Effective Analysis of Genomic Data

  • Paul R. Nelson
  • Andrew B. Goulter
  • Richard J. Davis
Part of the Methods in Molecular Medicine book series (MIMM, volume 104)

Abstract

High-throughput biotechnology has enabled genome-wide investigation of gene expression and has the potential to identify genes that have a role to play in focal cerebral ischemia, as well as many other interventions. The advent of this technology has also led to the generation of large amounts of expensive and complex expression data. One of the major problems with the generation of so much data is locating and extracting the relevant information to aid target identification and interpretation effectively and reliably. Statistical involvement is vital. Not only does it help to ensure effective extraction of information from the data, it also increases the likelihood that the data collected will embody the information about the differential expression of interest in the first place. The goal of this chapter is to recommend an effective process for investigating gene expression data. There are five stages in this process that we believe lead to reliable results when routinely applied to an expression dataset, once it has been appropriately generated and collected: (1) biological problem definition and design selection; (2) data examination, “preprocessing,” and reexamination; (3) data analysis step I: screening for differentially expressed genes; (4) data analysis step II: verifying differential expression; and (5) biological verification, interpretation, and communication.

Key Words

Differential expression experimental design data examination visualization preprocessing baseline features data analysis multivariate principal components analysis hierarchical cluster analysis partial least squares discriminant analysis regression coefficients variable influence on projection univariate analysis of variance covariate fold difference 

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Copyright information

© Humana Press Inc., Totowa, NJ 2005

Authors and Affiliations

  • Paul R. Nelson
    • 1
  • Andrew B. Goulter
    • 2
  • Richard J. Davis
    • 3
  1. 1.Prism Training and Consultancy Ltd.CambridgeUK
  2. 2.Exploratory Target ProfilingPharmagene plcRoystonUK
  3. 3.Pharmagene plcRoystonUK

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