A factor model to analyze heterogeneity in gene expression

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Blum, Yuna ^a,b   Le Mignon, Guillaume ^a,b   Lagarrigue, Sandrine ^a,b   Causeur, David ^a  

^a AGROCAMPUS OUEST   (France)

^b CEMAGREF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL INFORMATION; DIFFERENTIALLY EXPRESSED GENE; FUNCTIONAL CHARACTERIZATION; FUNCTIONAL INFORMATION; GENE EXPRESSION DATA; MICROARRAY TECHNOLOGIES; SIGNIFICANCE ANALYSIS; SIMULTANEOUS ANALYSIS;

FACTOR ANALYSIS; STATISTICAL TESTS; STATISTICS;

GENE EXPRESSION;

GALLUS GALLUS;

ABDOMINAL FAT; ALGORITHM; ANIMAL; ARTICLE; BIOLOGICAL MODEL; CHICKEN; CROSS BREEDING; DNA MICROARRAY; FEMALE; GENE EXPRESSION PROFILING; MALE; METHODOLOGY; PATHOLOGY; QUANTITATIVE TRAIT LOCUS;

ABDOMINAL FAT; ALGORITHMS; ANIMALS; CHICKENS; CROSSES, GENETIC; FEMALE; GENE EXPRESSION PROFILING; MALE; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; QUANTITATIVE TRAIT LOCI;

EID: 77954048300     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-368     Document Type: Article

References (18)

1. Kustra R, Shioda R, Zhu M. A factor analysis model for functional genomics. BMC bioinformatics 2006, 7:216. 10.1186/1471-2105-7-216, 1468435, 16630343.
2. Gordon A, Glazko G, Qiu X, Yakovlev A. Control of the mean number of false discoveries, Bonferroni, and stability of multiple testing. The Annals of Applied Statistics 2007, 1:179-190.
3. Leek J, Storey J. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genetics 2007, 3(9). 10.1371/journal.pgen.0030161, 1994707, 17907809.
4. Friguet C, Kloareg M, Causeur D. A factor model approach to multiple testing under dependence. JASA
5. Le Mignon G, Desert C, Pitel F, Leroux S, Demeure O, Pitel F, Guernec G, Pitel F, Douaire M, P LR, Pitel F, Lagarrigue S. Using trancriptome profiling to characterize QTL regions on chicken chromosome 5. BMC Genomics 2792231, 19954542.
6. Leek J, Storey J. A general framework for multiple testing dependence. Proceedings of the National Academy of Sciences 2008, 105(48):18718.
7. Peltola P, Pihlajamäki J, Koutnikova H, Ruotsalainen E, Salmenniemi U, Vauhkonen I, Kainulainen S, Gylling H, Miettinen T, Auwerx J, et al. Visceral Obesity is Associated with High Levels of Serum Squalene&ast. Obesity 2006, 14(7):1155-1163. 10.1038/oby.2006.132, 16899796.
8. Miettinen T, Gylling H. Cholesterol absorption efficiency and sterol metabolism in obesity. Atherosclerosis 2000, 153:241-248. 10.1016/S0021-9150(00)00404-4, 11058720.
9. MIETTINEN T. Cholesterol production in obesity. Circulation 1971, 44(5):842.
10. Spearman C. "General Intelligence," Objectively Determined and Measured. The American Journal of Psychology 1904, 15(2):201-292.
11. Rubin D, Thayer D. EM algorithms for ML factor analysis. Psychometrika 1982, 47:69-76.
12. Lê S, Josse J, Husson F. FactoMineR: An R package for multivariate analysis. Journal of Statistical Software 25:1-18.
13. Elsen J, Mangin B, Goffinet B, Boichard D, Le Roy P. Alternative models for QTL detection in livestock. I. General introduction. Genetics Selection Evolution 1999, 31(3):213-224.
14. Le Roy P, Elsen J, Boichard D, Mangin B, Bidanel J, Goffinet B. An algorithm for QTL detection in mixture of full and half sib families. Proceedings of the 6th World Congress on Genetics Applied to Livestock Production 1998, 26:257-260.
15. Casel P, Moreews F, Lagarrigue S, Klopp C. sigReannot: an oligo-set re-annotation pipeline based on similarities with the Ensembl transcripts and Unigene clusters. BMC proceedings, BioMed Central Ltd 2009, 3:S3.
16. ENSEMBL website. , http://www.ensembl/org
17. Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J, Davis A, Dolinski K, Dwight S, Eppig J, et al. Gene Ontology: tool for the unification of biology. Nature genetics 2000, 25:25-29. 10.1038/75556, 10802651.
18. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita K, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. From genomics to chemical genomics: new developments in KEGG. Nucleic acids research 2006, (34 Database):D354. 10.1093/nar/gkj102, 1347464, 16381885.