Grant Number:	5U01CA235487-03 Interpret this number
Primary Investigator:	Karnovsky, Alla
Organization:	University Of Michigan At Ann Arbor
Project Title:	Methods and Tools for Integrative Functional Enrichment Analysis of Metabolomics Data
Fiscal Year:	2020

Abstract Modern analytical methods allow simultaneous detection of hundreds of metabolites, generating increasingly large and complex data sets. Analysis of metabolomics data is a multi-step process that requires variety of bioinformatics and statistical tools. One of the biggest challenges in metabolomics is how alterations in metabolite levels can be linked to specific biological processes that are disrupted contributing to the development of disease, or reflecting the disease state. To address this challenge, we propose to develop methods and build computational tools to help researchers interrogate their metabolomics data and integrate them with other molecular phenotypes to build testable hypotheses and derive biological knowledge that could help addressing this challenge. Our team has extensive collaborative experience working together in the Phase I Common Fund-supported Regional Comprehensive Metabolomics Resource Core (MRC2) and in building computational methods and tools for the analysis of multi-dimensional `omics data. We propose to build on our past efforts to develop a novel functional enrichment testing (FET) approach that will not be limited to compounds found in canonical metabolic pathways and will include both known and unknown metabolites in the analysis. We will leverage our previously developed methodology for building partial correlation networks that allows identifying commonalities and differences in network structures derived from different experimental conditions. Exploring relationships between key metabolic changes and alterations in transcript, proteins and other molecular components can provide additional levels of information and help build biological insights from experimental data. The overarching goal of this proposal is to develop FET methods that would enable analysis of multi-condition, multi-layer `omics data sets. To that end, we propose a network-based data integration strategy that will help uncover relationships both within and between different molecular layers, identify subnetworks, containing metabolites, transcripts etc., and test their significance. We anticipate that the application of our methods will lead to better insights into molecular networks affected by many complex diseases. !




DNEA: an R package for fast and versatile data-driven network analysis of metabolomics data.
Authors: Patsalis C. , Iyer G. , Brandenburg M. , Karnovsky A. , Michailidis G. .
Source: Bmc Bioinformatics, 2024-12-18 00:00:00.0; 25(1), p. 383.
EPub date: 2024-12-18 00:00:00.0.
PMID: 39695921
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CorrelationCalculator and Filigree: Tools for Data-Driven Network Analysis of Metabolomics Data.
Authors: Iyer G. , Brandenburg M. , Patsalis C. , Michailidis G. , Karnovsky A. .
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Metabolomics identifies shared lipid pathways in independent amyotrophic lateral sclerosis cohorts.
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A generalized likelihood-based Bayesian approach for scalable joint regression and covariance selection in high dimensions.
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Lipidomic approaches to dissect dysregulated lipid metabolism in kidney disease.
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Application of Differential Network Enrichment Analysis for Deciphering Metabolic Alterations.
Authors: Iyer G.R. , Wigginton J. , Duren W. , LaBarre J.L. , Brandenburg M. , Burant C. , Michailidis G. , Karnovsky A. .
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Pathway Analysis for Targeted and Untargeted Metabolomics.
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Differential network enrichment analysis reveals novel lipid pathways in chronic kidney disease.
Authors: Ma J. , Karnovsky A. , Afshinnia F. , Wigginton J. , Rader D.J. , Natarajan L. , Sharma K. , Porter A.C. , Rahman M. , He J. , et al. .
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Untargeted Metabolomics Differentiates l-Carnitine Treated Septic Shock 1-Year Survivors and Nonsurvivors.
Authors: Evans C.R. , Karnovsky A. , Puskarich M.A. , Michailidis G. , Jones A.E. , Stringer K.A. .
Source: Journal Of Proteome Research, 2019-05-03 00:00:00.0; 18(5), p. 2004-2011.
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