RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites

Metabolites
Bofei ZhangEwy A Mathé

Abstract

The value of metabolomics in translational research is undeniable, and metabolomics data are increasingly generated in large cohorts. The functional interpretation of disease-associated metabolites though is difficult, and the biological mechanisms that underlie cell type or disease-specific metabolomics profiles are oftentimes unknown. To help fully exploit metabolomics data and to aid in its interpretation, analysis of metabolomics data with other complementary omics data, including transcriptomics, is helpful. To facilitate such analyses at a pathway level, we have developed RaMP (Relational database of Metabolomics Pathways), which combines biological pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, WikiPathways, and the Human Metabolome DataBase (HMDB). To the best of our knowledge, an off-the-shelf, public database that maps genes and metabolites to biochemical/disease pathways and can readily be integrated into other existing software is currently lacking. For consistent and comprehensive analysis, RaMP enables batch and complex queries (e.g., list all metabolites involved in glycolysis and lung cancer), can readily be integrated into pathway analysis tools, and supports pathway overrepresentat...Continue Reading

References

Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Jan 5, 2007·Nucleic Acids Research·David S WishartLori Querengesser
Sep 6, 2007·Genome Research·Sorin DraghiciRoberto Romero
Oct 28, 2008·Nucleic Acids Research·David S WishartIan Forsythe
Nov 8, 2008·Bioinformatics·Adi Laurentiu TarcaRoberto Romero
Dec 2, 2009·Nucleic Acids Research·Alex FrolkisDavid S Wishart
Nov 13, 2010·Nucleic Acids Research·Ethan G CeramiChris Sander
Mar 5, 2011·BMC Bioinformatics·Gang SuFan Meng
Nov 19, 2011·Nucleic Acids Research·Thomas KelderAlexander R Pico
Apr 27, 2012·Analytical Chemistry·Ralf TautenhahnGary Siuzdak
Nov 20, 2012·Nucleic Acids Research·David S WishartAugustin Scalbert
Jun 15, 2013·Nucleic Acids Research·Jianguo XiaRobert E W Hancock
Aug 7, 2013·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Geng ZhangS Perwez Hussain
Nov 10, 2013·Nucleic Acids Research·Timothy JewisonDavid S Wishart
Jan 1, 2012·Cancers·Marija MilacicLincoln Stein
Nov 19, 2013·Nucleic Acids Research·David CroftPeter D'Eustachio
Dec 10, 2013·The Journal of Clinical Investigation·Atsushi TerunumaStefan Ambs
Feb 4, 2014·Cancer Letters·Katherine M Aird, Rugang Zhang
Jan 15, 2015·Nature Reviews. Genetics·Marylyn D RitchieDokyoon Kim
Apr 22, 2015·Nucleic Acids Research·Jianguo XiaDavid S Wishart
Jun 20, 2015·BioMed Research International·Aihua ZhangXijun Wang
Sep 24, 2015·Biomarker Insights·Kwanjeera WanichthanarakDmitry Grapov
Oct 16, 2015·Briefings in Bioinformatics·Rachel CavillJacob Jan Briedé
Oct 18, 2015·Nucleic Acids Research·Minoru KanehisaMao Tanabe
Oct 21, 2015·Nucleic Acids Research·Martina KutmonAlexander R Pico
Mar 17, 2016·Nature Reviews. Molecular Cell Biology·Caroline H JohnsonGary Siuzdak
Sep 20, 2016·Metabolomics : Official Journal of the Metabolomic Society·Richard D BegerUNKNOWN for “Precision Medicine and Pharmacometabolomics Task Group”-Metabolomics Society Initiative
Dec 3, 2016·Nucleic Acids Research·Minoru KanehisaKanae Morishima
Feb 12, 2017·Cell·James E BradnerRichard A Young
Nov 15, 2017·Nucleic Acids Research·Denise N SlenterEgon L Willighagen
Apr 17, 2018·Non-coding RNA·Salvatore AlaimoAlfredo Pulvirenti

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Citations

May 17, 2019·BMC Bioinformatics·Daniel Domingo-FernándezMartin Hofmann-Apitius
Nov 18, 2018·Electrophoresis·Biswapriya B Misra, Subhashree Mohapatra
Jan 12, 2019·Frontiers in Immunology·Debajyoti GhoshTesfaye B Mersha
Jun 21, 2019·Metabolites·Su H ChuUNKNOWN Consortium of Metabolomics Studies Statistics Working Group
Mar 5, 2019·Metabolomics : Official Journal of the Metabolomic Society·Ksenia ShestakovaSvetlana A Appolonova
Sep 25, 2019·Metabolites·Jan StanstrupSteffen Neumann
Apr 16, 2021·Journal of Pharmaceutical and Biomedical Analysis·Sinem Nalbantoglu, Abdullah Karadag

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Software Mentioned

GenMAPP
PathVisio
Metabox
Python library urllib
MetaboAnalyst
Reactome
RaMP R
Metabolomics Workbench Refmet resource
XCMS
GeneMAPP

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