Metabolome

Metabolome^[1] refers to the complete set of small-molecule metabolites (such as metabolic intermediates, hormones and other signaling molecules, and secondary metabolites) to be found within a biological sample, such as a single organism. The word was coined in analogy with transcriptomics and proteomics; like the transcriptome and the proteome, the metabolome is dynamic, changing from second to second. Although the metabolome can be defined readily enough, it is not currently possible to analyse the entire range of metabolites by a single analytical method (see metabolomics). In January 2007 scientists at the University of Alberta and the University of Calgary finished a draft of the human metabolome. They have catalogued and characterized 2,500 metabolites, 1,200 drugs and 3,500 food components that can be found in the human body.

See also

• tumor metabolome
• Mass spectrometry | 2D gel | Protein sequencing.
• Databases: PIR | Swissprot | Pfam
• Bioinformatics

External links

• Proteome.org
• Metabolomics journal
• Bioinformatics Journal
• The Human Metabolome Project
• The Human Metabolome Database
• The Human Metabolite Library
• The Human Serum Metabolome Project (HUSERMET)
• PDF of Reporting Standards for Metabolomic Studies
• Scientists complete human metabalome

References

1. ^ First use of the term "metabolome" in the literature — Oliver SG, Winson MK, Kell DB, Baganz F (September 1998). "Systematic functional analysis of the yeast genome". Trends Biotechnol. 16 (9): 373–8. doi:10.1016/S0167-7799(98)01214-1. PMID 9744112. http://linkinghub.elsevier.com/retrieve/pii/S0167-7799(98)01214-1. 
2. First book on metabolomics — Harrigan, G. G. & Goodacre, R. (eds) (2003). Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis. Kluwer Academic Publishers (Boston). ISBN 1-4020-7370-4. 
3. Fiehn O, Kloska S, Altmann T (February 2001). "Integrated studies on plant biology using multiparallel techniques". Curr. Opin. Biotechnol. 12 (1): 82–6. doi:10.1016/S0958-1669(00)00165-8. PMID 11167078. http://linkinghub.elsevier.com/retrieve/pii/S0958-1669(00)00165-8. 
4. Fiehn O (2001). "Combining Genomics, Metabolome Analysis, and Biochemical Modelling to Understand Metabolic Networks". Comp. Funct. Genomics 2 (3): 155–68. doi:10.1002/cfg.82. PMC 2447208. PMID 18628911. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2447208. 

• Weckwerth W (2003). "Metabolomics in systems biology". Annu Rev Plant Biol 54: 669–89. doi:10.1146/annurev.arplant.54.031902.135014. PMID 14503007. 
• Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG, Kell DB (May 2004). "Metabolomics by numbers: acquiring and understanding global metabolite data". Trends Biotechnol. 22 (5): 245–52. doi:10.1016/j.tibtech.2004.03.007. PMID 15109811. 
• Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S, Fung C, Nikolai L, Lewis M, Coutouly M-A, Forsythe I, Tang P, Shrivastava S, Jeroncic K, Stothard P, Amegbey G, Block D, Hau DD, Wagner J, Miniaci J, Clements M, Gebremedhin M, Guo N, Zhang Y, Duggan GE, MacInnis GD, Weljie AM, Dowlatabadi R, Bamforth F, Clive D, Greiner R, Li L, Marrie T, Sykes BD, Vogel HJ, Querengesser L (January 2007). "HMDB: the Human Metabolome Database". Nucleic Acids Research 35 (Database issue) (Database issue): D521–6. doi:10.1093/nar/gkl923. PMC 1899095. PMID 17202168. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1899095. 
• Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, Mandal R, Sinelnikov I, Xia J, Jia L, Cruz JA, Lim E, Sobsey CA, Shrivastava S, Huang P, Liu P, Fang L, Peng J, Fradette R, Cheng D, Tzur D, Clements M, Lewis A, De Souza A, Zuniga A, Dawe M, Xiong Y, Clive D, Greiner R, Nazyrova A, Shaykhutdinov R, Li L, Vogel HJ, Forsythe I (January 2009). "HMDB: a knowledgebase for the human metabolome". Nucleic Acids Research 37 (Database issue) (Database issue): D603–10. doi:10.1093/nar/gkn810. PMC 2686599. PMID 18953024. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2686599. 
• Nicholson JK, Holmes E, Lindon JC, Wilson ID (October 2004). "The challenges of modeling mammalian biocomplexity". Nat. Biotechnol. 22 (10): 1268–74. doi:10.1038/nbt1015. PMID 15470467. . Stresses the role of intestinal microorganisms in contributing to the human metabolome.
• van der Greef J, Stroobant P, van der Heijden R (October 2004). "The role of analytical sciences in medical systems biology". Curr Opin Chem Biol 8 (5): 559–65. doi:10.1016/j.cbpa.2004.08.013. PMID 15450501. 
  • The importance of analytical sciences to omics and systems biology.
• Kell DB (June 2004). "Metabolomics and systems biology: making sense of the soup". Curr. Opin. Microbiol. 7 (3): 296–307. doi:10.1016/j.mib.2004.04.012. PMID 15196499. 
• Dunn W.B., Ellis D.I. (2005). "Metabolomics: current analytical platforms and methodologies". Trends in Analytical Chemistry 24 (4): 285–294. doi:10.1016/j.trac.2004.11.021. 
• Ellis DI, Goodacre R (August 2006). "Metabolic fingerprinting in disease diagnosis: biomedical applications of infrared and Raman spectroscopy". Analyst 131 (8): 875–85. doi:10.1039/b602376m. PMID 17028718. 
  • Metabolomic data as an input to systems biology models.