ADEMA: an algorithm to determine expected metabolite level alterations using mutual information.
Metabolomics is a relatively new "omics" platform, which analyzes a discrete set of metabolites detected in bio-fluids or tissue samples of organisms. It has been used in a diverse array of studies to detect biomarkers and to determine activity rates for pathways based on changes due to di...
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doaj-c05bcaadb1a14faf8b5671158475983c2020-11-24T21:12:26ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582013-01-0191e100285910.1371/journal.pcbi.1002859ADEMA: an algorithm to determine expected metabolite level alterations using mutual information.A Ercument CicekIlya BedermanLeigh HendersonMitchell L DrummGultekin OzsoyogluMetabolomics is a relatively new "omics" platform, which analyzes a discrete set of metabolites detected in bio-fluids or tissue samples of organisms. It has been used in a diverse array of studies to detect biomarkers and to determine activity rates for pathways based on changes due to disease or drugs. Recent improvements in analytical methodology and large sample throughput allow for creation of large datasets of metabolites that reflect changes in metabolic dynamics due to disease or a perturbation in the metabolic network. However, current methods of comprehensive analyses of large metabolic datasets (metabolomics) are limited, unlike other "omics" approaches where complex techniques for analyzing coexpression/coregulation of multiple variables are applied. This paper discusses the shortcomings of current metabolomics data analysis techniques, and proposes a new multivariate technique (ADEMA) based on mutual information to identify expected metabolite level changes with respect to a specific condition. We show that ADEMA better predicts De Novo Lipogenesis pathway metabolite level changes in samples with Cystic Fibrosis (CF) than prediction based on the significance of individual metabolite level changes. We also applied ADEMA's classification scheme on three different cohorts of CF and wildtype mice. ADEMA was able to predict whether an unknown mouse has a CF or a wildtype genotype with 1.0, 0.84, and 0.9 accuracy for each respective dataset. ADEMA results had up to 31% higher accuracy as compared to other classification algorithms. In conclusion, ADEMA advances the state-of-the-art in metabolomics analysis, by providing accurate and interpretable classification results.http://europepmc.org/articles/PMC3547803?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
A Ercument Cicek Ilya Bederman Leigh Henderson Mitchell L Drumm Gultekin Ozsoyoglu |
spellingShingle |
A Ercument Cicek Ilya Bederman Leigh Henderson Mitchell L Drumm Gultekin Ozsoyoglu ADEMA: an algorithm to determine expected metabolite level alterations using mutual information. PLoS Computational Biology |
author_facet |
A Ercument Cicek Ilya Bederman Leigh Henderson Mitchell L Drumm Gultekin Ozsoyoglu |
author_sort |
A Ercument Cicek |
title |
ADEMA: an algorithm to determine expected metabolite level alterations using mutual information. |
title_short |
ADEMA: an algorithm to determine expected metabolite level alterations using mutual information. |
title_full |
ADEMA: an algorithm to determine expected metabolite level alterations using mutual information. |
title_fullStr |
ADEMA: an algorithm to determine expected metabolite level alterations using mutual information. |
title_full_unstemmed |
ADEMA: an algorithm to determine expected metabolite level alterations using mutual information. |
title_sort |
adema: an algorithm to determine expected metabolite level alterations using mutual information. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS Computational Biology |
issn |
1553-734X 1553-7358 |
publishDate |
2013-01-01 |
description |
Metabolomics is a relatively new "omics" platform, which analyzes a discrete set of metabolites detected in bio-fluids or tissue samples of organisms. It has been used in a diverse array of studies to detect biomarkers and to determine activity rates for pathways based on changes due to disease or drugs. Recent improvements in analytical methodology and large sample throughput allow for creation of large datasets of metabolites that reflect changes in metabolic dynamics due to disease or a perturbation in the metabolic network. However, current methods of comprehensive analyses of large metabolic datasets (metabolomics) are limited, unlike other "omics" approaches where complex techniques for analyzing coexpression/coregulation of multiple variables are applied. This paper discusses the shortcomings of current metabolomics data analysis techniques, and proposes a new multivariate technique (ADEMA) based on mutual information to identify expected metabolite level changes with respect to a specific condition. We show that ADEMA better predicts De Novo Lipogenesis pathway metabolite level changes in samples with Cystic Fibrosis (CF) than prediction based on the significance of individual metabolite level changes. We also applied ADEMA's classification scheme on three different cohorts of CF and wildtype mice. ADEMA was able to predict whether an unknown mouse has a CF or a wildtype genotype with 1.0, 0.84, and 0.9 accuracy for each respective dataset. ADEMA results had up to 31% higher accuracy as compared to other classification algorithms. In conclusion, ADEMA advances the state-of-the-art in metabolomics analysis, by providing accurate and interpretable classification results. |
url |
http://europepmc.org/articles/PMC3547803?pdf=render |
work_keys_str_mv |
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