Predicting Network Activity from High Throughput Metabolomics

PLoS Computational Biology - Tập 9 Số 7 - Trang e1003123
Shuzhao Li1,2, Youngja Park3,4, Sai Duraisingham1,2, Frederick H. Strobel5, Nooruddin Khan1,2, Quinlyn A. Soltow4, Dean P. Jones4, Bali Pulendran1,2
1Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
2Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
3College of Pharmacy, Korea University, Seoul, South Korea
4Department of Medicine, Emory University, Atlanta, Georgia, United States of America
5Mass Spectrometry Center, Emory University, Atlanta, Georgia, United States of America

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S Biswas, 2012, Orchestration of metabolism by macrophages, Cell metabolism, 15, 432, 10.1016/j.cmet.2011.11.013

R DeBerardinis, 2012, Cellular metabolism and disease: what do metabolic outliers teach us?, Cell, 148, 1132, 10.1016/j.cell.2012.02.032

R Breitling, 2008, New surveyor tools for charting microbial metabolic maps, Nature Reviews Microbiology, 6, 156, 10.1038/nrmicro1797

R Kaddurah-Daouk, 2008, Metabolomics: a global biochemical approach to drug response and disease, Annu Rev Pharmacol Toxicol, 48, 653, 10.1146/annurev.pharmtox.48.113006.094715

G Patti, 2012, Metabolomics: the apogee of the omics trilogy, Nature Reviews Molecular Cell Biology, 13, 263, 10.1038/nrm3314

A Bordbar, 2012, Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation, Molecular Systems Biology, 8, 558, 10.1038/msb.2012.21

T Kind, 2010, Managing complexity-how many platforms do we need for metabolomics?, Journal of Biomolecular Techniques, 21, S6

Q Soltow, 2011, High-performance metabolic profiling with dual chromatography-fourier-transform mass spectrometry (dc-ftms) for study of the exposome, Metabolomics, 9, 132, 10.1007/s11306-011-0332-1

Y Park, 2012, High-performance metabolic profiling of plasma from seven mammalian species for simultaneous environmental chemical surveillance and bioeffect monitoring, Toxicology, 295, 47, 10.1016/j.tox.2012.02.007

J Roede, 2012, Detailed mitochondrial phenotyping by high resolution metabolomics, PloS ONE, 7, e33020, 10.1371/journal.pone.0033020

R Caspi, 2012, The metacyc database of metabolic pathways and enzymes and the biocyc collection of pathway/genome databases, Nucleic Acids Research, 40, D742, 10.1093/nar/gkr1014

M Oberhardt, 2009, Applications of genome-scale metabolic reconstructions, Molecular Systems Biology, 5, 320, 10.1038/msb.2009.77

I Thiele, 2010, A protocol for generating a high-quality genome-scale metabolic reconstruction, Nature Protocols, 5, 93, 10.1038/nprot.2009.203

C Henry, 2010, High-throughput generation, optimization and analysis of genome-scale metabolic models, Nature Biotechnology, 28, 977, 10.1038/nbt.1672

N Duarte, 2007, Global reconstruction of the human metabolic network based on genomic and bibliomic data, Proceedings of the National Academy of Sciences, 104, 1777, 10.1073/pnas.0610772104

H Ma, 2007, The edinburgh human metabolic network reconstruction and its functional analysis, Molecular Systems Biology, 3, 135, 10.1038/msb4100177

T Livnat Jerby, 2010, Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism, Molecular Systems Biology, 6, 401, 10.1038/msb.2010.56

M Sigurdsson, 2010, A detailed genome-wide reconstruction of mouse metabolism based on human recon 1, BMC Systems Biology, 4, 140, 10.1186/1752-0509-4-140

A Bordbar, 2011, A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology, BMC Systems Biology, 5, 180, 10.1186/1752-0509-5-180

R Agren, 2012, Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using init, PLoS Computational Biology, 8, e1002518, 10.1371/journal.pcbi.1002518

G Plata, 2010, Reconstruction and ux-balance analysis of the plasmodium falciparum metabolic network, Molecular Systems Biology, 6, 408, 10.1038/msb.2010.60

