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deepBase v3.0: expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data

Eukaryotic genomes encode thousands of small and large non-coding RNAs (ncRNAs). However, the expression, functions and evolution of these ncRNAs are still largely unknown. In this study, we have updated deepBase to version 3.0 (deepBase v3.0, http://rna.sysu.edu.cn/deepbase3/index.html), an increas...

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Autores principales: Xie, Fangzhou, Liu, Shurong, Wang, Junhao, Xuan, Jiajia, Zhang, Xiaoqin, Qu, Lianghu, Zheng, Lingling, Yang, Jianhua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778966/
https://www.ncbi.nlm.nih.gov/pubmed/33175131
http://dx.doi.org/10.1093/nar/gkaa1039
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author Xie, Fangzhou
Liu, Shurong
Wang, Junhao
Xuan, Jiajia
Zhang, Xiaoqin
Qu, Lianghu
Zheng, Lingling
Yang, Jianhua
author_facet Xie, Fangzhou
Liu, Shurong
Wang, Junhao
Xuan, Jiajia
Zhang, Xiaoqin
Qu, Lianghu
Zheng, Lingling
Yang, Jianhua
author_sort Xie, Fangzhou
collection PubMed
description Eukaryotic genomes encode thousands of small and large non-coding RNAs (ncRNAs). However, the expression, functions and evolution of these ncRNAs are still largely unknown. In this study, we have updated deepBase to version 3.0 (deepBase v3.0, http://rna.sysu.edu.cn/deepbase3/index.html), an increasingly popular and openly licensed resource that facilitates integrative and interactive display and analysis of the expression, evolution, and functions of various ncRNAs by deeply mining thousands of high-throughput sequencing data from tissue, tumor and exosome samples. We updated deepBase v3.0 to provide the most comprehensive expression atlas of small RNAs and lncRNAs by integrating ∼67 620 data from 80 normal tissues and ∼50 cancer tissues. The extracellular patterns of various ncRNAs were profiled to explore their applications for discovery of noninvasive biomarkers. Moreover, we constructed survival maps of tRNA-derived RNA Fragments (tRFs), miRNAs, snoRNAs and lncRNAs by analyzing >45 000 cancer sample data and corresponding clinical information. We also developed interactive webs to analyze the differential expression and biological functions of various ncRNAs in ∼50 types of cancers. This update is expected to provide a variety of new modules and graphic visualizations to facilitate analyses and explorations of the functions and mechanisms of various types of ncRNAs.
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spelling pubmed-77789662021-01-06 deepBase v3.0: expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data Xie, Fangzhou Liu, Shurong Wang, Junhao Xuan, Jiajia Zhang, Xiaoqin Qu, Lianghu Zheng, Lingling Yang, Jianhua Nucleic Acids Res Database Issue Eukaryotic genomes encode thousands of small and large non-coding RNAs (ncRNAs). However, the expression, functions and evolution of these ncRNAs are still largely unknown. In this study, we have updated deepBase to version 3.0 (deepBase v3.0, http://rna.sysu.edu.cn/deepbase3/index.html), an increasingly popular and openly licensed resource that facilitates integrative and interactive display and analysis of the expression, evolution, and functions of various ncRNAs by deeply mining thousands of high-throughput sequencing data from tissue, tumor and exosome samples. We updated deepBase v3.0 to provide the most comprehensive expression atlas of small RNAs and lncRNAs by integrating ∼67 620 data from 80 normal tissues and ∼50 cancer tissues. The extracellular patterns of various ncRNAs were profiled to explore their applications for discovery of noninvasive biomarkers. Moreover, we constructed survival maps of tRNA-derived RNA Fragments (tRFs), miRNAs, snoRNAs and lncRNAs by analyzing >45 000 cancer sample data and corresponding clinical information. We also developed interactive webs to analyze the differential expression and biological functions of various ncRNAs in ∼50 types of cancers. This update is expected to provide a variety of new modules and graphic visualizations to facilitate analyses and explorations of the functions and mechanisms of various types of ncRNAs. Oxford University Press 2020-11-11 /pmc/articles/PMC7778966/ /pubmed/33175131 http://dx.doi.org/10.1093/nar/gkaa1039 Text en © The Author(s) 2020. 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
Xie, Fangzhou
Liu, Shurong
Wang, Junhao
Xuan, Jiajia
Zhang, Xiaoqin
Qu, Lianghu
Zheng, Lingling
Yang, Jianhua
deepBase v3.0: expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data
title deepBase v3.0: expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data
title_full deepBase v3.0: expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data
title_fullStr deepBase v3.0: expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data
title_full_unstemmed deepBase v3.0: expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data
title_short deepBase v3.0: expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data
title_sort deepbase v3.0: expression atlas and interactive analysis of ncrnas from thousands of deep-sequencing data
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778966/
https://www.ncbi.nlm.nih.gov/pubmed/33175131
http://dx.doi.org/10.1093/nar/gkaa1039
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