Multivariate analysis of variance test for gene set analysis

Bioinformatics

Volumn 25, Issue 7, 2009, Pages 897-903

  Tsai, Chen An ^a   Chen, James J ^b  

^a CHINA MEDICAL UNIVERSITY   (Taiwan)

^b NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS OF COVARIANCE; ANALYTICAL ERROR; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; COVARIANCE; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE NUMBER; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; MONTE CARLO METHOD; MULTIVARIATE ANALYSIS OF VARIANCE; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; SIMULATION;

ANALYSIS OF VARIANCE; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 63549122405     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp098     Document Type: Article

References (31)

1. Adewale,A.J. et al. (2008) Pathway analysis of microarray data via regression. J. Comput. Biol., 15, 269-277.
2. Chen,J.J. et al. (2007) Significance analysis of groups of genes in expression profiling studies. Bioinformatics, 23, 2104-2112.
3. Draghici,S. et al. (2003) Global functional profiling of gene expression. Genomics, 81, 98-104.
4. Dinu,I. et al. (2007) Improving gene set analysis of microarray data by SAM-GS. BMC Bioinformatics, 8, 242.
5. Efron,B. and Tibshirani,R. (2007) On testing the significance of set s of genes. Ann. Appl. Stat., 1, 107-129.
6. Goeman,J.J. and Bühlmann,P. (2007) Analyzing gene expression data in terms of gene sets: Methodological issues. Bioinformatics, 23 980-987.
7. Goeman1,J.J. and Mansmann,U. (2008) Multiple testing on the directed acyclic graph of gene ontology. Bioinformatics, 24, 537-544.
8. Goeman,J.J. et al. (2004) A global test for groups of genes: testing association with a clinical outcome. Bioinformatics, 20 93-99.
9. Hummel,M. et al. (2008) GlobalANCOVA: Exploration and assessment of gene group effects. Bioinformatics, 24, 78-85.
10. Irrizarry,R.A. et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 239-264.
11. Johnson,R.A. and Wichern,D.W. (2000) Applied Multivariate Statistical Analysis. 5th edn. Prentice Hall, NY.
12. Khatri,P. and Draghici,S. (2005) Ontological analysis of gene expression data: Current tools, limitations, and open problems. Bioinformatics 21, 3587-3595.
13. Kim,B.S. et al. (2005) Statistical methods of translating microarray data into clinically relevant diagnostic information in colorectal cancer. Bioinformatics, 21, 517-528.
14. Kong,S.W. et al. (2006) A multivariate approach for integrating genome wide expression data and biological knowledge. Bioinformatics 22, 2373-2380.
15. Läuter,J. (1996) Exact t and F tests for analyzing studies with multiple endpoints. Biometrics, 52, 964-970.
16. Liu,Q. et al. (2007) Comparative evaluation of gene-set analysis methods. BMC Bioinformatics, 8, 431.
17. Lu,Y. et al. (2005) Hotelling's T2 multivariate profiling for detecting differential expression in microarrays. Bioinformatics, 21, 3105-3113.
18. Mansmann,U. and Meister,R. (2005) Testing differential gene expression in functional groups: Goeman's global test versus an ANCOVA approach. Method. Inform. in Med., 44, 449-453.
19. Marcus,R. et al. (1976) On closed testing procedures with special reference to ordered analysis of variance. Biometrika, 63, 655-660.
20. Mootha,V.K. et al. (2003) PGC-1 alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet., 34, 267-273.
21. Nam,D. and Kim,S.Y. (2008) Gene-set approach for expression pattern analysis. Brief. Bioinformatics, 9, 189-197.
22. O'Brien,P.C. (1984) Procedure for comparing samples with multiple endpoints. Biometrics, 40, 1079-1087.
23. Pavlidis,P. et al. (2004) Using the gene ontology for microarray data mining: A comparison of methods and application to age effects in human prefrontal cortex. Neurochem. Res., 29, 1213-1222.
24. Rivals,I. et al. (2007) Enrichment or depletion of a GO category within a class of genes: Which test? Bioinformatics, 23, 401-407.
25. Schäfer,J. and Strimmer,K. (2005) A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Statist. Appl. Genet. Mol. Biol., 4, 32.
26. Subramanian,A. et al. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 102, 15545-15550.
27. Szabo,A. et al. (2003) Multivariate exploratory tools for microarray data analysis. Biostatistics, 4, 555-567.
28. Tian,L. et al. (2005) Discovering statistically significant pathways in expression profiling studies. Proc. Natl Acad. of Sci. USA, 102, 13544-13549.
29. Tomfohr,J. et al. (2005) Pathway level analysis of gene expression using singular value decomposition. BMC Bioinformatics, 6, 225.
30. Tusher,V.G. et al. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116-5121.
31. Van't Veer,H. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature, 415, 530-536.