MassTRIX Reloaded: Combined Analysis and Visualization of Transcriptome and Metabolome Data

PLoS ONE - Tập 7 Số 7 - Trang e39860
Brigitte Wägele1,2, Michael Witting1,3, Philippe Schmitt‐Kopplin4,3, Karsten Suhre5,2
1Department of Genome oriented Bioinformatics, Life and Food Science Center Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
2Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
3Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
4Chair of Analytical Food Chemistry, Technische Universität München, Freising-Weihenstephan, Germany
5Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City – Qatar Foundation, Doha, Qatar

Tóm tắt

Từ khóa


Tài liệu tham khảo

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

DP Leader, 2011, Pathos: A web facility that uses metabolic maps to display experimental changes in metabolites identified by mass spectrometry., Rapid Communications in Mass Spectrometry, 25, 3422, 10.1002/rcm.5245

F García-Alcalde, 2011, Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data., Bioinformatics, 27, 137, 10.1093/bioinformatics/btq594

M Kanehisa, 2000, KEGG: kyoto encyclopedia of genes and genomes., Nucleic Acids Res, 28, 27, 10.1093/nar/28.1.27

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

DS Wishart, 2009, HMDB: a knowledgebase for the human metabolome., D603

M Sud, 2007, LMSD: LIPID MAPS structure database., Nucleic Acids Research, 35, D527, 10.1093/nar/gkl838

R Caspi, 2008, The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases., Nucleic Acids Research, 36, D623, 10.1093/nar/gkm900

K Suhre, 2008, MassTRIX: mass translator into pathways., Nucleic Acids Research, 36, W481, 10.1093/nar/gkn194

N Huang, 1999, Automation of a Fourier transform ion cyclotron resonance mass spectrometer for acquisition, analysis, and e-mailing of high-resolution exact-mass electrospray ionization mass spectral data., Journal of the American Society for Mass Spectrometry, 10, 1166, 10.1016/S1044-0305(99)00089-6

Y Shinbo, 2006, KNApSAcK: A Comprehensive Species-Metabolite Relationship DatabasePlant Metabolomics., 165