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A tool for analyzing and visualizing ribo-seq data at the isoform level

BACKGROUND: Translational regulation is one important aspect of gene expression regulation. Dysregulation of translation results in abnormal cell physiology and leads to diseases. Ribosome profiling (RP), also called ribo-seq, is a powerful experimental technique to study translational regulation. I...

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Autores principales: Wu, Wei-Sheng, Tsao, Yi-Hong, Shiue, Sheng-Cian, Chen, Ting-Yu, Tseng, Yan-Yuan, Tseng, Joseph T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8323483/
https://www.ncbi.nlm.nih.gov/pubmed/34058988
http://dx.doi.org/10.1186/s12859-021-04192-7
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author Wu, Wei-Sheng
Tsao, Yi-Hong
Shiue, Sheng-Cian
Chen, Ting-Yu
Tseng, Yan-Yuan
Tseng, Joseph T.
author_facet Wu, Wei-Sheng
Tsao, Yi-Hong
Shiue, Sheng-Cian
Chen, Ting-Yu
Tseng, Yan-Yuan
Tseng, Joseph T.
author_sort Wu, Wei-Sheng
collection PubMed
description BACKGROUND: Translational regulation is one important aspect of gene expression regulation. Dysregulation of translation results in abnormal cell physiology and leads to diseases. Ribosome profiling (RP), also called ribo-seq, is a powerful experimental technique to study translational regulation. It can capture a snapshot of translation by deep sequencing of ribosome-protected mRNA fragments. Many ribosome profiling data processing tools have been developed. However, almost all tools analyze ribosome profiling data at the gene level. Since different isoforms of a gene may produce different proteins with distinct biological functions, it is advantageous to analyze ribosome profiling data at the isoform level. To meet this need, previously we developed a pipeline to analyze 610 public human ribosome profiling data at the isoform level and constructed HRPDviewer database. RESULTS: To allow other researchers to use our pipeline as well, here we implement our pipeline as an easy-to-use software tool called RPiso. Compared to Ribomap (a widely used tool which provides isoform-level ribosome profiling analyses), our RPiso (1) estimates isoform abundance more accurately, (2) supports analyses on more species, and (3) provides a web-based viewer for interactively visualizing ribosome profiling data on the selected mRNA isoforms. CONCLUSIONS: In this study, we developed RPiso software tool (http://cosbi7.ee.ncku.edu.tw/RPiso/) to provide isoform-level ribosome profiling analyses. RPiso is very easy to install and execute. RPiso also provides a web-based viewer for interactively visualizing ribosome profiling data on the selected mRNA isoforms. We believe that RPiso is a useful tool for researchers to analyze and visualize their own ribosome profiling data at the isoform level. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04192-7.
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spelling pubmed-83234832021-08-02 A tool for analyzing and visualizing ribo-seq data at the isoform level Wu, Wei-Sheng Tsao, Yi-Hong Shiue, Sheng-Cian Chen, Ting-Yu Tseng, Yan-Yuan Tseng, Joseph T. BMC Bioinformatics Research BACKGROUND: Translational regulation is one important aspect of gene expression regulation. Dysregulation of translation results in abnormal cell physiology and leads to diseases. Ribosome profiling (RP), also called ribo-seq, is a powerful experimental technique to study translational regulation. It can capture a snapshot of translation by deep sequencing of ribosome-protected mRNA fragments. Many ribosome profiling data processing tools have been developed. However, almost all tools analyze ribosome profiling data at the gene level. Since different isoforms of a gene may produce different proteins with distinct biological functions, it is advantageous to analyze ribosome profiling data at the isoform level. To meet this need, previously we developed a pipeline to analyze 610 public human ribosome profiling data at the isoform level and constructed HRPDviewer database. RESULTS: To allow other researchers to use our pipeline as well, here we implement our pipeline as an easy-to-use software tool called RPiso. Compared to Ribomap (a widely used tool which provides isoform-level ribosome profiling analyses), our RPiso (1) estimates isoform abundance more accurately, (2) supports analyses on more species, and (3) provides a web-based viewer for interactively visualizing ribosome profiling data on the selected mRNA isoforms. CONCLUSIONS: In this study, we developed RPiso software tool (http://cosbi7.ee.ncku.edu.tw/RPiso/) to provide isoform-level ribosome profiling analyses. RPiso is very easy to install and execute. RPiso also provides a web-based viewer for interactively visualizing ribosome profiling data on the selected mRNA isoforms. We believe that RPiso is a useful tool for researchers to analyze and visualize their own ribosome profiling data at the isoform level. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04192-7. BioMed Central 2021-05-25 /pmc/articles/PMC8323483/ /pubmed/34058988 http://dx.doi.org/10.1186/s12859-021-04192-7 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Wu, Wei-Sheng
Tsao, Yi-Hong
Shiue, Sheng-Cian
Chen, Ting-Yu
Tseng, Yan-Yuan
Tseng, Joseph T.
A tool for analyzing and visualizing ribo-seq data at the isoform level
title A tool for analyzing and visualizing ribo-seq data at the isoform level
title_full A tool for analyzing and visualizing ribo-seq data at the isoform level
title_fullStr A tool for analyzing and visualizing ribo-seq data at the isoform level
title_full_unstemmed A tool for analyzing and visualizing ribo-seq data at the isoform level
title_short A tool for analyzing and visualizing ribo-seq data at the isoform level
title_sort tool for analyzing and visualizing ribo-seq data at the isoform level
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8323483/
https://www.ncbi.nlm.nih.gov/pubmed/34058988
http://dx.doi.org/10.1186/s12859-021-04192-7
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