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miRPathDB 2.0：miRNA 通路词典数据库的新版本。

miRPathDB 2.0: a novel release of the miRNA Pathway Dictionary Database.

机构信息

Chair for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany.

Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.

出版信息

Nucleic Acids Res. 2020 Jan 8;48(D1):D142-D147. doi: 10.1093/nar/gkz1022.

DOI:10.1093/nar/gkz1022
PMID:31691816
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7145528/
Abstract

Since the initial release of miRPathDB, tremendous progress has been made in the field of microRNA (miRNA) research. New miRNA reference databases have emerged, a vast amount of new miRNA candidates has been discovered and the number of experimentally validated target genes has increased considerably. Hence, the demand for a major upgrade of miRPathDB, including extended analysis functionality and intuitive visualizations of query results has emerged. Here, we present the novel release 2.0 of the miRNA Pathway Dictionary Database (miRPathDB) that is freely accessible at https://mpd.bioinf.uni-sb.de/. miRPathDB 2.0 comes with a ten-fold increase of pre-processed data. In total, the updated database provides putative associations between 27 452 (candidate) miRNAs, 28 352 targets and 16 833 pathways for Homo sapiens, as well as interactions of 1978 miRNAs, 24 898 targets and 6511 functional categories for Mus musculus. Additionally, we analyzed publications citing miRPathDB to identify common use-cases and further extensions. Based on this evaluation, we added new functionality for interactive visualizations and down-stream analyses of bulk queries. In summary, the updated version of miRPathDB, with its new custom-tailored features, is one of the most comprehensive and advanced resources for miRNAs and their target pathways.

摘要

自 miRPathDB 首次发布以来，miRNA 研究领域取得了巨大的进展。新的 miRNA 参考数据库已经出现，大量新的 miRNA 候选物被发现，并且经过实验验证的靶基因数量也大大增加。因此，对 miRPathDB 进行重大升级的需求已经出现，包括扩展分析功能和直观显示查询结果。在这里，我们展示了 miRNA 通路词典数据库（miRPathDB）的新版本 2.0，可在 https://mpd.bioinf.uni-sb.de/ 免费访问。miRPathDB 2.0 的预处理数据增加了十倍。总的来说，更新后的数据库为智人提供了 27452 个（候选）miRNA、28352 个靶基因和 16833 个途径之间的假定关联，以及 1978 个 miRNA、24898 个靶基因和 6511 个功能类别之间的相互作用。此外，我们分析了引用 miRPathDB 的出版物，以确定常见的用例和进一步的扩展。基于此评估，我们为批量查询的交互式可视化和下游分析添加了新功能。总之，更新后的 miRPathDB 版本具有新的定制功能，是 miRNA 及其靶途径的最全面和先进的资源之一。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/09ec/7145528/5b5f9e235dc6/gkz1022fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/09ec/7145528/3cfc829ec80b/gkz1022fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/09ec/7145528/a5b66d6b9643/gkz1022fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/09ec/7145528/5b5f9e235dc6/gkz1022fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/09ec/7145528/3cfc829ec80b/gkz1022fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/09ec/7145528/a5b66d6b9643/gkz1022fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/09ec/7145528/5b5f9e235dc6/gkz1022fig3.jpg

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本文引用的文献

[1]
MirGeneDB 2.0: the metazoan microRNA complement.

Nucleic Acids Res. 2020-1-8

[2]
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Cells. 2019-4-23

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Nucleic Acids Res. 2019-5-21

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Nucleic Acids Res. 2019-4-23

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Nucleic Acids Res. 2019-1-8

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Nucleic Acids Res. 2019-1-8

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PLoS One. 2018-10-18

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Nucleic Acids Res. 2019-1-8

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Small non-coding RNAs are altered by short-term sprint interval training in men.

Physiol Rep. 2018-4

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