Identifying genes from up-down properties of microarray expression series

Autor: Jean-Pierre Nadal, François Radvanyi, Thomas M. A. Fink, Karen Willbrand, Jean Paul Thiery
Přispěvatelé: Laboratoire de Physique Statistique de l'ENS (LPS), Université Paris Diderot - Paris 7 (UPD7)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Compartimentation et dynamique cellulaires (CDC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS)
Rok vydání: 2005
Předmět:
Statistics and Probability
Time Factors
Microarray
MESH: Algorithms
Computational biology
computer.software_genre
Biochemistry
Pattern Recognition
Automated

MESH: Gene Expression Profiling
03 medical and health sciences
0302 clinical medicine
MESH: Pattern Recognition
Automated

Molecular Biology
Gene
Oligonucleotide Array Sequence Analysis
030304 developmental biology
Mathematics
Sequence (medicine)
0303 health sciences
Series (mathematics)
Gene Expression Profiling
MESH: Time Factors
Function (mathematics)
Expression (computer science)
MESH: Gene Expression Regulation
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Computer Science Applications
Computational Mathematics
Data point
Gene Expression Regulation
Computational Theory and Mathematics
MESH: Oligonucleotide Array Sequence Analysis
Data mining
DNA microarray
computer
Algorithms
030217 neurology & neurosurgery
Zdroj: Bioinformatics
Bioinformatics, Oxford University Press (OUP), 2005, 21 (20), pp.3859-64. ⟨10.1093/bioinformatics/bti549⟩
Bioinformatics, 2005, 21 (20), pp.3859-64. ⟨10.1093/bioinformatics/bti549⟩
ISSN: 1460-2059
1367-4803
1367-4811
DOI: 10.1093/bioinformatics/bti549
Popis: International audience; MOTIVATION: We consider any collection of microarrays that can be ordered to form a progression; for example, as a function of time, severity of disease or dose of a stimulant. By plotting the expression level of each gene as a function of time, or severity, or dose, we form an expression series, or curve, for each gene. While most of these curves will exhibit random fluctuations, some will contain a pattern, and these are the genes that are most likely associated with the quantity used to order them. RESULTS: We introduce a method of identifying the pattern and hence genes in microarray expression curves without knowing what kind of pattern to look for. Key to our approach is the sequence of ups and downs formed by pairs of consecutive data points in each curve. As a benchmark, we blindly identified genes from yeast cell cycles without selecting for periodic or any other anticipated behaviour. CONTACT: tmf20@cam.ac.uk SUPPLEMENTARY INFORMATION: The complete versions of Table 2 and Figure 4, as well as other material, can be found at http://www.lps.ens.fr/~willbran/up-down/ or http://www.tcm.phy.cam.ac.uk/~tmf20/up-down/
Databáze: OpenAIRE
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