Predictive response-relevant clustering of expression data provides insights into disease processes

Nucleic Acids Research

Volumn 38, Issue 20, 2010, Pages 6831-6840

  Hopcroft, Lisa E M ^a   McBride, Martin W ^b   Harris, Keith J ^a   Sampson, Amanda K ^b   McClure, John D ^b   Graham, Delyth ^b   Young, Graham ^a   Holyoake, Tessa L ^a   Girolami, Mark A ^a   Dominiczak, Anna F ^b  

^a UNIVERSITY OF GLASGOW   (United Kingdom)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BASIC HELIX LOOP HELIX TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR ARNTL;

CANONICAL ANALYSIS; CIRCADIAN RHYTHM; DATA ANALYSIS; GENE CLUSTER; GENE EXPRESSION; HUMAN; HYPERTENSION; MICROARRAY ANALYSIS; NONHUMAN; PATHOPHYSIOLOGY; PREDICTION; PRIORITY JOURNAL; REVIEW; SIGNAL TRANSDUCTION; SODIUM INTAKE; STATISTICAL MODEL; TRANSCRIPTION INITIATION;

ANIMALS; CIRCADIAN RHYTHM; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HUMANS; HYPERTENSION; KIDNEY; LEUKEMIA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RATS; REGRESSION ANALYSIS;

RATTUS;

EID: 78651305584     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq550     Document Type: Review

References (35)

