On the Use of Correlation and MI as a Measure of Metabolite-Metabolite Association for Network Differential Connectivity Analysis

Metabolites
Sanjeevan Jahagirdar, Edoardo Saccenti

Abstract

Metabolite differential connectivity analysis has been successful in investigating potential molecular mechanisms underlying different conditions in biological systems. Correlation and Mutual Information (MI) are two of the most common measures to quantify association and for building metabolite-metabolite association networks and to calculate differential connectivity. In this study, we investigated the performance of correlation and MI to identify significantly differentially connected metabolites. These association measures were compared on (i) 23 publicly available metabolomic data sets and 7 data sets from other fields, (ii) simulated data with known correlation structures, and (iii) data generated using a dynamic metabolic model to simulate real-life observed metabolite concentration profiles. In all cases, we found more differentially connected metabolites when using correlation indices as a measure for association than MI. We also observed that different MI estimation algorithms resulted in difference in performance when applied to data generated using a dynamic model. We concluded that there is no significant benefit in using MI as a replacement for standard Pearson's or Spearman's correlation when the application is t...Continue Reading

References

Nov 23, 2000·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·H Matsuda
Sep 1, 1996·Chaos·Thomas Schurmann, Peter Grassberger
Jul 13, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Alexander KraskovPeter Grassberger
Jul 13, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Ilya NemenmanRob de Ruyter van Steveninck
Oct 14, 2004·Bioinformatics·Juliane Schäfer, Korbinian Strimmer
Apr 11, 2006·Biostatistics·Yaqian GuoRobert Tibshirani
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Juliane Schäfer, Korbinian Strimmer
Jun 17, 2009·Journal of Proteome Research·Patrizia BerniniLeonardo Tenori
May 18, 2011·The Plant Journal : for Cell and Molecular Biology·Camila CaldanaMatthew A Hannah
Sep 16, 2011·Science Signaling·Avi Ma'ayan
Nov 1, 2011·Bioinformatics·Daniel J Stekhoven, Peter Bühlmann
Oct 12, 2013·International Journal of Cancer. Journal International Du Cancer·Mika HilvoSibylle Loibl
Jan 7, 2014·PloS One·Dragana StanleyRobert J Moore
Nov 28, 2014·Journal of Proteome Research·Edoardo SaccentiLeonardo Tenori
Aug 19, 2015·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Johannes F FahrmannSuzanne Miyamoto
Dec 10, 2015·British Journal of Cancer·Angela W ChanDavid Broadhurst
Apr 20, 2016·Proceedings of the National Academy of Sciences of the United States of America·Juan ZhaoLuonan Chen
Dec 21, 2016·Bioinformatics·Stefano CacciatoreDavid A MacIntyre
Nov 2, 2017·Journal of Proteome Research·Alessia VignoliEdoardo Saccenti
Nov 4, 2017·PLoS Computational Biology·Florian RohartKim-Anh Lê Cao
Mar 6, 2018·Metabolomics : Official Journal of the Metabolomic Society·Antonio RosatoEdoardo Saccenti
Jul 13, 2018·Angewandte Chemie·Alessia VignoliClaudio Luchinat
Oct 6, 2018·Essays in Biochemistry·Iman TavassolyRavi Iyengar
Dec 12, 2018·Nature Microbiology·Eric A FranzosaRamnik J Xavier
Dec 18, 2018·Analytical Biochemistry·Yijun YouTianlu Chen
Mar 5, 2019·Metabolomics : Official Journal of the Metabolomic Society·Victoria L StevensSusan M Gapstur
Jun 30, 2019·Metabolites·Abdul-Hamid EmwasDavid S Wishart
Oct 20, 2019·Nature Communications·Rani K PowersJoaquin M Espinosa
Nov 7, 2019·Nucleic Acids Research·Kenneth HaugClaire O'Donovan
Nov 9, 2019·Nucleic Acids Research·Rahuman S Malik-SheriffHenning Hermjakob

Citations

Jan 2, 2021·Computational and Structural Biotechnology Journal·Sandrien DesmetKris Morreel

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