R Deo, 2010, Interpreting metabolomic profiles using unbiased pathway models, PLoS Computational Biology, 6, e1000692, 10.1371/journal.pcbi.1000692

W Dunn, 2012, Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics, Metabolomics, 9, 44, 10.1007/s11306-012-0434-4

C Smith, 2006, Xcms: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification, Analytical chemistry, 78, 779, 10.1021/ac051437y

T Yu, 2009, aplcmsadaptive processing of high-resolution lc/ms data, Bioinformatics, 25, 1930, 10.1093/bioinformatics/btp291

T Pluskal, 2010, Mzmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data, BMC bioinformatics, 11, 395, 10.1186/1471-2105-11-395

J Xia, 2010, Metpa: a web-based metabolomics tool for pathway analysis and visualization, Bioinformatics, 26, 2342, 10.1093/bioinformatics/btq418

L Cottret, 2010, Metexplore: a web server to link metabolomic experiments and genome-scale metabolic networks, Nucleic acids research, 38, W132, 10.1093/nar/gkq312

J Gao, 2010, Metscape: a cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks, Bioinformatics, 26, 971, 10.1093/bioinformatics/btq048

J Xia, 2011, Web-based inference of biological patterns, functions and pathways from metabolomic data using metaboanalyst, Nature Protocols, 6, 743, 10.1038/nprot.2011.319

G Kastenmüller, 2010, metap-server: a web-based metabolomics data analysis tool, Journal of Biomedicine and Biotechnology, 2011

E Melamud, 2010, Metabolomic analysis and visualization engine for lcms data, Analytical chemistry, 82, 9818, 10.1021/ac1021166

T Kind, 2006, Metabolomic database annotations via query of elemental compositions: mass accuracy is insufficient even at less than 1 ppm, BMC bioinformatics, 7, 234, 10.1186/1471-2105-7-234

T Kind, 2007, Seven golden rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry, BMC bioinformatics, 8, 105, 10.1186/1471-2105-8-105

M Brown, 2009, Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics, Analyst, 134, 1322, 10.1039/b901179j

D Wishart, 2009, Hmdb: a knowledgebase for the human metabolome, Nucleic Acids Research, 37, D603, 10.1093/nar/gkn810

R Tautenhahn, 2012, An accelerated workow for untargeted metabolomics using the metlin database, Nature Biotechnology, 30, 826, 10.1038/nbt.2348

M Kanehisa, 2006, From genomics to chemical genomics: new developments in KEGG, Nucleic Acids Research, 34, D354, 10.1093/nar/gkj102

S Li, 2010, Constructing a fish metabolic network model, Genome Biology, 11, R115, 10.1186/gb-2010-11-11-r115

E Ravasz, 2002, Hierarchical organization of modularity in metabolic networks, Science, 297, 1551, 10.1126/science.1073374

H Ma, 2004, Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph, Bioinformatics, 20, 1870, 10.1093/bioinformatics/bth167

M Newman, 2004, Finding and evaluating community structure in networks, Physical Review E, 69, 26113, 10.1103/PhysRevE.69.026113

M Newman, 2006, Modularity and community structure in networks, Proceedings of the National Academy of Sciences, 103, 8577, 10.1073/pnas.0601602103

G Berriz, 2003, Characterizing gene sets with funcassociate, Bioinformatics, 19, 2502, 10.1093/bioinformatics/btg363

D Hosack, 2003, Identifying biological themes within lists of genes with ease, Genome Biol, 4, R70, 10.1186/gb-2003-4-10-r70

W Paul, 2011, Bridging innate and adaptive immunity, Cell, 147, 1212, 10.1016/j.cell.2011.11.036

I Amit, 2009, Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses, Science, 326, 257, 10.1126/science.1179050

B Pulendran, 2010, Systems vaccinology, Immunity, 33, 516, 10.1016/j.immuni.2010.10.006

