CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines.
Chinese hamster ovary (CHO) cell lines are widely used in industry for biological drug production. During cell culture development, considerable effort is invested to understand the factors that greatly impact cell growth, specific productivity and product qualities of the biotherapeutics. While hig...
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2020-12-01
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Series: | PLoS Computational Biology |
Online Access: | https://doi.org/10.1371/journal.pcbi.1008498 |
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doaj-849744a569d14e8f84cf44db421cb4252021-04-21T16:39:51ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582020-12-011612e100849810.1371/journal.pcbi.1008498CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines.Dongdong LinHima B YalamanchiliXinmin ZhangNathan E LewisChristina S AlvesJoost GrootJohnny ArnsdorfSara P BjørnTune WulffBjørn G VoldborgYizhou ZhouBaohong ZhangChinese hamster ovary (CHO) cell lines are widely used in industry for biological drug production. During cell culture development, considerable effort is invested to understand the factors that greatly impact cell growth, specific productivity and product qualities of the biotherapeutics. While high-throughput omics approaches have been increasingly utilized to reveal cellular mechanisms associated with cell line phenotypes and guide process optimization, comprehensive omics data analysis and management have been a challenge. Here we developed CHOmics, a web-based tool for integrative analysis of CHO cell line omics data that provides an interactive visualization of omics analysis outputs and efficient data management. CHOmics has a built-in comprehensive pipeline for RNA sequencing data processing and multi-layer statistical modules to explore relevant genes or pathways. Moreover, advanced functionalities were provided to enable users to customize their analysis and visualize the output systematically and interactively. The tool was also designed with the flexibility to accommodate other types of omics data and thereby enabling multi-omics comparison and visualization at both gene and pathway levels. Collectively, CHOmics is an integrative platform for data analysis, visualization and management with expectations to promote the broader use of omics in CHO cell research.https://doi.org/10.1371/journal.pcbi.1008498 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Dongdong Lin Hima B Yalamanchili Xinmin Zhang Nathan E Lewis Christina S Alves Joost Groot Johnny Arnsdorf Sara P Bjørn Tune Wulff Bjørn G Voldborg Yizhou Zhou Baohong Zhang |
spellingShingle |
Dongdong Lin Hima B Yalamanchili Xinmin Zhang Nathan E Lewis Christina S Alves Joost Groot Johnny Arnsdorf Sara P Bjørn Tune Wulff Bjørn G Voldborg Yizhou Zhou Baohong Zhang CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines. PLoS Computational Biology |
author_facet |
Dongdong Lin Hima B Yalamanchili Xinmin Zhang Nathan E Lewis Christina S Alves Joost Groot Johnny Arnsdorf Sara P Bjørn Tune Wulff Bjørn G Voldborg Yizhou Zhou Baohong Zhang |
author_sort |
Dongdong Lin |
title |
CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines. |
title_short |
CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines. |
title_full |
CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines. |
title_fullStr |
CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines. |
title_full_unstemmed |
CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines. |
title_sort |
chomics: a web-based tool for multi-omics data analysis and interactive visualization in cho cell lines. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS Computational Biology |
issn |
1553-734X 1553-7358 |
publishDate |
2020-12-01 |
description |
Chinese hamster ovary (CHO) cell lines are widely used in industry for biological drug production. During cell culture development, considerable effort is invested to understand the factors that greatly impact cell growth, specific productivity and product qualities of the biotherapeutics. While high-throughput omics approaches have been increasingly utilized to reveal cellular mechanisms associated with cell line phenotypes and guide process optimization, comprehensive omics data analysis and management have been a challenge. Here we developed CHOmics, a web-based tool for integrative analysis of CHO cell line omics data that provides an interactive visualization of omics analysis outputs and efficient data management. CHOmics has a built-in comprehensive pipeline for RNA sequencing data processing and multi-layer statistical modules to explore relevant genes or pathways. Moreover, advanced functionalities were provided to enable users to customize their analysis and visualize the output systematically and interactively. The tool was also designed with the flexibility to accommodate other types of omics data and thereby enabling multi-omics comparison and visualization at both gene and pathway levels. Collectively, CHOmics is an integrative platform for data analysis, visualization and management with expectations to promote the broader use of omics in CHO cell research. |
url |
https://doi.org/10.1371/journal.pcbi.1008498 |
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