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Pattern Identification in Time-Course Gene Expression Data with the CoGAPS Matrix Factorization

  • Elana J. Fertig
  • Genevieve Stein-O’Brien
  • Andrew Jaffe
  • Carlo Colantuoni
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1101)

Abstract

Patterns in time-course gene expression data can represent the biological processes that are active over the measured time period. However, the orthogonality constraint in standard pattern-finding algorithms, including notably principal components analysis (PCA), confounds expression changes resulting from simultaneous, non-orthogonal biological processes. Previously, we have shown that Markov chain Monte Carlo nonnegative matrix factorization algorithms are particularly adept at distinguishing such concurrent patterns. One such matrix factorization is implemented in the software package CoGAPS. We describe the application of this software and several technical considerations for identification of age-related patterns in a public, prefrontal cortex gene expression dataset.

Key words

Markov Chain Monte Carlo Gene expression Nonnegative matrix factorization 

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Copyright information

© Springer Science+Business Media, LLC 2014

Authors and Affiliations

  • Elana J. Fertig
    • 1
  • Genevieve Stein-O’Brien
    • 2
    • 3
  • Andrew Jaffe
    • 3
  • Carlo Colantuoni
    • 3
  1. 1.Oncology Biostatistics and BioinformaticsJohns Hopkins UniversityBaltimoreUSA
  2. 2.Institute of Genetic Medicine, Human Genetics Graduate ProgramJohns Hopkins University School of MedicineBaltimoreUSA
  3. 3.Lieber Institute for Brain DevelopmentBaltimoreUSA

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