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      miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions

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          Abstract

          MicroRNAs (miRNAs) are small non-coding RNAs of ∼ 22 nucleotides that are involved in negative regulation of mRNA at the post-transcriptional level. Previously, we developed miRTarBase which provides information about experimentally validated miRNA-target interactions (MTIs). Here, we describe an updated database containing 422 517 curated MTIs from 4076 miRNAs and 23 054 target genes collected from over 8500 articles. The number of MTIs curated by strong evidence has increased ∼1.4-fold since the last update in 2016. In this updated version, target sites validated by reporter assay that are available in the literature can be downloaded. The target site sequence can extract new features for analysis via a machine learning approach which can help to evaluate the performance of miRNA-target prediction tools. Furthermore, different ways of browsing enhance user browsing specific MTIs. With these improvements, miRTarBase serves as more comprehensively annotated, experimentally validated miRNA-target interactions databases in the field of miRNA related research. miRTarBase is available at http://miRTarBase.mbc.nctu.edu.tw/.

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          Most cited references 49

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          Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.

          DAVID bioinformatics resources consists of an integrated biological knowledgebase and analytic tools aimed at systematically extracting biological meaning from large gene/protein lists. This protocol explains how to use DAVID, a high-throughput and integrated data-mining environment, to analyze gene lists derived from high-throughput genomic experiments. The procedure first requires uploading a gene list containing any number of common gene identifiers followed by analysis using one or more text and pathway-mining tools such as gene functional classification, functional annotation chart or clustering and functional annotation table. By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.
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            MicroRNAs: genomics, biogenesis, mechanism, and function.

             David Bartel (2004)
            MicroRNAs (miRNAs) are endogenous approximately 22 nt RNAs that can play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. Although they escaped notice until relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in multicellular organisms and likely influence the output of many protein-coding genes.
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              miRBase: annotating high confidence microRNAs using deep sequencing data

              We describe an update of the miRBase database (http://www.mirbase.org/), the primary microRNA sequence repository. The latest miRBase release (v20, June 2013) contains 24 521 microRNA loci from 206 species, processed to produce 30 424 mature microRNA products. The rate of deposition of novel microRNAs and the number of researchers involved in their discovery continue to increase, driven largely by small RNA deep sequencing experiments. In the face of these increases, and a range of microRNA annotation methods and criteria, maintaining the quality of the microRNA sequence data set is a significant challenge. Here, we describe recent developments of the miRBase database to address this issue. In particular, we describe the collation and use of deep sequencing data sets to assign levels of confidence to miRBase entries. We now provide a high confidence subset of miRBase entries, based on the pattern of mapped reads. The high confidence microRNA data set is available alongside the complete microRNA collection at http://www.mirbase.org/. We also describe embedding microRNA-specific Wikipedia pages on the miRBase website to encourage the microRNA community to contribute and share textual and functional information.
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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                04 January 2018
                06 November 2017
                06 November 2017
                : 46
                : Database issue , Database issue
                : D296-D302
                Affiliations
                Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
                Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
                Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 350, Taiwan
                Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 106, Taiwan
                Center for Bioinformatics Research, National Chiao Tung University, Hsinchu, 300, Taiwan
                Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan
                Clinical Research Center, Chung Shan Medical University Hospital, Taichung, 402, Taiwan
                Interdisciplinary Program of Life Science, National Tsing Hua University, Hsinchu, 300, Taiwan
                Department of Pediatrics, National Taiwan University Hospital Hsinchu Branch, Hsinchu, 300, Taiwan
                Delivery Room, Department of Nursing, National Taiwan University Hospital Hsinchu Branch, Hsinchu, 300, Taiwan
                Gynecologic Cancer Center, Department of Obstetrics and Gynecology, Cathay General Hospital, Taipei, 106, Taiwan
                Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, 300, Taiwan
                Mackay Medicine, Nursing and Management College, Taipei, 112, Taiwan
                Department of Medicine, Mackay Medical College, New Taipei City, 252, Taiwan
                Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan
                Warshel Institute for Computational Biology, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong Province, 518172, China
                School of Science and Engineering, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong Province, 518172, China
                Author notes
                To whom correspondence should be addressed. Tel: +886 3 5712121 (Ext. 56952); Email: bryan@ 123456mail.nctu.edu.tw

                These authors contributed equally to this work as first authors.

                Article
                gkx1067
                10.1093/nar/gkx1067
                5753222
                29126174
                © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

                Page count
                Pages: 7
                Product
                Categories
                Database Issue

                Genetics

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