Stratégies pour l'analyse statistique de données transcriptomiques

Alain Baccini; Philippe Besse; Sébastien Déjean; Pascal G. P. Martin; Christèle Robert-Granié; Magali San Cristobal

Journal de la société française de statistique (2005)

  • Volume: 146, Issue: 1-2, page 5-44
  • ISSN: 1962-5197

How to cite


Baccini, Alain, et al. "Stratégies pour l'analyse statistique de données transcriptomiques." Journal de la société française de statistique 146.1-2 (2005): 5-44. <>.

author = {Baccini, Alain, Besse, Philippe, Déjean, Sébastien, Martin, Pascal G. P., Robert-Granié, Christèle, San Cristobal, Magali},
journal = {Journal de la société française de statistique},
language = {fre},
number = {1-2},
pages = {5-44},
publisher = {Société française de statistique},
title = {Stratégies pour l'analyse statistique de données transcriptomiques},
url = {},
volume = {146},
year = {2005},

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
PB - Société française de statistique
VL - 146
IS - 1-2
SP - 5
EP - 44
LA - fre
UR -
ER -


  1. AKAIKE H. (1974). A new look at the statistical model identification, IEEE Transaction on Automatic control, AC-19, 716-723. Zbl0314.62039MR423716
  2. 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. 
  3. 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. 
  4. 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, 
  5. 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. 
  6. 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. Zbl1037.92023MR2016987
  7. 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. Zbl0809.62014MR1325392
  8. 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. 
  9. BLAND J., ALTMAN D. (1995). Multiple significance tests : the Bonferroni method, British medical Journal, 310, 170. 
  10. 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. 
  11. BREIMAN L. (2001). Random forest, Machine Leaming, 45, 5-32. Zbl1007.68152
  12. BREIMAN L., FRIEDMAN J.H., OLSHEN R.A., STONE C.J. (1984). Classification and regression trees, Wadsworth & Brooks, Cole Advanced Books & Software. Zbl0541.62042MR726392
  13. 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. 
  14. 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. 
  15. DALMASSO C., BROËT P., MOREAU T. (2005). A simple procedure for estimating the false discovery rate, Bioinformatics, 21(5), 660-668. 
  16. 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. Zbl05188670MR2134596
  17. DRAGHICI S. (2003). Data Analysis Tools for DNA Microarrays, Mathematical Biology and Medicine Series, Chapman & Hall/CRC. Zbl1031.62096MR1991810
  18. DUDOIT S., POPPER J., BOLDRICK J.C. (2003), Multiple Hypothesis Testing in Microarray Experiments, Statistical Science, 18(1), 71-103. Zbl1048.62099MR1997066
  19. 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. Zbl1004.62088MR1894191
  20. 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. 
  21. 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. 
  22. 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. 
  23. KERR K., MARTIN M., CHURCHILL G. (2000). Analysis of variance for gene expression microarray data, Journal of Computational Biology, 7, 819-837. 
  24. LEBART L., MORINEAU A., PIRON M. (1995). Statistique exploratoire multidimensionnelle, Dunod. Zbl0920.62077
  25. 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. 
  26. MARDIA K., KENT J., BIBBY J. (1979). Multivariate analysis, Academic Press. Zbl0432.62029
  27. 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 : 
  28. 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. 
  29. MCLACHLAN G.J., DO K.-A., AMBROISE C. (2004). Analysing microarray gene expression data, Wiley. Zbl1140.92010
  30. 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. 
  31. 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. 
  32. 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. Zbl05374072MR2086486
  33. 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. 
  34. 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. 
  35. 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. 
  36. SAPORTA G. (1990). Probabilités analyse des données et statistique, Paris : Éditions Technip. Zbl0703.62003
  37. SCHWARZ G. (1978). Estimating the dimension of a model, Annals of Statistics, 6, 461-464. Zbl0379.62005MR468014
  38. SPEED T. (2003). Statistical Analysis of Gene Expression Microarray Data, Interdisciplinary Statistics, Chapman & Hall/CRC. Zbl1108.62331

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