Cited by 304Gene expression and cancer classificationBioinformatics and Genomic NetworksGene Regulatory Network Analysis

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

Open access
Alter, Orly, Brown, Patrick O., Botstein, David·2003·Proceedings of the National Academy of Sciences

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.

Integrity signals

Registry

Crossref · 10.1073/pnas.0530258100

Cites

14 of 14 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Alter, O., Brown, P. O., & Botstein, D.
Affiliations
Stanford University (US)
Venue
Proceedings of the National Academy of Sciences
Published
2003-03-11
Volume
100
Issue
6
Pages
3351-3356
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
OpenAlex
W2129256542
Cited by
304
References
14
Citations by year
2026: 4 · 2025: 6 · 2024: 2 · 2023: 6 · 2022: 5 · 2021: 8 · 2020: 15 · 2019: 13 · 2018: 9 · 2017: 9 · 2016: 16 · 2015: 10 · 2014: 29 · 2013: 13 · 2012: 8
FWCI
7.58
Type
journal article
Language
en
Open access
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • National Human Genome Research Institute (5 K01 HG00038-01, K01HG000038)
  • National Cancer Institute (CA85129, CA 77097, R01CA077097, U01CA085129)
  • National Institute of General Medical Sciences (GM46406, R37GM046406, R01GM046406)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Keywords
generalized singular value decomposition, regulatory programs, biological processes, experimental artifacts, gene classification, yeast cell cycle, cross-species comparison
MeSH terms
Cell Cycle, Data Interpretation, Statistical, Genes, Fungal, Humans, Pheromones, RNA, Fungal, RNA, Messenger, Saccharomyces cerevisiae, Stress, Physiological, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Genomics, Databases, Genetic

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review