SUMMER, a shiny utility for metabolomics and multiomics exploratory research

INTRODUCTION: Cellular metabolites are generated by a complex network of biochemical reactions. This makes interpreting changes in metabolites exceptionally challenging. OBJECTIVES: To develop a computational tool that integrates multiomics data at the level of reactions. METHODS: Changes in metabol...

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Detalles Bibliográficos
Autores principales: Huang, Ling, Currais, Antonio, Shokhirev, Maxim N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer US 2020
Materias:
Short Communication
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7723939/
https://www.ncbi.nlm.nih.gov/pubmed/33294943
http://dx.doi.org/10.1007/s11306-020-01750-7
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author Huang, Ling
Currais, Antonio
Shokhirev, Maxim N.
author_facet Huang, Ling
Currais, Antonio
Shokhirev, Maxim N.
author_sort Huang, Ling
collection PubMed
description INTRODUCTION: Cellular metabolites are generated by a complex network of biochemical reactions. This makes interpreting changes in metabolites exceptionally challenging. OBJECTIVES: To develop a computational tool that integrates multiomics data at the level of reactions. METHODS: Changes in metabolic reactions are modeled with input from transcriptomics/proteomics measurements of enzymes and metabolomic measurements of metabolites. RESULTS: We developed SUMMER, which identified more relevant signals, key metabolic reactions, and relevant underlying biological pathways in a real-world case study. CONCLUSION: SUMMER performs integrative analysis for data interpretation and exploration. SUMMER is freely accessible at http://summer.salk.edu and the code is available at https://bitbucket.org/salkigc/summer. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11306-020-01750-7) contains supplementary material, which is available to authorized users.
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spelling pubmed-77239392020-12-14 SUMMER, a shiny utility for metabolomics and multiomics exploratory research Huang, Ling Currais, Antonio Shokhirev, Maxim N. Metabolomics Short Communication INTRODUCTION: Cellular metabolites are generated by a complex network of biochemical reactions. This makes interpreting changes in metabolites exceptionally challenging. OBJECTIVES: To develop a computational tool that integrates multiomics data at the level of reactions. METHODS: Changes in metabolic reactions are modeled with input from transcriptomics/proteomics measurements of enzymes and metabolomic measurements of metabolites. RESULTS: We developed SUMMER, which identified more relevant signals, key metabolic reactions, and relevant underlying biological pathways in a real-world case study. CONCLUSION: SUMMER performs integrative analysis for data interpretation and exploration. SUMMER is freely accessible at http://summer.salk.edu and the code is available at https://bitbucket.org/salkigc/summer. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11306-020-01750-7) contains supplementary material, which is available to authorized users. Springer US 2020-12-09 2020 /pmc/articles/PMC7723939/ /pubmed/33294943 http://dx.doi.org/10.1007/s11306-020-01750-7 Text en © The Author(s) 2020 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/.
spellingShingle Short Communication
Huang, Ling
Currais, Antonio
Shokhirev, Maxim N.
SUMMER, a shiny utility for metabolomics and multiomics exploratory research
title SUMMER, a shiny utility for metabolomics and multiomics exploratory research
title_full SUMMER, a shiny utility for metabolomics and multiomics exploratory research
title_fullStr SUMMER, a shiny utility for metabolomics and multiomics exploratory research
title_full_unstemmed SUMMER, a shiny utility for metabolomics and multiomics exploratory research
title_short SUMMER, a shiny utility for metabolomics and multiomics exploratory research
title_sort summer, a shiny utility for metabolomics and multiomics exploratory research
topic Short Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7723939/
https://www.ncbi.nlm.nih.gov/pubmed/33294943
http://dx.doi.org/10.1007/s11306-020-01750-7
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