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PMID: 12631705 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 100 ·No. 6 ·2003-03-18 ·Pages 3351-6

Alter O, Brown PO, Botstein D

Abstract

We describe a comparative mathematical framework for two genome-scale expression data sets. This framework formulates expression as superposition of the effects of regulatory programs, biological processes, and experimental artifacts common to both data sets, as well as those that are exclusive to one data set or the other, by using generalized singular value decomposition. This framework enables comparative reconstruction and classification of the genes and arrays of both data sets. We illustrate this framework with a comparison of yeast and human cell-cycle expression data sets.

MeSH Terms
Cell Cycle/genetics Data Interpretation, Statistical Databases, Genetic Gene Expression Profiling/statistics & numerical data Genes, Fungal/drug effects Genomics/statistics & numerical data Humans Oligonucleotide Array Sequence Analysis/statistics & numerical data Pheromones/pharmacology RNA, Fungal/genetics,metabolism RNA, Messenger/genetics,metabolism Saccharomyces cerevisiae/cytology,genetics,metabolism Stress, Physiological/genetics
Chemicals
Pheromones RNA, Fungal RNA, Messenger
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Alter Orly
Department of Genetics, Stanford University, Stanford, CA 94305. [email protected]
Brown Patrick O
Botstein David
References (11)
11 references, click to expand
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.0530258100
Email
[email protected]
Published
2003-03-18
Epub
2003-00-11
Pages
3351-6
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC152296
Subset
IM
Grants
NCI NIH HHS · U01 CA085129 · United States
NIGMS NIH HHS · R01 GM046406 · United States
NCI NIH HHS · R01 CA077097 · United States
NHGRI NIH HHS · 5K01 HG 00038-01 · United States
NIGMS NIH HHS · R37 GM046406 · United States
NHGRI NIH HHS · K01 HG000038 · United States
NCI NIH HHS · CA 85129 · United States
NIGMS NIH HHS · GM 46406 · United States
NCI NIH HHS · CA 77097 · United States
External Links
PubMed source DOI: 10.1073/pnas.0530258100 PMC Full Text View journal details
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