Beruflich Dokumente
Kultur Dokumente
Hypothesis Generation
Data Analysis
Data
Network Mapping
1. Generate Connections 2. Calculate Mappings 3. Create Network
Grapov D., Fiehn O., Multivariate and network tools for analysis and visualization of metabolomic data, ASMS, June 08, 2013, Minneapolis, MN
Biochemical Relationships
http://www.genome.jp/dbget-bin/www_bget?rn:R00975
Structural Similarity
http://pubchem.ncbi.nlm.nih.gov//score_matrix/score_matrix.cgi
Empirical Associations
How are the variables related given my experiment?
Types of associations: Correlation Partial correlation Bayesian Other
simple to calculate
can offer insight when the biology is unknown
Partial correlations can help simplify networks and preference direct over indirect associations.
10.1007/978-1-4614-1689-0_17
B
The observed changes can be summarized into three groups, A, B and central inversely correlated group
A) 1. increase in 5-Deoxy-5-(methylthio)adenosine (MTA) suggests deficiency of enzyme 5'-methylthioadenosine phosphorylase (MTAP) important for Sadenosylmethionine (AdoMet) salvage shown to be decreased in cancer inhibits spermidine synthase [PMID:6896990, PMID:21135097] vital for cell survival 2. increased 5,6-dihydrouracil is observed in prostate cancer [PMID:23824564] 3. increased xanthine indicates tissue depletion of ATP [PMID:3062020] and product uric acid is a pro-oxidant (in cells) [PMID:18600514] 4. biosynthesis of UDP-GlcNAc involves glutamate B) 1. ornithine and citrulline linked through ornithine transcarbamylase [PMID:11849441] 2. decrease in citrulline, allantoic acid and biuret may suggest reduction in urea cycle 3. nicotinamide induces L-ornithine decarboxylase [PMID: 153228, heart] which is necessary for putrescine synthesis
$20K earnings
Automated Data Analysis and Reporting
Primary Metabolomics
1. Dmitry Grapov, Caitlin Campbell, Oliver Fiehn, Carol J. Chandler, Dustin J. Burnett, Elaine C. Souza, John K. Meissen, Kohei Takeuchi, Gretchen A. Casazza, Mary B. Gustafson, Nancy L. Keim, John W. Newman, Gary R. Hunter, Jose R. Fernandez, W. Timothy Garvey, Mary-Ellen Harper, Charles L. Hoppel, and Sean H. Adams, Altered patterns of plasma metabolites of endogenous and gut origin in insulin-resistant obese women following a weight loss and fitness intervention, Nov. 2013, Plos ONE (accepted) Dmitry Grapov, Johannes Fahrmann, Manami Hara, Oliver Fiehn, Type 1 diabetes associated metabolic perturbations. (in preparation) William R. Wikoff, Dmitry Grapov, Brian Defelice*, Oliver Fiehn*, Suzanne Miyamoto, William Rom, Harvey Pass, Karen Kelly, David Gandara, Kyoungmi Kim, Early Stage Adenocarcinoma Affects Multiple Metabolic Pathways in Lung Tissue. Cancer research (in preparation) Brian D. Piccolo, Dmitry Grapov, W. Timothy Garvey, Mary-Ellen Harper, Oliver Fiehn, Sean H. Adams, John W. Newman, Impact of a human missense UCP3 polymorphism on the plasma metabolomic profile: support for a mitochondrial fuel-partitioning role for UCP3 (in preparation)
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Lipidomics
1. Dmitry Grapov, Stuart G. Snowden, Heli Nygren,Magnus Settergren, Fabio Luiz DAlexandri, Jesper Z. Haeggstrm, Tuulia Hytylinen, Theresa L. Pedersen, John W. Newman, Matej Orei, John Pernow, Craig E. Wheelock, High dose simvastatin exhibits enhanced lipid lowering effects relative to simvastatin/ezetimibe combination therapy. Circulation Cardiovascular Genetics, Nov. 2013 (submitted)
2.
Schuster GU, Bratt JM, Jiang X, Pedersen TL, Grapov D, Adkins Y, Kelley DS, Newman JW, Kenyon NJ, Stephensen CB. Dietary Long-Chain Omega-3 Fatty Acids do not Diminish Eosinophilic Pulmonary Inflammation in Mice. Am J Respir Cell Mol Biol. 2013 Oct 17.
Denis J. Glenn, Michelle C. Cardema, Wei Ni, Yan Zhang, Yerem Yeghiazarians, Dmitry Grapov, Oliver Fiehn and David G. Gardner, Cardiac Steatosis Potentiates Angiotensin II Effects in the Heart. Sept. 2013, Circulation (in review)
3.
Bioinformatics
1. Dmitry Grapov, Oliver Fiehn, MetaMapR: a Metabolomic Network Generation and Analysis Tool. Bioinformatics (in preparation)
2.
Dmitry Grapov, Oliver Fiehn, Devium: Dynamic Multivariate Data Analysis and Visualization Platform. Bioinformatics (in development)
Method Development
1. Dmitry Grapov, Theresa Pedersen, John W. Newman, Quantitative analysis of Sterol Ester, Triglyceride and Phospholipid Bound Fatty Acids and Oxylipins. (in preparation)