Planta 0, Madrid, 28029 , Spain"},{"name":"Centro de Diagn\u00f3stico de Enfermedades Moleculares, Centro de Biolog\u00eda Molecular-SO UAM-CSIC, Universidad Aut\u00f3noma de Madrid , Campus de Cantoblanco, Madrid , Spain"},{"name":"Instituto de Investigaci\u00f3n Sanitaria IdiPaZ , Madrid , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2399-4103","authenticated-orcid":false,"given":"Pascual","family":"Sanz","sequence":"additional","affiliation":[{"name":"CIBER de Enfermedades Raras (CIBERER) , Avda. Monforte de Lemos, 3-5, Pabell\u00f3n 11, Planta 0, Madrid, 28029 , Spain"},{"name":"Consejo Superior de Investigaciones Cient\u00edficas, Instituto de Biomedicina de Valencia , Jaime Roig 11, 46010, Valencia , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9514-8910","authenticated-orcid":false,"given":"Matthias","family":"Kohl","sequence":"additional","affiliation":[{"name":"Faculty of Medical and Life Sciences , Furtwangen University , Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2678-710X","authenticated-orcid":false,"given":"Elena","family":"Rojano","sequence":"additional","affiliation":[{"name":"Departamento de Biolog\u00eda Molecular y Bioqu\u00edmica , Facultad de Ciencias, , Bulevar Louis Pasteur, 31, M\u00e1laga, 29010 , Spain"},{"name":"Universidad de M\u00e1laga , Facultad de Ciencias, , Bulevar Louis Pasteur, 31, M\u00e1laga, 29010 , Spain"},{"name":"Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND) , C\/ Severo Ochoa, 35, Parque Tecnol\u00f3gico de Andaluc\u00eda (PTA), Campanillas, M\u00e1laga, 29590 , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3020-1415","authenticated-orcid":false,"given":"Pedro","family":"Seoane","sequence":"additional","affiliation":[{"name":"Departamento de Biolog\u00eda Molecular y Bioqu\u00edmica , Facultad de Ciencias, , Bulevar Louis Pasteur, 31, M\u00e1laga, 29010 , Spain"},{"name":"Universidad de M\u00e1laga , Facultad de Ciencias, , Bulevar Louis Pasteur, 31, M\u00e1laga, 29010 , Spain"},{"name":"Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND) , C\/ Severo Ochoa, 35, Parque Tecnol\u00f3gico de Andaluc\u00eda (PTA), Campanillas, M\u00e1laga, 29590 , Spain"},{"name":"CIBER de Enfermedades Raras (CIBERER) , Avda. Monforte de Lemos, 3-5, Pabell\u00f3n 11, Planta 0, Madrid, 28029 , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0327-1837","authenticated-orcid":false,"given":"Juan A G","family":"Ranea","sequence":"additional","affiliation":[{"name":"Departamento de Biolog\u00eda Molecular y Bioqu\u00edmica , Facultad de Ciencias, , Bulevar Louis Pasteur, 31, M\u00e1laga, 29010 , Spain"},{"name":"Universidad de M\u00e1laga , Facultad de Ciencias, , Bulevar Louis Pasteur, 31, M\u00e1laga, 29010 , Spain"},{"name":"Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND) , C\/ Severo Ochoa, 35, Parque Tecnol\u00f3gico de Andaluc\u00eda (PTA), Campanillas, M\u00e1laga, 29590 , Spain"},{"name":"CIBER de Enfermedades Raras (CIBERER) , Avda. Monforte de Lemos, 3-5, Pabell\u00f3n 11, Planta 0, Madrid, 28029 , Spain"},{"name":"Instituto Nacional de Bioinform\u00e1tica (INB\/ELIXIR-ES), Instituto de Salud Carlos III (ISCIII) , C\/ Sinesio Delgado, 4, Madrid, 28029 , Spain"}]}],"member":"286","published-online":{"date-parts":[[2024,3,2]]},"reference":[{"issue":"10","key":"2024030413432475700_ref1","doi-asserted-by":"crossref","first-page":"e1008755","DOI":"10.1371\/journal.pcbi.1008755","article-title":"Network potential identifies therapeutic miRNA cocktails in Ewing sarcoma","volume":"17","author":"Weaver","year":"2021","journal-title":"PLoS Comput Biol"},{"key":"2024030413432475700_ref2","doi-asserted-by":"crossref","first-page":"20218","DOI":"10.1038\/s41598-020-76995-2","article-title":"Circulating miRNA-181b-5p, miRNA-223-3p, miRNA-210-3p, let 7i-5p, miRNA-21-5p and miRNA-29a-3p in patients with localized scleroderma as potential biomarkers","volume":"10","author":"Wolska-Gawron","year":"2020","journal-title":"Sci Rep"},{"issue":"1","key":"2024030413432475700_ref3","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1186\/s13058-020-01295-6","article-title":"Secreted breast tumor interstitial fluid microRNAs and their target genes are associated with triple-negative breast cancer, tumor grade, and immune infiltration","volume":"22","author":"Terkelsen","year":"2020","journal-title":"Breast Cancer Res"},{"issue":"4","key":"2024030413432475700_ref4","doi-asserted-by":"crossref","first-page":"1465","DOI":"10.1093\/bib\/bbz082","article-title":"Critical microRNAs and regulatory motifs in cleft palate identified by a conserved miRNA-TF-gene network approach in humans and mice","volume":"21","author":"Li","year":"2020","journal-title":"Brief Bioinform"},{"key":"2024030413432475700_ref5","doi-asserted-by":"crossref","first-page":"6635925","DOI":"10.1155\/2021\/6635925","article-title":"Whole-transcriptome RNA sequencing reveals significant differentially expressed mRNAs, miRNAs, and lncRNAs and related regulating biological pathways in the peripheral blood of COVID-19 patients","volume":"2021","author":"Li","year":"2021","journal-title":"Mediators Inflamm"},{"issue":"6472","key":"2024030413432475700_ref6","doi-asserted-by":"crossref","first-page":"eaav1741","DOI":"10.1126\/science.aav1741","article-title":"The biochemical basis of microRNA targeting efficacy","volume":"366","author":"McGeary","year":"2019","journal-title":"Science"},{"issue":"10","key":"2024030413432475700_ref7","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1038\/ng2135","article-title":"The role of site accessibility in microRNA target recognition","volume":"39","author":"Kertesz","year":"2007","journal-title":"Nat Genet"},{"issue":"1","key":"2024030413432475700_ref8","doi-asserted-by":"crossref","first-page":"R1","DOI":"10.1186\/gb-2003-5-1-r1","article-title":"MicroRNA targets in drosophila","volume":"5","author":"Enright","year":"2003","journal-title":"Genome Biol"},{"issue":"1","key":"2024030413432475700_ref9","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-019-1629-z","article-title":"Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data","volume":"20","author":"Liu","year":"2019","journal-title":"Genome Biol"},{"key":"2024030413432475700_ref10","volume-title":"MicroRNA Target Identification: Methods and Protocols. 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