A procedure to statistically evaluate agreement of differential expression for cross-species genomics

Bioinformatics

Volumn 27, Issue 15, 2011, Pages 2098-2103

  Pounds, Stan ^a   Gao, Cuilan Lani ^a   Johnson, Robert A ^b   Wright, Karen D ^a   Poppleton, Helen ^a   Finkelstein, David ^a   Leary, Sarah E S ^c   Gilbertson, Richard J ^a  

^a ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

^b THE OHIO STATE UNIVERSITY COLLEGE OF MEDICINE   (United States)

^c SEATTLE CHILDREN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; MUS;

ANIMAL; ARTICLE; BIOLOGY; COMPARATIVE STUDY; DISEASE MODEL; EPENDYMOMA; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; HUMAN; META ANALYSIS (TOPIC); METHODOLOGY; MOUSE; STATISTICAL MODEL; VALIDATION STUDY;

ANIMALS; COMPUTATIONAL BIOLOGY; DISEASE MODELS, ANIMAL; EPENDYMOMA; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; META-ANALYSIS AS TOPIC; MICE; MODELS, STATISTICAL;

EID: 79960410568     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr362     Document Type: Article

References (21)

1. Allison,D.B. et al., (2006) Microarray data analysis: from disarray to consolidation and consensus. Nat. Rev. Genet., 7, 55-65.
2. Barry,W.T. et al. (2005) Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics, 21, 1943-1949.
3. Fitzpatrick,P.M. (1996) Advanced Calculus: a Course in Mathematical Analysis. PWS Publishing Company, Boston, MA.
4. Gadbury,G. et al. (2003) Randomization tests for small samples: an application for genetic expression data. Appl. Stat., 52, 365-376.
5. Gibson,P. et al. (2010) Subtypes of medulloblastoma have distinct developmental origins. Nature, 468, 1095-1099.
6. Goeman,J.J and Bühlmann,P. (2007) Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics, 23, 980-987.
7. Good,P. (2010) Permutation, Parametric, and Bootstrap Tests of Hypotheses, 3rd edn. Springer, New York.
8. Irizarry,R.A. et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 249-264.
9. Johnson,R. et al. (2010) Cross-species genomics matches driver mutations and cell compartments to model ependymoma. Nature, 466, 632-636.
10. Mullighan,C.G. et al. (2007) Genes regulating B cell development are mutated in acute lymphoid leukaemia. Nature, 446, 758-764.
11. Poisson,L.M. and Ghosh,D. (2007) Statistical issues and analysis of in vivo and in vitro genomic data in order to identify clinically relevant profiles. Cancer Informat., 3, 231-243.
12. Pounds,S. and Cheng,C. (2005a) Statistical development and evaluation of gene expression data filters. J. Comput. Biol., 12, 482-495.
13. Pounds,S. and Cheng,C. (2005b) Sample size determination for the false discovery rate. Bioinformatics, 21, 4263-4271.
14. Pounds,S. (2006) Estimation and control of multiple testing error rates for the analysis of microarray data. Brief. Bioinformatics, 7, 25-36.
15. Pounds,S. and Dyer,M. (2008) Statistical analysis of data collected in retroviral clonal experiments in the developing retina. Brain Res., 1192, 178-185.
16. Pounds,S. et al. (2009a) Reference alignment of SNP microarray signals for copy number analysis of tumors. Bioinformatics, 25, 315-321.
17. Pounds,S. et al. (2009b) PROMISE: a tool to identify genomic variables with a specific biologically interesting pattern of associations with multiple endpoint variables. Bioinformatics, 25, 2013-2019.
18. Pounds,S. et al. (2011) Integrated analysis of pharmacokinetic, clinical, and SNP microarray data using projection onto the most interesting statistical evidence with adaptive permutation testing. Int. J. Data Min. Bioinformatics, 5, 143-157.
19. Sandberg,R. and Ernberg,I. (2005) Assessment of tumor characteristic gene expression in cell lines using a tissue similarity index (TSI). Proc. Natl Acad. Sci. USA, 102, 2052-2057.
20. Stouffer,S.A. et al. (1949) The American Soldier. Vol. 1, Adjustment during Army Life. Princeton University Press, Princeton, NJ.
21. Zheng-Bradley,X. et al. (2010) Large scale comparison of global gene expression patterns in human and mouse. Genome Biol., 11, r124.