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ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species
The increasing application of RNA sequencing to study non-model species demands easy-to-use and efficient bioinformatics tools to help researchers quickly uncover biological and functional insights. We developed ExpressAnalyst (www.expressanalyst.ca), a web-based platform for processing, analyzing,...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10209063/ https://www.ncbi.nlm.nih.gov/pubmed/37225696 http://dx.doi.org/10.1038/s41467-023-38785-y |
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author | Liu, Peng Ewald, Jessica Pang, Zhiqiang Legrand, Elena Jeon, Yeon Seon Sangiovanni, Jonathan Hacariz, Orcun Zhou, Guangyan Head, Jessica A. Basu, Niladri Xia, Jianguo |
author_facet | Liu, Peng Ewald, Jessica Pang, Zhiqiang Legrand, Elena Jeon, Yeon Seon Sangiovanni, Jonathan Hacariz, Orcun Zhou, Guangyan Head, Jessica A. Basu, Niladri Xia, Jianguo |
author_sort | Liu, Peng |
collection | PubMed |
description | The increasing application of RNA sequencing to study non-model species demands easy-to-use and efficient bioinformatics tools to help researchers quickly uncover biological and functional insights. We developed ExpressAnalyst (www.expressanalyst.ca), a web-based platform for processing, analyzing, and interpreting RNA-sequencing data from any eukaryotic species. ExpressAnalyst contains a series of modules that cover from processing and annotation of FASTQ files to statistical and functional analysis of count tables or gene lists. All modules are integrated with EcoOmicsDB, an ortholog database that enables comprehensive analysis for species without a reference transcriptome. By coupling ultra-fast read mapping algorithms with high-resolution ortholog databases through a user-friendly web interface, ExpressAnalyst allows researchers to obtain global expression profiles and gene-level insights from raw RNA-sequencing reads within 24 h. Here, we present ExpressAnalyst and demonstrate its utility with a case study of RNA-sequencing data from multiple non-model salamander species, including two that do not have a reference transcriptome. |
format | Online Article Text |
id | pubmed-10209063 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-102090632023-05-26 ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species Liu, Peng Ewald, Jessica Pang, Zhiqiang Legrand, Elena Jeon, Yeon Seon Sangiovanni, Jonathan Hacariz, Orcun Zhou, Guangyan Head, Jessica A. Basu, Niladri Xia, Jianguo Nat Commun Article The increasing application of RNA sequencing to study non-model species demands easy-to-use and efficient bioinformatics tools to help researchers quickly uncover biological and functional insights. We developed ExpressAnalyst (www.expressanalyst.ca), a web-based platform for processing, analyzing, and interpreting RNA-sequencing data from any eukaryotic species. ExpressAnalyst contains a series of modules that cover from processing and annotation of FASTQ files to statistical and functional analysis of count tables or gene lists. All modules are integrated with EcoOmicsDB, an ortholog database that enables comprehensive analysis for species without a reference transcriptome. By coupling ultra-fast read mapping algorithms with high-resolution ortholog databases through a user-friendly web interface, ExpressAnalyst allows researchers to obtain global expression profiles and gene-level insights from raw RNA-sequencing reads within 24 h. Here, we present ExpressAnalyst and demonstrate its utility with a case study of RNA-sequencing data from multiple non-model salamander species, including two that do not have a reference transcriptome. Nature Publishing Group UK 2023-05-24 /pmc/articles/PMC10209063/ /pubmed/37225696 http://dx.doi.org/10.1038/s41467-023-38785-y Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Liu, Peng Ewald, Jessica Pang, Zhiqiang Legrand, Elena Jeon, Yeon Seon Sangiovanni, Jonathan Hacariz, Orcun Zhou, Guangyan Head, Jessica A. Basu, Niladri Xia, Jianguo ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species |
title | ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species |
title_full | ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species |
title_fullStr | ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species |
title_full_unstemmed | ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species |
title_short | ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species |
title_sort | expressanalyst: a unified platform for rna-sequencing analysis in non-model species |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10209063/ https://www.ncbi.nlm.nih.gov/pubmed/37225696 http://dx.doi.org/10.1038/s41467-023-38785-y |
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