Share Email Print
cover

Proceedings Paper

Processing and modeling genome-wide expression data using singular value decomposition
Author(s): Orly Alter; Patrick O. Brown; David Botstein
Format Member Price Non-Member Price
PDF $14.40 $18.00
cover GOOD NEWS! Your organization subscribes to the SPIE Digital Library. You may be able to download this paper for free. Check Access

Paper Abstract

We describe the use of singular value decomposition in transforming genome-wide expression data from genes x arrays space to reduced diagonalized eigengenes x eigenarrays space, where the eigengenes (or eigenarrays) are unique orthonormal superpositions of the genes (or arrays). Normalizing the data by filtering out the eigengenes (and eigenarrays) that are inferred to represent additive or multiplicative noise, experimental artifacts, or even irrelevant biological processes enables meaningful comparison of the expression of different genes across different arrays in different experiments. Sorting the data according to the eigengenes and eigenarrays gives a global picture of the dynamics of gene expression, in which individual genes and arrays appear to be classified into groups of similar regulation and function, or similar cellular state and biological phenotype, respectively. After normalization and sorting, the significant eigengenes and eigenarrays can be associated with observed genome-wide effects of regulators, or with measured samples, in which these regulators are overactive or underactive, respectively.

Paper Details

Date Published: 4 June 2001
PDF: 16 pages
Proc. SPIE 4266, Microarrays: Optical Technologies and Informatics, (4 June 2001); doi: 10.1117/12.427986
Show Author Affiliations
Orly Alter, Stanford Univ. (United States)
Patrick O. Brown, Stanford Univ. (United States)
David Botstein, Stanford Univ. (United States)


Published in SPIE Proceedings Vol. 4266:
Microarrays: Optical Technologies and Informatics
Michael L. Bittner; Yidong Chen; Andreas N. Dorsel; Edward R. Dougherty, Editor(s)

© SPIE. Terms of Use
Back to Top