Application of Differential Network Enrichment Analysis for Deciphering Metabolic Alterations
Modern analytical methods allow for the simultaneous detection of hundreds of metabolites, generating increasingly large and complex data sets. The analysis of metabolomics data is a multi-step process that involves data processing and normalization, followed by statistical analysis. One of the bigg...
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doaj-5c3d8939e6fc417cb1729c6818e544e12020-11-27T07:56:14ZengMDPI AGMetabolites2218-19892020-11-011047947910.3390/metabo10120479Application of Differential Network Enrichment Analysis for Deciphering Metabolic AlterationsGayatri R. Iyer0Janis Wigginton1William Duren2Jennifer L. LaBarre3Marci Brandenburg4Charles Burant5George Michailidis6Alla Karnovsky7Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USAMichigan Regional Comprehensive Metabolomics Resource Core, Biomedical Research Core Facilities, University of Michigan Medical School, Ann Arbor, MI 48109, USADepartment of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USADepartment of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USADepartment of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USADepartment of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USAMichigan Regional Comprehensive Metabolomics Resource Core, Biomedical Research Core Facilities, University of Michigan Medical School, Ann Arbor, MI 48109, USADepartment of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USAModern analytical methods allow for the simultaneous detection of hundreds of metabolites, generating increasingly large and complex data sets. The analysis of metabolomics data is a multi-step process that involves data processing and normalization, followed by statistical analysis. One of the biggest challenges in metabolomics is linking alterations in metabolite levels to specific biological processes that are disrupted, contributing to the development of disease or reflecting the disease state. A common approach to accomplishing this goal involves pathway mapping and enrichment analysis, which assesses the relative importance of predefined metabolic pathways or other biological categories. However, traditional knowledge-based enrichment analysis has limitations when it comes to the analysis of metabolomics and lipidomics data. We present a Java-based, user-friendly bioinformatics tool named Filigree that provides a primarily data-driven alternative to the existing knowledge-based enrichment analysis methods. Filigree is based on our previously published differential network enrichment analysis (DNEA) methodology. To demonstrate the utility of the tool, we applied it to previously published studies analyzing the metabolome in the context of metabolic disorders (type 1 and 2 diabetes) and the maternal and infant lipidome during pregnancy.https://www.mdpi.com/2218-1989/10/12/479partial correlation networksdifferential networksenrichment analysismetabolic disordersmetabolomics and lipidomics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Gayatri R. Iyer Janis Wigginton William Duren Jennifer L. LaBarre Marci Brandenburg Charles Burant George Michailidis Alla Karnovsky |
spellingShingle |
Gayatri R. Iyer Janis Wigginton William Duren Jennifer L. LaBarre Marci Brandenburg Charles Burant George Michailidis Alla Karnovsky Application of Differential Network Enrichment Analysis for Deciphering Metabolic Alterations Metabolites partial correlation networks differential networks enrichment analysis metabolic disorders metabolomics and lipidomics |
author_facet |
Gayatri R. Iyer Janis Wigginton William Duren Jennifer L. LaBarre Marci Brandenburg Charles Burant George Michailidis Alla Karnovsky |
author_sort |
Gayatri R. Iyer |
title |
Application of Differential Network Enrichment Analysis for Deciphering Metabolic Alterations |
title_short |
Application of Differential Network Enrichment Analysis for Deciphering Metabolic Alterations |
title_full |
Application of Differential Network Enrichment Analysis for Deciphering Metabolic Alterations |
title_fullStr |
Application of Differential Network Enrichment Analysis for Deciphering Metabolic Alterations |
title_full_unstemmed |
Application of Differential Network Enrichment Analysis for Deciphering Metabolic Alterations |
title_sort |
application of differential network enrichment analysis for deciphering metabolic alterations |
publisher |
MDPI AG |
series |
Metabolites |
issn |
2218-1989 |
publishDate |
2020-11-01 |
description |
Modern analytical methods allow for the simultaneous detection of hundreds of metabolites, generating increasingly large and complex data sets. The analysis of metabolomics data is a multi-step process that involves data processing and normalization, followed by statistical analysis. One of the biggest challenges in metabolomics is linking alterations in metabolite levels to specific biological processes that are disrupted, contributing to the development of disease or reflecting the disease state. A common approach to accomplishing this goal involves pathway mapping and enrichment analysis, which assesses the relative importance of predefined metabolic pathways or other biological categories. However, traditional knowledge-based enrichment analysis has limitations when it comes to the analysis of metabolomics and lipidomics data. We present a Java-based, user-friendly bioinformatics tool named Filigree that provides a primarily data-driven alternative to the existing knowledge-based enrichment analysis methods. Filigree is based on our previously published differential network enrichment analysis (DNEA) methodology. To demonstrate the utility of the tool, we applied it to previously published studies analyzing the metabolome in the context of metabolic disorders (type 1 and 2 diabetes) and the maternal and infant lipidome during pregnancy. |
topic |
partial correlation networks differential networks enrichment analysis metabolic disorders metabolomics and lipidomics |
url |
https://www.mdpi.com/2218-1989/10/12/479 |
work_keys_str_mv |
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