Stratégies pour l'analyse statistique de données transcriptomiques
Journal de la Société française de statistique, Tome 146 (2005) no. 1-2, pp. 5-44.
@article{JSFS_2005__146_1-2_5_0,
     author = {Baccini, Alain and Besse, Philippe and D\'ejean, S\'ebastien and Martin, Pascal G. P. and Robert-Grani\'e, Christ\`ele and San Cristobal, Magali},
     title = {Strat\'egies pour l'analyse statistique de donn\'ees transcriptomiques},
     journal = {Journal de la Soci\'et\'e fran\c{c}aise de statistique},
     pages = {5--44},
     publisher = {Soci\'et\'e fran\c{c}aise de statistique},
     volume = {146},
     number = {1-2},
     year = {2005},
     language = {fr},
     url = {http://www.numdam.org/item/JSFS_2005__146_1-2_5_0/}
}
TY  - JOUR
AU  - Baccini, Alain
AU  - Besse, Philippe
AU  - Déjean, Sébastien
AU  - Martin, Pascal G. P.
AU  - Robert-Granié, Christèle
AU  - San Cristobal, Magali
TI  - Stratégies pour l'analyse statistique de données transcriptomiques
JO  - Journal de la Société française de statistique
PY  - 2005
SP  - 5
EP  - 44
VL  - 146
IS  - 1-2
PB  - Société française de statistique
UR  - http://www.numdam.org/item/JSFS_2005__146_1-2_5_0/
LA  - fr
ID  - JSFS_2005__146_1-2_5_0
ER  - 
%0 Journal Article
%A Baccini, Alain
%A Besse, Philippe
%A Déjean, Sébastien
%A Martin, Pascal G. P.
%A Robert-Granié, Christèle
%A San Cristobal, Magali
%T Stratégies pour l'analyse statistique de données transcriptomiques
%J Journal de la Société française de statistique
%D 2005
%P 5-44
%V 146
%N 1-2
%I Société française de statistique
%U http://www.numdam.org/item/JSFS_2005__146_1-2_5_0/
%G fr
%F JSFS_2005__146_1-2_5_0
Baccini, Alain; Besse, Philippe; Déjean, Sébastien; Martin, Pascal G. P.; Robert-Granié, Christèle; San Cristobal, Magali. Stratégies pour l'analyse statistique de données transcriptomiques. Journal de la Société française de statistique, Tome 146 (2005) no. 1-2, pp. 5-44. http://www.numdam.org/item/JSFS_2005__146_1-2_5_0/

Akaike H. (1974). A new look at the statistical model identification, IEEE Transaction on Automatic control, AC-19, 716-723. | MR | Zbl

Aoyama T., Peters J.M., Iritani N., Nakajima T., Furihata K., Hashimoto T., Gonzalez F.J. (1998). Altered constitutive expression of fatty acidmetabolizing enzymes in mice lacking the peroxisome proliferator-activated receptor alpha (PPARalpha), Journal of Biological Chemistry, 273(10), 5678-84.

Aubert J., Bar-Hen A., Daudin J.-J., Robin S. (2004). Determination of the differentially expressed genes in microarray experiments using local FDR, BMC Bioinformatics, 5, 125.

Baccini A., Besse Ph., Déjean S., Martin , P., Robert-Granié C., San Cristobal M. (2005). Analyse statistique des données d'expression génomique, support de formation disponible en ligne, www.lsp.ups-tlse.fr/Biopuces.

Baccini A., Besse Ph., Déjean S., Martin , P., Robert-Granié C., San Cristobal M. (2005). Étude de données cinétiques issues de biopuces, XXXVIIèmes Journées de Statistique, juin 2005, Pau.

Bar-Hen A., Robin S. (2003). An iterative procedure for differential analysis of gene expression, Comptes rendus de l'Académie des sciences, Série I, 337, 343-346. | MR | Zbl

Benjamini Y., Hochberg Y. (1995). Controlling the false discovery rate : a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society - Series B, 85, 289-300. | MR | Zbl

Berger A., Mutch D.M., German J.B., Roberts M.A. (2002). Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression, Lipids in Health and Disease, 1 :2.

Bland J., Altman D. (1995). Multiple significance tests : the Bonferroni method, British medical Journal, 310, 170.

Bonnet A., Benne F., Dantec C., Gobert N., Frappart P.O., San Cristobal M., Hatey F., Tosser-Klopp G. (2004). Identification of genes and gene networks involved in pig ovarian follicular development, by using c-DNA microarrays, XIII International Workshop on the Development and Function of Reproductive organs, 12-15 July 2004, Copenhagen, Denmark.

Breiman L. (2001). Random forest, Machine Leaming, 45, 5-32. | Zbl

Breiman L., Friedman J.H., Olshen R.A., Stone C.J. (1984). Classification and regression trees, Wadsworth & Brooks, Cole Advanced Books & Software. | MR | Zbl

Broët P., Lewin A., Richardson S., Dalmasso C., Magdelenat H. (2005). A mixture model-based strategy for selecting sets of genes in multiclass response microarray experiments, Bioinformatics, 20(16), 2562-2571.

