MetPA: a web-based metabolomics tool for pathway analysis and visualization

Bioinformatics
Jianguo Xia, David S Wishart

Abstract

MetPA (Metabolomics Pathway Analysis) is a user-friendly, web-based tool dedicated to the analysis and visualization of metabolomic data within the biological context of metabolic pathways. MetPA combines several advanced pathway enrichment analysis procedures along with the analysis of pathway topological characteristics to help identify the most relevant metabolic pathways involved in a given metabolomic study. The results are presented in a Google-map style network visualization system that supports intuitive and interactive data exploration through point-and-click, dragging and lossless zooming. Additional features include a comprehensive compound library for metabolite name conversion, automatic generation of analysis report, as well as the implementation of various univariate statistical procedures that can be accessed when users click on any metabolite node on a pathway map. MetPA currently enables analysis and visualization of 874 metabolic pathways, covering 11 common model organisms. Freely available at http://metpa.metabolomics.ca.

References

Feb 7, 2002·Genomics·Purvesh KhatriStephen A Krawetz
Mar 7, 2003·Genomics·Sorin DraghiciStephen A Krawetz
Dec 25, 2003·Bioinformatics·Jelle J GoemanHans C van Houwelingen
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Aug 2, 2006·Briefings in Bioinformatics·Tero Aittokallio, Benno Schwikowski
Sep 6, 2007·Genome Research·Sorin DraghiciRoberto Romero
Sep 15, 2007·Bioinformatics·Seth I BergerAvi Ma'ayan
Nov 21, 2007·Bioinformatics·Manuela HummelUlrich Mansmann
Dec 14, 2007·Nucleic Acids Research·Minoru KanehisaYoshihiro Yamanishi
Oct 28, 2008·Nucleic Acids Research·David S WishartIan Forsythe
Nov 8, 2008·Bioinformatics·Adi Laurentiu TarcaRoberto Romero
Mar 25, 2009·Bioinformatics·Jitao David Zhang, Stefan Wiemann
May 12, 2009·Nucleic Acids Research·Jianguo XiaDavid S Wishart
Mar 26, 2010·Bioinformatics·Enrico GlaabAlfonso Valencia

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Citations

Oct 13, 2011·Analytical Chemistry·Gregory D TredwellJacob G Bundy
Oct 16, 2012·Briefings in Bioinformatics·Monica Chagoyen, Florencio Pazos
May 4, 2012·Nucleic Acids Research·Jianguo XiaDavid S Wishart
Jun 15, 2013·Nucleic Acids Research·Jianguo XiaRobert E W Hancock
Dec 18, 2012·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Mukesh VermaJohn P A Ioannidis
Jul 19, 2013·PLoS Computational Biology·Shuzhao LiBali Pulendran
Jan 18, 2014·Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology·Hervé Colinet, David Renault
Apr 2, 2013·Metabolomics : Official Journal of the Metabolomic Society·Jianguo XiaDavid S Wishart
Feb 26, 2016·Frontiers in Molecular Biosciences·Benjamin MerletFabien Jourdan
Feb 21, 2016·Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences·Hang ChuXijun Wang
Feb 26, 2015·Diabetes·Kelli M SasSubramaniam Pennathur
Jan 26, 2016·Journal of Pharmaceutical and Biomedical Analysis·Ya-Xiao ChenDong-Zi Yang
Nov 20, 2015·Toxicological Sciences : an Official Journal of the Society of Toxicology·Rance NaultTimothy R Zacharewski
Nov 28, 2014·Molecular Neurobiology·Arvind Kumar ShuklaMohana Krishna Reddy Mudiam
Nov 13, 2014·Analytical Chemistry·Caroline H JohnsonGary Siuzdak
Mar 5, 2016·Scientific Reports·Thomas J VelenosiBradley L Urquhart
Nov 5, 2014·BMC Bioinformatics·Maysson IbrahimKenneth Langlands
Nov 12, 2015·Analytical Chemistry·Abhinav DubeyHanudatta Sastry Atreya
Jan 26, 2013·Plant, Cell & Environment·Maria C DavisDion G Durnford
Jan 10, 2012·Academic Emergency Medicine : Official Journal of the Society for Academic Emergency Medicine·Deborah B DiercksMark Sutter
Nov 14, 2014·Electrophoresis·Raúl González-DomínguezJosé Luis Gómez-Ariza
Mar 30, 2016·International Journal of Medical Microbiology : IJMM·Dirk K WissenbachMartin von Bergen
Oct 1, 2015·Immunity, Inflammation and Disease·Michael J McGeachieJessica A Lasky-Su

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