Chapter 3 Matrix Factorization for Recovery of Biological Processes from Microarray Data

Andrew V. Kossenkov, Michael F. Ochs

Research output: Contribution to journalArticle

Abstract

We explore a number of matrix factorization methods in terms of their ability to identify signatures of biological processes in a large gene expression study. We focus on the ability of these methods to find signatures in terms of gene ontology enhancement and on the interpretation of these signatures in the samples. Two Bayesian approaches, Bayesian Decomposition (BD) and Bayesian Factor Regression Modeling (BFRM), perform best. Differences in the strength of the signatures between the samples suggest that BD will be most useful for systems modeling and BFRM for biomarker discovery.

Original languageEnglish (US)
Pages (from-to)59-77
Number of pages19
JournalMethods in Enzymology
Volume467
Issue numberC
DOIs
StatePublished - 2009

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Biological Phenomena
Microarrays
Factorization
Decomposition
Recovery
Gene Ontology
Bayes Theorem
Biomarkers
Gene expression
Ontology
Genes
Gene Expression

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Chapter 3 Matrix Factorization for Recovery of Biological Processes from Microarray Data. / Kossenkov, Andrew V.; Ochs, Michael F.

In: Methods in Enzymology, Vol. 467, No. C, 2009, p. 59-77.

Research output: Contribution to journalArticle

Kossenkov, Andrew V. ; Ochs, Michael F. / Chapter 3 Matrix Factorization for Recovery of Biological Processes from Microarray Data. In: Methods in Enzymology. 2009 ; Vol. 467, No. C. pp. 59-77.
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