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非编码 RNA 网络资源在植物科学研究中的综合评述

A comprehensive review of web-based resources of non-coding RNAs for plant science research.

机构信息

Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500,China.

Yunnan key laboratory of Panax notoginseng, Kunming, Yunnan, 650500, China.

出版信息

Int J Biol Sci. 2018 May 22;14(8):819-832. doi: 10.7150/ijbs.24593. eCollection 2018.

DOI:10.7150/ijbs.24593
PMID:29989090
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6036741/
Abstract

Non-coding RNAs (ncRNAs) are transcribed from genome but not translated into proteins. Many ncRNAs are key regulators of plants growth and development, metabolism and stress tolerance. In order to make the web-based ncRNA resources for plant science research be more easily accessible and understandable, we made a comprehensive review for 83 web-based resources of three types, including genome databases containing ncRNA data, microRNA (miRNA) databases and long non-coding RNA (lncRNA) databases. To facilitate effective usage of these resources, we also suggested some preferred resources of miRNAs and lncRNAs for performing meaningful analysis.

摘要

非编码 RNA(ncRNAs) 是从基因组中转录而来的，但不翻译成蛋白质。许多 ncRNAs 是植物生长发育、代谢和应激耐受的关键调节剂。为了使植物科学研究的基于网络的 ncRNA 资源更易于访问和理解，我们对三种类型的 83 个基于网络的资源进行了全面综述，包括包含 ncRNA 数据的基因组数据库、microRNA(miRNA)数据库和长非编码 RNA(lncRNA)数据库。为了便于有效地使用这些资源，我们还为进行有意义的分析推荐了一些 miRNA 和 lncRNA 的首选资源。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/30e8/6036741/a3fc95c2691b/ijbsv14p0819g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/30e8/6036741/a3fc95c2691b/ijbsv14p0819g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/30e8/6036741/a3fc95c2691b/ijbsv14p0819g001.jpg

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[1]
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[3]
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[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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本文引用的文献

[1]
PlantCircNet: a database for plant circRNA-miRNA-mRNA regulatory networks.

Database (Oxford). 2017-1-1

[2]
funRiceGenes dataset for comprehensive understanding and application of rice functional genes.

Gigascience. 2018-1-1

[3]
miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions.

Nucleic Acids Res. 2018-1-4

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Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.

Nucleic Acids Res. 2018-1-4

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Rice Expression Database (RED): An integrated RNA-Seq-derived gene expression database for rice.

J Genet Genomics. 2017-5-4

[6]
CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features.

Nucleic Acids Res. 2017-7-3

[7]
PlantcircBase: A Database for Plant Circular RNAs.

Mol Plant. 2017-8-7

[8]
Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes.

Plant Cell Physiol. 2017-1-1

[9]
PeTMbase: A Database of Plant Endogenous Target Mimics (eTMs).

PLoS One. 2016-12-9

[10]
The BIG Data Center: from deposition to integration to translation.

Nucleic Acids Res. 2017-1-4

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