Dataset Information

SUMMER, a shiny utility for metabolomics and multiomics exploratory research.

ABSTRACT:

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 .

SUBMITTER: Huang L

PROVIDER: S-EPMC7723939 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Publications

SUMMER, a shiny utility for metabolomics and multiomics exploratory research.

Huang Ling L Currais Antonio A Shokhirev Maxim N MN

Metabolomics : Official journal of the Metabolomic Society 20201209 12

<h4>Introduction</h4>Cellular metabolites are generated by a complex network of biochemical reactions. This makes interpreting changes in metabolites exceptionally challenging.<h4>Objectives</h4>To develop a computational tool that integrates multiomics data at the level of reactions.<h4>Methods</h4>Changes in metabolic reactions are modeled with input from transcriptomics/proteomics measurements of enzymes and metabolomic measurements of metabolites.<h4>Results</h4>We developed SUMMER, which id ...[more]

PMID: 33294943

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Project description:BACKGROUND:Clinical study reports (CSRs) have been increasingly utilised within academic research in recent years. European Medicines Agency (EMA) Policy 0070 'Phase 1,' which came into effect in January 2015, requires the publication of regulatory documents such as CSRs from central applications in an anonymised format. EMA Policy 0070 requires sponsors to demonstrate careful consideration of data utility within anonymised CSRs published within the scope of the policy, yet the concept of data utility is not clearly defined in the associated anonymisation guidance. OBJECTIVE:To review the use of data from CSRs in published academic research and to hypothesise the potential data utility of CSRs anonymised under the objectives of EMA Policy 0070 for future academic research. METHODS:Review of the objectives, research methodologies and findings of academic research reports using unpublished data from CSRs (prior to EMA Policy 0070). Semi-structured interviews with authors of academic research reports, including questions related to data utility of anonymised CSRs published under EMA Policy 0070. RESULTS:Thirteen academic research reports were identified and reviewed. The research purposes ranged from assessment of reporting bias, comparison of methods and results with published data sources, detailed evaluation of harms and adverse events, re-analysis and novel analyses including systematic reviews and meta-analysis. All of the examples identified required access to the methods and results sections of CSRs (including aggregated summary tables) and research purposes relating to evaluation of adverse events also required access to participant narratives. Retaining anonymised participant narratives relating to interventions, findings and events, while maintaining an acceptably low risk of participant re-identification, may provide an important gain in data utility and further understanding of drug safety profiles. CONCLUSIONS:This work provides an initial insight into the previous use of CSR data and current practices for including regulatory data in academic research. This work also provides early guidance to qualitatively assess and document data utility within anonymised CSRs published under EMA Policy 0070.

Dataset Information

SUMMER, a shiny utility for metabolomics and multiomics exploratory research.

Introduction

Objectives

Methods

Results

Conclusion

Publications

SUMMER, a shiny utility for metabolomics and multiomics exploratory research.

Similar Datasets

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