Chen H.W., Yang J.J., Tsai C.W., Wu J.J., Sheen L.Y., Ou C.C., Lii C.K. (2001). Dietary fat and garlic oil independently regulate hepatic cytochrome p(450) 2B1 and the placental form of glutathione S-transferase expression in rats, The Journal of Nutrition, 131(5), 1438-43.

Dalmasso C., Broët P., Moreau T. (2005). A simple procedure for estimating the false discovery rate, Bioinformatics, 21(5), 660-668.

Delmar P., Robin S., Tronik-Leroux D., Daudin J.-J. (2005). Mixture model on the variance for the differential analysis of gene expression data, Journal of the Royal Statistical Society - Series C, Applied Statistics, 54, 1-20. | MR

Draghici S. (2003). Data Analysis Tools for DNA Microarrays, Mathematical Biology and Medicine Series, Chapman & Hall/CRC. | MR | Zbl

Dudoit S., Popper J., Boldrick J.C. (2003), Multiple Hypothesis Testing in Microarray Experiments, Statistical Science, 18(1), 71-103. | MR | Zbl

Dudoit S., Yang Y., Speed T., Callow M. (2002), Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments, Statistica Sinica, 12(1), 111-139. | MR | Zbl

Eisen M.B., Spellman P.T., Brown P.O., Botstein D. (1998), Cluster analysis and display of genome-wide expression patterns, Proceedings of the National Academy of Sciences of the USA, 95(25), 14863-14868.

Forman B.M., Chen J., Evans R.M. (1997). Hypolipidemic drugs, polyunsaturated fatty acids, and eicosanoids are ligands for peroxisome proliferator-activated receptors alpha and delta, Proceedings of the National Academy of Sciences of the USA, 94(9), 4312-7.

Foulley J.-L., Jaffrezic F., Robert-Granié C. (2000), EM-REML estimation of cavariances parameters in Gaussian mixed models for longitudinal data analysis, Genetics Selection Evolution, 32, 129-141.

Kerr K., Martin M., Churchill G. (2000). Analysis of variance for gene expression microarray data, Journal of Computational Biology, 7, 819-837.

Lebart L., Morineau A., Piron M. (1995). Statistique exploratoire multidimensionnelle, Dunod. | Zbl

Lee S.S., Pineau T., Drago J., Lee E.J., Owens J.W., Kroetz D.L., Fernandez-Salguero P.M., Westphal H., Gonzalez F.J. (1995). Targeted disruption of the alpha isoform of the peroxisome proliferator-activated receptor gene in mice results in abolishment of the pleiotropic effects of peroxisome proliferators, Molecular and Cellular Biology 15(6), 3012-22.

Mardia K., Kent J., Bibby J. (1979). Multivariate analysis, Academic Press. | Zbl

Martin P.G.P., Lasserre F., Calleja C., Van Es A., Roulet A., Concordet D., Cantiello M., Barnouin R., Gauthier B., Pineau T. ( 2005a). Transcriptional modulations by RXR agonists are only partially subordinated to PPARalpha signaling and attest additional, organ-specific, molecular crosstalks, Gene Expression. Voir également le matériel supplémentaire associé à l'article à l'adresse : http://www.inra.fr/Internet/Centres/toulouse/pharmacologie/pharmaco-moleculaire/valorisations.

Martin P.G.P. et al. ( 2005b). A nutrigenomic approach in mice reveals new aspects of PPARα-deficient phenotype with important implications in pharmacology, en préparation.

Mclachlan G.J., Do K.-A., Ambroise C. (2004). Analysing microarray gene expression data, Wiley. | Zbl

Murakami K., Ide T., Suzuki M., Mochizuki T., Kadowaki T. (1999). Evidence for direct binding of fatty acids and eicosanoids to human peroxisome proliferators-activated receptor alpha, Biochemical and Biophysical Research Communications, 260(3), 609-13.

Nakamura M.T., Nara T.Y. (2004). Structure, function, and dietary regulation of delta6, delta5, and delta9 desaturases. Annual Review of Nutrition, 24, 345-76.

Nguyen D.V. (2004). On estimating the proportion of true null hypothesis for false discovery rate controlling procedures in exploratory DNA microarrays studies. Computational Statistics and Data Analysis, 47, 611-637. | MR

Peterfy M., Phan J., Xu P., Reue K. (2001). Lipodystrophy in the fld mouse results from mutation of a new gene encoding a nuclear protein, lipin, Nature Genetics, 27(1), 121-4.

Robert-Granié C., Bonaiti B., Boichard D., Barbat A. (1999). Accounting for variance heterogeneity in French dairy cattle genetic evaluation, Livestock Production Science, 60, 343-357.

San Cristobal M., Robert-Granié C., Foulley J-L. (2002). Hétéroscédasticité et modèles linéaires mixtes : théorie et applications en génétique quantitative, Journal de la Société Française de Statistique, 143, 1-2.

Saporta G. (1990). Probabilités analyse des données et statistique, Paris : Éditions Technip. | Zbl

Schwarz G. (1978). Estimating the dimension of a model, Annals of Statistics, 6, 461-464. | MR | Zbl

Speed T. (2003). Statistical Analysis of Gene Expression Microarray Data, Interdisciplinary Statistics, Chapman & Hall/CRC. | Zbl