The CRASSS plug-in for integrating annotation data with hierarchical clustering results

Bioinformatics

Volumn 20, Issue 17, 2004, Pages 3266-3269

  Buehler, Eugen C ^a   Sachs, Jeffrey R ^a   Shao, Kui ^a   Bagchi, Ansuman ^a   Ungar, Lyle H ^b  

^a MERCK RESEARCH LABORATORIES   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLUSTER ANALYSIS; DATA ANALYSIS; GENE EXPRESSION; GENETIC ALGORITHM; PRIORITY JOURNAL; STATISTICAL SIGNIFICANCE;

EID: 10244264786     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth362     Document Type: Article

References (18)

1. Alon,U., Barkai,N., Notterman,D., Gish,K., Ybarra,S., Mack,D. and Levine,A. (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl Acad. Sci., USA, 96, 6745-6750.
2. Draghici,S., Khatri,P., Martins,R.P., Ostermeier,G.C. and Krawetz,S.A. (2003) Global functional profiling of gene expression. Genomics, 81, 98-104.
3. Eisen,M., Spellman,P., Brown,P. and Botstein,D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci., USA, 95, 14863-14868.
4. Fisher,R.A. (1935) Design of Experiments. Hafner, New York.
5. Goss-Tusher,V., Tibshirani,R. and Chu,G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci., USA, 98, 5116-5121.
6. Holder,D.J., Pikounis,V.B., Raubertas,R., Svetnik,V. and Soper,K.A. (2004) Statistical analysis of high density oligonucleotide arrays: a SAFER approach. In: Proceedings of the American Statistical Association.
7. Kahn,J., Simon,R., Bittner,M., Chen,P.Y., Leighton,S.B., Pohida,T. and Smith,P.D. (1998) Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays. Cancer Res., 58, 5009-5013.
8. Kaminski,N., Allard,J.D., Pittet,J.F., Zuo,F., Griffiths, M.J.D., Morris,D., Huang,X., Sheppard,D. and Heller,R.A. (2000) Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosis. Proc. Natl Acad. Sci., USA, 97, 1778-1783.
9. Levenstien,M.A., Yang,Y. and Ott,J. (2003) Statistical significance for hierarchical clustering in genetic association and microarray expression studies. BMC Bioinformatics, 4, 62.
10. Lockhart,D., Dong,H., Byrne,M., Follettie,M., Gallo,M., Chee,M., Mittmann,M., Wang,C., Kobayashi,M.H. and Brown,E. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol., 14, 1675-1680.
11. Pitman,E.J.G. (1937) Significance tests which may be applied to any population. Stat. Soc. Suppl., 4, 119-130, 225-232.
12. Pitman,E.J.G. (1938) Significance tests which may be applied to any population. Part III. The analysis of variance test. Biometrika 29, 322-335.
13. Primig,M., Williams,R.M., Winzeler,E.A., Tevzadze,G.G., Conway,A.R., Hwang,S.Y., Davis,R.W. and Esposito,R.E. (2000) The core meiotic transcriptome in budding yeast. Nat. Genet., 26, 415-423.
14. Shaffer,J.P. (1995) Multiple hypothesis testing. Ann. Rev. Psychol., 46, 561-584.
15. Snedecor,G.W. and Cochran,W.G. (1989) Statistical Methods Iowa State University Press, Ames, Iowa.
16. Tavazoie,S., Hughes,J.D., Campbell,M.J., Cho,R.J. and Church,G.M. (1999) Systematic determination of genetic network architecture. Nat. Genet., 22, 281-285.
17. Weinstein,J.N., Myers,T.G., O'Connor,P.M., Friend,S.H., Fornace, A.J., Jr, Kohn,K.W., Fojo,T., Bates,S.E., Rubinstein,L.V., Anderson,L.N. (1997) An information-intensive approach to the molecular pharmacology of cancer. Science, 275, 343-349.
18. Welsh,J.B., Zarrinkar,P.P., Sapinoso,L.M., Kern,S.G., Behling,C.A., Monk,B.J., Lockhart,D.J., Burger,R.A. and Hampton,G.M. (2001) Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. Proc. Natl Acad. Sci., USA, 98, 1176-1181.