Clinically driven semi-supervised class discovery in gene expression data

Bioinformatics

Volumn 24, Issue 16, 2008, Pages

  Steinfeld, Israel ^a   Navon, Roy ^a   Ardigò, Diego ^b   Zavaroni, Ivana ^b   Yakhini, Zohar ^a  

^a Agilent Laboratories   (Israel)

^b UNIVERSITY OF PARMA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ARTERY INTIMA PROLIFERATION; ATHEROSCLEROSIS; BIOSENSOR; CARDIOVASCULAR DISEASE; CARDIOVASCULAR RISK; COMPUTER PROGRAM; CONFERENCE PAPER; CONTROLLED STUDY; GENDER BIAS; GENE EXPRESSION PROFILING; GENETIC ALGORITHM; HUMAN; HUMAN CELL; MATHEMATICAL COMPUTING; MICROARRAY ANALYSIS; NORMAL HUMAN; PERIPHERAL BLOOD MONONUCLEAR CELL; PHENOTYPIC VARIATION; PRIORITY JOURNAL; QUANTITATIVE GENETICS; QUANTITATIVE TRAIT; RISK ASSESSMENT; SCORING SYSTEM;

EID: 49549087973     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn279     Document Type: Conference Paper

References (27)

1. Alizadeh,A.A. et al. (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature, 403 503-511.
2. Ardigo,D. et al. (2007) Application of leukocyte transcriptomes to assess systemic consequences of risk factors for cardiovascular disease. Clin. Chem. Lab. Med., 45, 1109-1120.
3. Ben-Dor,A. et al. (2001a) Tissue classification with gene expression profiles. J. Comput. Biol., 7, 559-583.
4. Ben-Dor,A. et al. (2001b) Class discovery in gene expression data. In Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB'01). ACM Press, pp. 31-38.
5. Benjamini,Y. and Hochberg,Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. B, 57, 289-300.
6. Bittner,M. et al. (2000) Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature, 406 536-540.
7. Bots,M.L. (2006) Carotid intima-media thickness as a surrogate marker for cardiovascular disease in intervention studies. Curr. Med. Res. Opin., 22, 2181-2190.
8. Cui,X. and Churchill,G.A. (2003) Statistical tests for differential expression in cDNA microarray experiments. Genome Biol., 4, 210.
9. Dietzsch,J. et al. (2006) Mayday - a microarray data analysis workbench. Bioinformatics, 22, 1010-1012.
10. Eden,E. et al. (200) Discovering motifs in ranked lists of DNA Sequences. PloS Comput. Biol., 3, e39.
11. Golub,T.R. et al. (1999) Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 286, 531-537.
12. Harris,M.A. et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res., 32, D258-D261.
13. Hurst,R.T. et al. (2007) Clinical use of carotid intima-media thickness: Review of the literature. J. Am. Soc. Echocardiogr., 20, 907-914.
14. Kanehisa,M. (2002) The KEGG database. Novartis Found Symp., 247 91-101.
15. Kirkpatrick,S. et al. (1983) Optimization by simulated annealing. Science, 220, 671-680.
16. Libby,P. et al. (2002) Inflammation and atherosclerosis. Circulation, 105, 1135-1143.
17. Lorenz,M.W. et al. (2007) Prediction of clinical cardiovascular events with carotid intima-media thickness: A systematic review and meta-analysis. Circulation, 115, 459-467.
18. Maglott,D. et al. (2005) Entrez gene: Gene-centered information at NCBl. Nucleic Acids Res., 33 (Database issue), D54-D58.
19. Packard,R.R. and Libby,P. (2008) Inflammation in atherosclerosis: From vascular biology to biomarker discovery and risk prediction. Clin. Chem., 54, 24-38.
20. Steinfeld,I. et al. (2007) Semi-supervised class discovery using quantitative phenotypes - CVD as a case study. BMC Bioinformatics, 8 (Suppl. 8), S6.
21. 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.
22. Touboul,P.J. et al. (200) Mannheim carotid intima-media thickness consensus (2004-2006). An update on behalf of the advisory board of the 3rd and 4th watching the risk symposium, 13th and 15th European stroke conferences, Mannheim, Germany, 2004, and Brussels, Belgium, 2006. Cerebrovasc Dis., 23, 75-80.
23. Tusher,V.G. et al. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116-5121.
24. von Heydebreck,A. et al. (2001) Identifying splits with clear separation: A new class discovery method for gene expression data. Bioinformatics, 17, S107-S114.
25. van't Veer,L. et al. (2002). Gene expression profiling predicts clinical outcome of breast cancer. Nature, 415, 530-536.
26. Zavaroni,I. et al. (1989) Risk factors for coronary artery disease in healthy persons with hyperinsulinemia and normal glucose tolerance. N. Engl. J. Med., 320, 702-706.
27. Zavaroni,I. et al. (1999) Hyperinsulinemia in a normal population as a predictor of non-insulin-dependent diabetes mellitus, hypertension, and coronary heart disease: The Barilla factory revisited. Metabolism 48, 989-994.