Global test for metabolic pathway differences between conditions

Analytica Chimica Acta
Diana M HendrickxAge K Smilde

Abstract

In many metabolomics applications there is a need to compare metabolite levels between different conditions, e.g., case versus control. There exist many statistical methods to perform such comparisons but only few of these explicitly take into account the fact that metabolites are connected in pathways or modules. Such a priori information on pathway structure can alleviate problems in, e.g., testing on individual metabolite level. In gene-expression analysis, Goeman's global test is used to this extent to determine whether a group of genes has a different expression pattern under changed conditions. We examined if this test can be generalized to metabolomics data. The goal is to determine if the behavior of a group of metabolites, belonging to the same pathway, is significantly related to a particular outcome of interest, e.g., case/control or environmental conditions. The results show that the global test can indeed be used in such situations. This is illustrated with extensive intracellular metabolomics data from Escherichia coli and Saccharomyces cerevisiae under different environmental conditions.

References

Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Oct 26, 2000·Comparative Biochemistry and Physiology. Toxicology & Pharmacology : CBP·D SpassovaA K Singh
Jul 18, 2002·Nature Reviews. Drug Discovery·Jeremy K NicholsonElaine Holmes
Dec 25, 2003·Bioinformatics·Jelle J GoemanHans C van Houwelingen
Feb 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Jian WuStephen G Oliver
Jun 28, 2005·Nucleic Acids Research·André BoorsmaHarmen J Bussemaker
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Dec 31, 2005·Nucleic Acids Research·Minoru KanehisaMika Hirakawa
Feb 10, 2006·Proceedings of the National Academy of Sciences of the United States of America·Sergio RossellHans V Westerhoff
Aug 5, 2006·Proteomics·Katherine HollywoodRoyston Goodacre
Oct 4, 2006·Molecular Systems Biology·Tunahan CakirJens Nielsen
Nov 28, 2006·Bioinformatics·Zhen Jiang, Robert Gentleman
Dec 13, 2006·Proceedings of the National Academy of Sciences of the United States of America·Matthew J BrauerJoshua D Rabinowitz
Jun 8, 2007·Bioinformatics·James J ChenChen-An Tsai
Jul 7, 2007·BMC Bioinformatics·Irina DinuYutaka Yasui
Sep 4, 2007·Analytical Biochemistry·Mariët J van der WerfThomas Hankemeier
Jan 19, 2008·Briefings in Bioinformatics·Dougu Nam, Seon-Young Kim
Feb 25, 2009·Analytical Chemistry·Jörg Martin BüscherNicola Zamboni
Mar 4, 2009·Bioinformatics·Chen-An Tsai, James J Chen
Nov 3, 2009·Nucleic Acids Research·Minoru KanehisaMika Hirakawa
Jan 7, 2011·Bioinformatics·Monica Chagoyen, Florencio Pazos
Feb 16, 2011·Omics : a Journal of Integrative Biology·Mones S Abu-AsabHakima Amri
May 10, 2011·Bioinformatics·Matti KankainenMatej Oresic
Jun 4, 2011·PLoS Computational Biology·Frank Emmert-Streib, Galina V Glazko
Jun 24, 2011·PloS One·Edoardo SaccentiMargriet M W B Hendriks

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Citations

Mar 6, 2018·Metabolomics : Official Journal of the Metabolomic Society·Antonio RosatoEdoardo Saccenti
Oct 16, 2014·Molecular BioSystems·A Marcel WillemsenAntoine H C van Kampen
Apr 5, 2019·Neurology·Gerrit L J OnderwaterUNKNOWN BBMRI Metabolomics Consortium
Jul 12, 2012·Molecular BioSystems·Diana M HendrickxAge K Smilde
Jun 20, 2018·BMC Systems Biology·Abel Folch-FortunyAlberto Ferrer
Mar 5, 2019·Metabolomics : Official Journal of the Metabolomic Society·Parastoo FazelzadehJohn van Duynhoven
Sep 25, 2019·Journal of Clinical Medicine·Angela CaragnanoAntonio Paolo Beltrami
Mar 17, 2020·Journal of Proteome Research·Lingli DengJiyang Dong
May 19, 2021·Journal of Proteome Research·Lingli DengJiyang Dong

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