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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...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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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. |
format | Online Article Text |
id | pubmed-7778966 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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