T Querec, 2006, Yellow fever vaccine yf-17d activates multiple dendritic cell subsets via tlr2, 7, 8, and 9 to stimulate polyvalent immunity, The Journal of experimental medicine, 203, 413, 10.1084/jem.20051720

T Querec, 2009, Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans, Nature Immunology, 10, 116, 10.1038/ni.1688

B Pulendran, 2009, Learning immunology from the yellow fever vaccine: innate immunity to systems vaccinology, Nature Reviews Immunology, 9, 741, 10.1038/nri2629

D Lembo, 2000, Expression of an altered ribonucleotide reductase activity associated with the replication of murine cytomegalovirus in quiescent fibroblasts, Journal of virology, 74, 11557, 10.1128/JVI.74.24.11557-11565.2000

G Gribaudo, 2000, Murine cytomegalovirus stimulates cellular thymidylate synthase gene expression in quiescent cells and requires the enzyme for replication, Journal of virology, 74, 4979, 10.1128/JVI.74.11.4979-4987.2000

L Vastag, 2011, Divergent effects of human cytomegalovirus and herpes simplex virus-1 on cellular metabolism, PLoS Pathogens, 7, e1002124, 10.1371/journal.ppat.1002124

J Peterson, 1998, Glutathione levels in antigen-presenting cells modulate th1 versus th2 response patterns, Proceedings of the National Academy of Sciences, 95, 3071, 10.1073/pnas.95.6.3071

G Angelini, 2002, Antigen-presenting dendritic cells provide the reducing extracellular microenvironment required for t lymphocyte activation, Proceedings of the National Academy of Sciences, 99, 1491, 10.1073/pnas.022630299

Z Yan, 2009, Extracellular redox modulation by regulatory t cells, Nature chemical biology, 5, 721, 10.1038/nchembio.212

V Bronte, 2005, Regulation of immune responses by l-arginine metabolism, Nature Reviews Immunology, 5, 641, 10.1038/nri1668

S Morris Jr, 2010, Arginine: master and commander in innate immune responses, Science Signalling, 3, pe27

J Kopincová, 2011, Biochemical aspects of nitric oxide synthase feedback regulation by nitric oxide, Interdisciplinary toxicology, 4, 63, 10.2478/v10102-011-0012-z

N Serbina, 2003, Tnf/inos-producing dendritic cells mediate innate immune defense against bacterial infection, Immunity, 19, 59, 10.1016/S1074-7613(03)00171-7

L Tong, 2011, Nitric oxide: A regulator of eukaryotic initiation factor 2 kinases, Free Radical Biology and Medicine, 50, 1717, 10.1016/j.freeradbiomed.2011.03.032

A Roux, 2012, Annotation of the human adult urinary metabolome and metabolite identification using ultra high performance liquid chromatography coupled to a ltq-orbitrap mass spectrometer, Analytical Chemistry, 84, 6429, 10.1021/ac300829f

MF Clasquin, 2011, Riboneogenesis in yeast, Cell, 145, 969, 10.1016/j.cell.2011.05.022

C Smith, 2005, Metlin: a metabolite mass spectral database, Therapeutic drug monitoring, 27, 747, 10.1097/01.ftd.0000179845.53213.39

Q Cui, 2008, Metabolite identification via the madison metabolomics consortium database, Nature biotechnology, 26, 162, 10.1038/nbt0208-162

CG Rivera, 2010, Nemo: network module identification in cytoscape, BMC bioinformatics, 11, S61, 10.1186/1471-2105-11-S1-S61

MT Dittrich, 2008, Identifying functional modules in protein–protein interaction networks: an integrated exact approach, Bioinformatics, 24, i223, 10.1093/bioinformatics/btn161

S Rogers, 2009, Probabilistic assignment of formulas to mass peaks in metabolomics experiments, Bioinformatics, 25, 512, 10.1093/bioinformatics/btn642

E Gaquerel, 2013, Computational annotation of plant metabolomics profiles via a novel network-assisted approach, Metabolomics

K Haug, 2013, Metabolightsan open-access general-purpose repository for metabolomics studies and associated meta-data, Nucleic Acids Research, 41, D781, 10.1093/nar/gks1004