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miRDB: an online database for prediction of functional microRNA targets
MicroRNAs (miRNAs) are small noncoding RNAs that act as master regulators in many biological processes. miRNAs function mainly by downregulating the expression of their gene targets. Thus, accurate prediction of miRNA targets is critical for characterization of miRNA functions. To this end, we have...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943051/ https://www.ncbi.nlm.nih.gov/pubmed/31504780 http://dx.doi.org/10.1093/nar/gkz757 |
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author | Chen, Yuhao Wang, Xiaowei |
author_facet | Chen, Yuhao Wang, Xiaowei |
author_sort | Chen, Yuhao |
collection | PubMed |
description | MicroRNAs (miRNAs) are small noncoding RNAs that act as master regulators in many biological processes. miRNAs function mainly by downregulating the expression of their gene targets. Thus, accurate prediction of miRNA targets is critical for characterization of miRNA functions. To this end, we have developed an online database, miRDB, for miRNA target prediction and functional annotations. Recently, we have performed major updates for miRDB. Specifically, by employing an improved algorithm for miRNA target prediction, we now present updated transcriptome-wide target prediction data in miRDB, including 3.5 million predicted targets regulated by 7000 miRNAs in five species. Further, we have implemented the new prediction algorithm into a web server, allowing custom target prediction with user-provided sequences. Another new database feature is the prediction of cell-specific miRNA targets. miRDB now hosts the expression profiles of over 1000 cell lines and presents target prediction data that are tailored for specific cell models. At last, a new web query interface has been added to miRDB for prediction of miRNA functions by integrative analysis of target prediction and Gene Ontology data. All data in miRDB are freely accessible at http://mirdb.org. |
format | Online Article Text |
id | pubmed-6943051 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-69430512020-01-08 miRDB: an online database for prediction of functional microRNA targets Chen, Yuhao Wang, Xiaowei Nucleic Acids Res Database Issue MicroRNAs (miRNAs) are small noncoding RNAs that act as master regulators in many biological processes. miRNAs function mainly by downregulating the expression of their gene targets. Thus, accurate prediction of miRNA targets is critical for characterization of miRNA functions. To this end, we have developed an online database, miRDB, for miRNA target prediction and functional annotations. Recently, we have performed major updates for miRDB. Specifically, by employing an improved algorithm for miRNA target prediction, we now present updated transcriptome-wide target prediction data in miRDB, including 3.5 million predicted targets regulated by 7000 miRNAs in five species. Further, we have implemented the new prediction algorithm into a web server, allowing custom target prediction with user-provided sequences. Another new database feature is the prediction of cell-specific miRNA targets. miRDB now hosts the expression profiles of over 1000 cell lines and presents target prediction data that are tailored for specific cell models. At last, a new web query interface has been added to miRDB for prediction of miRNA functions by integrative analysis of target prediction and Gene Ontology data. All data in miRDB are freely accessible at http://mirdb.org. Oxford University Press 2020-01-08 2019-08-31 /pmc/articles/PMC6943051/ /pubmed/31504780 http://dx.doi.org/10.1093/nar/gkz757 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Database Issue Chen, Yuhao Wang, Xiaowei miRDB: an online database for prediction of functional microRNA targets |
title | miRDB: an online database for prediction of functional microRNA targets |
title_full | miRDB: an online database for prediction of functional microRNA targets |
title_fullStr | miRDB: an online database for prediction of functional microRNA targets |
title_full_unstemmed | miRDB: an online database for prediction of functional microRNA targets |
title_short | miRDB: an online database for prediction of functional microRNA targets |
title_sort | mirdb: an online database for prediction of functional microrna targets |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943051/ https://www.ncbi.nlm.nih.gov/pubmed/31504780 http://dx.doi.org/10.1093/nar/gkz757 |
work_keys_str_mv | AT chenyuhao mirdbanonlinedatabaseforpredictionoffunctionalmicrornatargets AT wangxiaowei mirdbanonlinedatabaseforpredictionoffunctionalmicrornatargets |