Analytical and Bioanalytical Chemistry

, Volume 380, Issue 3, pp 419–429 | Cite as

Using chemometrics for navigating in the large data sets of genomics, proteomics, and metabonomics (gpm)

  • Lennart Eriksson
  • Henrik Antti
  • Johan Gottfries
  • Elaine Holmes
  • Erik Johansson
  • Fredrik Lindgren
  • Ingrid Long
  • Torbjörn Lundstedt
  • Johan Trygg
  • Svante Wold
Review
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Abstract

This article describes the applicability of multivariate projection techniques, such as principal-component analysis (PCA) and partial least-squares (PLS) projections to latent structures, to the large-volume high-density data structures obtained within genomics, proteomics, and metabonomics. PCA and PLS, and their extensions, derive their usefulness from their ability to analyze data with many, noisy, collinear, and even incomplete variables in both X and Y. Three examples are used as illustrations: the first example is a genomics data set and involves modeling of microarray data of cell cycle-regulated genes in the microorganism Saccharomyces cerevisiae. The second example contains NMR-metabonomics data, measured on urine samples of male rats treated with either of the drugs chloroquine or amiodarone. The third and last data set describes sequence-function classification studies in a set of G-protein-coupled receptors using hierarchical PCA.

Keywords

PCA PLS Hierarchical modeling Multivariate analysis Omics data analysis 
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Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Lennart Eriksson
    • 1
  • Henrik Antti
    • 2
    • 4
  • Johan Gottfries
    • 3
    • 4
  • Elaine Holmes
    • 2
  • Erik Johansson
    • 1
  • Fredrik Lindgren
    • 5
  • Ingrid Long
    • 6
  • Torbjörn Lundstedt
    • 6
  • Johan Trygg
    • 4
  • Svante Wold
    • 4
  1. 1.Umetrics ABUmeåSweden
  2. 2.Biological Chemistry, Biomedical Sciences Division, Faculty of MedicineImperial College of Science Technology and MedicineLondonUK
  3. 3.AstraZenecaR&D MölndalMölndalSweden
  4. 4.Institute of ChemistryUmeå UniversityUmeåSweden
  5. 5.Umetrics ABMalmö OfficeMalmöSweden
  6. 6.Department of Pharmaceutical ChemistryUppsala UniversityUppsalaSweden

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