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Combining Metabonomics and Other -omics Data

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Metabonomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1277))

Abstract

Combining molecular profiling data from multiple -omics platforms has the potential to provide a more comprehensive characterization of the biological system as well as improved prediction models for diagnostic applications compared to information derived from a single molecular profiling platform. In this chapter we outline analysis strategies for characterization of the genetic drivers of metabolism, joint pathway analysis in metabonomic and transcriptomic data and how metabonomic, and other -omics data can be combined to improve prediction models.

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References

  1. Dumas ME, Wilder SP, Bihoreau MT et al (2007) Direct quantitative trait locus mapping of mammalian metabolic phenotypes in diabetic and normoglycemic rat models. Nat Genet 39(5):666–672

    Article  CAS  PubMed  Google Scholar 

  2. Gieger C, Geistlinger L, Altmaier E et al (2008) Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum. PLoS Genet 4(11):e1000282

    Article  PubMed Central  PubMed  Google Scholar 

  3. Illig T, Gieger C, Zhai G et al (2010) A genome-wide perspective of genetic variation in human metabolism. Nat Genet 42(2):137–141

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  4. Kettunen J, Tukiainen T, Sarin AP et al (2012) Genome-wide association study identifies multiple loci influencing human serum metabolite levels. Nat Genet 44(3):269–276

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. Nicholson G, Rantalainen M, Li JV et al (2011) A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. PLoS Genet 7(9):e1002270

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  6. Khatri P, Sirota M, Butte AJ (2012) Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol 8(2):e1002375

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. Ramanan VK, Shen L, Moore JH et al (2012) Pathway analysis of genomic data: concepts, methods, and prospects for future development. Trends Genet 28(7):323–332

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  8. Subramanian A, Tamayo P, Mootha VK et al (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102(43):15545–15550

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. Astrakas L, Blekas KD, Constantinou C et al (2011) Combining magnetic resonance spectroscopy and molecular genomics offers better accuracy in brain tumor typing and prediction of survival than either methodology alone. Int J Oncol 38(4):1113–1127

    CAS  PubMed  Google Scholar 

  10. Bjerrum JT, Rantalainen M, Wang Y et al (2013) Integration of transcriptomics and metabonomics: improving diagnostics, biomarker identification and phenotyping in ulcerative colitis. Metabolomics 10(2):280–290

    Google Scholar 

  11. Borgan E, Sitter B, Lingjaerde OC et al (2010) Merging transcriptomics and metabolomics–advances in breast cancer profiling. BMC Cancer 10:628

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  12. Tibshirani R (1996) Regression shrinkage and selection via the lasso. J Roy Stat Soc B Meth 58(1):267–288

    Google Scholar 

  13. Wold S, Sjöström M, Eriksson L (2001) PLS-regression: a basic tool of chemometrics. Chemometr Intell Lab 58(2):109–130

    Article  CAS  Google Scholar 

  14. Bylesjö M, Rantalainen M, Cloarec O et al (2007) OPLS discriminant analysis: combining the strengths of PLS-DA and SIMCA classification. J Chemometr 20(8–10):341–351

    Google Scholar 

  15. R Core Team (2013) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/

  16. McCarthy MI, Abecasis GR, Cardon LR et al (2008) Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 9(5):356–369

    Article  CAS  PubMed  Google Scholar 

  17. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc B Meth 57(1):289–300

    Google Scholar 

  18. Storey J (2003) The positive false discovery rate: a Bayesian interpretation and the q-value. Ann Stat 31(6):2013–2035

    Article  Google Scholar 

  19. Curtis RK, Oresic M, Vidal-Puig A (2005) Pathways to the analysis of microarray data. Trends Biotechnol 23(8):429–435

    Article  CAS  PubMed  Google Scholar 

  20. Mootha VK, Lindgren CM, Eriksson KF et al (2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34(3):267–273

    Article  CAS  PubMed  Google Scholar 

  21. Cavill R, Kamburov A, Ellis JK et al (2011) Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells. PLoS Comput Biol 7(3):e1001113

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  22. Kamburov A, Cavill R, Ebbels TM et al (2011) Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA. Bioinformatics 27(20):2917–2918

    Article  CAS  PubMed  Google Scholar 

  23. Brown CD, Davis HT (2006) Receiver operating characteristics curves and related decision measures: a tutorial. Chemometr Intell Lab 80(1):24–38

    Article  CAS  Google Scholar 

  24. Delong ER, Delong DM, Clarkepearson DI (1988) Comparing the areas under 2 or more correlated receiver operating characteristic curves – a nonparametric approach. Biometrics 44(3):837–845

    Article  CAS  PubMed  Google Scholar 

  25. Vickers AJ, Cronin AM, Begg CB (2011) One statistical test is sufficient for assessing new predictive markers. BMC Med Res Methodol 11(1):13

    Article  PubMed Central  PubMed  Google Scholar 

  26. Turner S, Armstrong LL, Bradford Y et al (2011) Quality control procedures for genome-wide association studies. Current protocols in human genetics/editorial board, Jonathan L. Haines (et al.) Chapter 1:Unit1. 19

    Google Scholar 

  27. Steinhoff C, Vingron M (2006) Normalization and quantification of differential expression in gene expression microarrays. Brief Bioinform 7(2):166–177

    Article  CAS  PubMed  Google Scholar 

  28. Soneson C, Delorenzi M (2013) A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinformatics 14(1):91

    Article  PubMed Central  PubMed  Google Scholar 

  29. Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28(1):27–30

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  30. Matthews L, Gopinath G, Gillespie M et al (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 37(Database issue):D619–D622

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  31. Fonville JM, Richards SE, Barton RH et al (2010) The evolution of partial least squares models and related chemometric approaches in metabonomics and metabolic phenotyping. J Chemometr 24(11–12):636–649

    Article  CAS  Google Scholar 

  32. Varma S, Simon R (2006) Bias in error estimation when using cross-validation for model selection. BMC Bioinformatics 7:91

    Article  PubMed Central  PubMed  Google Scholar 

  33. Spicker JS, Brunak S, Frederiksen KS et al (2008) Integration of clinical chemistry, expression, and metabolite data leads to better toxicological class separation. Toxicol Sci 102(2):444–454

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

M. R. acknowledges funding received from Karolinska Institutet.

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Correspondence to Mattias Rantalainen .

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© 2015 Springer Science+Business Media New York

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Rantalainen, M. (2015). Combining Metabonomics and Other -omics Data. In: Bjerrum, J. (eds) Metabonomics. Methods in Molecular Biology, vol 1277. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2377-9_12

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  • DOI: https://doi.org/10.1007/978-1-4939-2377-9_12

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2376-2

  • Online ISBN: 978-1-4939-2377-9

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