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DIANA-LncBase v3：在非编码转录本上索引实验支持的 miRNA 靶标。

DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts.

机构信息

DIANA-Lab, Department of Electrical and Computer Engineering, Univ. of Thessaly, 38221 Volos, Greece.

Hellenic Pasteur Institute, 11521 Athens, Greece.

出版信息

Nucleic Acids Res. 2020 Jan 8;48(D1):D101-D110. doi: 10.1093/nar/gkz1036.

DOI:10.1093/nar/gkz1036
PMID:31732741
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7145509/
Abstract

DIANA-LncBase v3.0 (www.microrna.gr/LncBase) is a reference repository with experimentally supported miRNA targets on non-coding transcripts. Its third version provides approximately half a million entries, corresponding to ∼240 000 unique tissue and cell type specific miRNA-lncRNA pairs. This compilation of interactions is derived from the manual curation of publications and the analysis of >300 high-throughput datasets. miRNA targets are supported by 14 experimental methodologies, applied to 243 distinct cell types and tissues in human and mouse. The largest part of the database is highly confident, AGO-CLIP-derived miRNA-binding events. LncBase v3.0 is the first relevant database to employ a robust CLIP-Seq-guided algorithm, microCLIP framework, to analyze 236 AGO-CLIP-Seq libraries and catalogue ∼370 000 miRNA binding events. The database was redesigned from the ground up, providing new functionalities. Known short variant information, on >67,000 experimentally supported target sites and lncRNA expression profiles in different cellular compartments are catered to users. Interactive visualization plots, portraying correlations of miRNA-lncRNA pairs, as well as lncRNA expression profiles in a wide range of cell types and tissues, are presented for the first time through a dedicated page. LncBase v3.0 constitutes a valuable asset for ncRNA research, providing new insights to the understanding of the still widely unexplored lncRNA functions.

摘要

DIANA-LncBase v3.0（www.microrna.gr/LncBase）是一个参考数据库，其中包含经过实验验证的非编码转录本上的 miRNA 靶标。它的第三个版本提供了大约 50 万个条目，对应于约 240000 个独特的组织和细胞类型特异性 miRNA-lncRNA 对。这些相互作用的组合是通过对出版物的手动注释和对 >300 个高通量数据集的分析得出的。miRNA 靶标得到了 14 种实验方法的支持，这些方法应用于人类和小鼠的 243 种不同的细胞类型和组织。该数据库的最大部分是高度可信的，AGO-CLIP 衍生的 miRNA 结合事件。LncBase v3.0 是第一个采用强大的 CLIP-Seq 引导算法（microCLIP 框架）来分析 236 个 AGO-CLIP-Seq 文库并编目约 370000 个 miRNA 结合事件的相关数据库。该数据库从头开始重新设计，提供了新的功能。针对 >67000 个实验支持的靶位点和不同细胞区室中的 lncRNA 表达谱的已知短变异信息，满足了用户的需求。通过专门的页面，首次呈现了描绘 miRNA-lncRNA 对以及广泛的细胞类型和组织中 lncRNA 表达谱相关性的交互式可视化图。LncBase v3.0 是 ncRNA 研究的宝贵资产，为理解仍广泛未知的 lncRNA 功能提供了新的见解。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/86c9/7145509/4cd10e9538b1/gkz1036fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/86c9/7145509/f8f10bcd70c6/gkz1036fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/86c9/7145509/8824238748a6/gkz1036fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/86c9/7145509/030c5eefe565/gkz1036fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/86c9/7145509/7e0b900e968b/gkz1036fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/86c9/7145509/4cd10e9538b1/gkz1036fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/86c9/7145509/f8f10bcd70c6/gkz1036fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/86c9/7145509/8824238748a6/gkz1036fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/86c9/7145509/030c5eefe565/gkz1036fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/86c9/7145509/7e0b900e968b/gkz1036fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/86c9/7145509/4cd10e9538b1/gkz1036fig5.jpg

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4
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IET Syst Biol. 2025 Jan-Dec;19(1):e70015. doi: 10.1049/syb2.70015.
5
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6
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7
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8
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9
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10
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