1. de Snoo, F., Bender, R., Glas, A. and Rutgers, E. (2009) Gene expression profiling: decoding breast cancer. Surgical Oncology, 18, 366-378.
2. Harris, K., McMillan, L. and Girolami, M. (2009) Inferring meta-covariates in classification. Pattern Recogn. Bioinform. LNBI., 5780, 150-161.
3. Hanczar, B., Courtin, M., Benis, A., Henegar, C., Clement, K. and Zucker, J. D. (2003) Improving classification of microarray data using prototype-based feature selection. SIGKCC Explorations, 5, 23-30.
4. Park, M. Y., Hastie, T. and Tibshirani, R. (2007) Averaged gene expressions for regression. Biostatistics, 8, 212-227.
5. Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J. P., Coller, H., Loh, M. L., Downing, J. R., Caligiuri, M. A. et al. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science, 286, 531-537.
6. Dudoit, S., Fridlyand, J. and Speed, T. P. (2000) Comparison of discrimination methods for the classification of tumors using gene expression data. J. Am. Stat. Assoc., 97, 77-87.
7. Clark, J. S., Jeffs, B., Davidson, A. O., Lee, W. K., Anderson, N. H., Bihoreau, M. T., Brosnan, M. J., Devlin, A. M., Kelman, A. W., Lindpaintner, K. et al. (1996) Quantitative trait loci in genetically hypertensive rats. Possible sex specificity. Hypertension, 28, 898-906.
8. Jeffs, B., Negrin, C. D., Graham, D., Clark, J. S., Anderson, N. H., Gauguier, D. and Dominiczak, A. F. (2000) Applicability of a "speed" congenic strategy to dissect blood pressure quantitative trait loci on rat chromosome 2. Hypertension, 35, 179-187.
9. Irizarry, R. A., Hobbs, B., Collin, F., Beazer-Barclay, Y. D., Antonellis, K. J., Scherf, U. and Speed, T. P. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 249-264.
10. Breitling, R., Armengaud, P., Amtmann, A. and Herzyk, P. (2004) Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett., 573, 83-92.
11. Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate-a practical and powerful approach to multiple testing. JRSS-B, 57, 289-300.
12. Bishop, C. M. (2006) Pattern Recognition and Machine Learning. Springer, New York, 2006.
13. Hoffbrand, A. V., Moss, P. A. H. and Pettit, J. E. (2006) Essential Haematology, 5th edn. Blackwell Publishing, Malden, MA, USA.
14. Bae, K. and Mallick, B. K. (2004) Gene selection using a two-level hierarchical Bayesian model. Bioinformatics, 20, 3423-3430.
15. Lee, Y. and Lee, C.-K. (2003) Classification of multiple cancer types by multicategory support vector machines using gene expression data. Bioinformatics, 19, 1132-1139.
16. Tibshirani, R., Hastie, T., Narasimhan, B. and Chu, G. (2002) Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc. Natl Acad. Sci. USA, 99, 6567-6572.
17. Lee, K. E., Sha, N., Dougherty, E. R., Vannucci, M. and Mallick, B. K. (2003) Gene selection: a Bayesian variable selection approach. Bioinformatics, 19, 90-97.
18. Bennett, J. M., Catovsky, D., Daniel, M. T., Flandrin, G., Galton, D. A., Gralnick, H. R. and Sultan, C. (1976) Proposals for the classification of the acute leukaemias. French-American-British (FAB) co-operative group. Br. J. Haematol, 33, 451-458.
19. Bach, J.-P., Rinn, B., Meyer, B., Dodel, R. and Bacher, M. (2008) Role of MIF in inflammation and tumorigenesis. Oncology, 75, 127-133.
20. Abe, R., Peng, T., Sailors, J., Bucala, R. and Metz, C. N. (2001) Regulation of the CTL response by macrophage migration inhibitory factor. J. Immunol., 166, 747-753. (Pubitemid 32060224)
21. Ziino, O., D'Urbano, L. E., De Benedetti, F., Conter, V., Barisone, E., De Rossi, G., Basso, G. and Arica, M. (2005) The MIF-173G/C polymorphism does not contribute to prednisone poor response in vivo in childhood acute lymphoblastic leukemia. Leukemia, 19, 2346-2347.
22. Gore, Y., Starlets, D., Maharshak, N., Becker-Herman, S., Kaneyuki, U., Leng, L., Bucala, R. and Shachar, I. (2008) Macrophage migration inhibitory factor induces B cell survival by activation of a CD74-CD44 receptor complex. J. Biol. Chem., 283, 2784-2792.
23. Stein, R., Mattes, M. J., Cardillo, T. M., Hansen, H. J., Chang, C.-H., Burton, J., Govindan, S. and Goldenberg, D. M. (2007) CD74: a new candidate target for the immunotherapy of B-cell neoplasms. Clin. Cancer Res., 13, 5556s-5563s.
24. Kearney, P. M., Whelton, M., Reynolds, K., Muntner, P., Whelton, P. K. and He, J. (2005) Global burden of hypertension: analysis of worldwide data. Lancet, 365, 217-223.
25. Weinberger, M. H. (1996) Salt sensitivity of blood pressure in humans. Hypertension, 27, 481-490.
26. McBride, M. W., Graham, D., Delles, C. and Dominiczak, A. F. (2006) Functional genomics in hypertension. Curr. Opin. Nephrol. Hypertens., 15, 145-151.
27. Graham, D., McBride, M. W., Gaasenbeek, M., Gilday, K., Beattie, E., Miller, W. H., McClure, J. D., Polke, J. M., Montezano, A., Touyz, R. M. et al. (2007) Candidate genes that determine response to salt in the stroke-prone spontaneously hypertensive rat: congenic analysis. Hypertension, 50, 1134-1141.
28. Hubert, L. and Arabie, P. (1985) Comparing partitions. J. Classif., 2, 193-218.
29. Vinh, N. X., Epps, J. and Bailey, J. (2009) Information theoretic measures for clusterings comparison: Is a correction for chance necessary? Proceedings of the 26th International Conference on Machine Learning, Montreal, Canada.
30. Bunger, M. K., Wilsbacher, L. D., Moran, S. M., Clendenin, C., Radcliffe, L. A., Hogenesch, J. B., Simon, M. C., Takahashi, J. S. and Bradfield, C. A. (2000) Mop3 is an essential component of the master circadian pacemaker in mammals. Cell, 103, 1009-1017.
31. Huffman, J. L., Mokashi, A., Bachinger, H. P. and Brennan, R. G. (2001) The basic helix-loop-helix domain of the aryl hydrocarbon receptor nuclear transporter (ARNT) can oligomerize and bind E-box DNA specifically. J. Biol. Chem., 276, 40537-40544.
32. Woon, P. Y., Kaisaki, P. J., Braganca, J., Bihoreau, M.-T., Levy, J. C., Farrall, M. and Gauguier, D. (2007) Aryl hydrocarbon receptor nuclear translocator-like (BMAL1) is associated with susceptibility to hypertension and type 2 diabetes. Proc. Natl Acad. Sci. USA, 104, 14412-14417.
33. Doi, M., Takahashi, Y., Komatsu, R., Yamazaki, F., Yamada, H., Haraguchi, S., Emoto, N., Okuno, Y., Tsujimoto, G., Kanematsu, A. et al. (2010) Salt-sensitive hypertension in circadian clock-deficient cry-null mice involves dysregulated adrenal hsd3b6. Nat. Med., 16, 67-74.
34. Zuber, A. M., Centeno, G., Pradervand, S., Nikolaeva, S., Maquelin, L., Cardinaux, L., Bonny, O. and Firsov, D. (2009) Molecular clock is involved in predictive circadian adjustment of renal function. Proc. Natl Acad. Sci. USA, 106, 16523-16528.
35. Mohri, T., Emoto, N., Nonaka, H., Fukuya, H., Yagita, K., Okamura, H. and Yokoyama, M. (2003) Alterations of circadian expressions of clock genes in Dahl salt-sensitive rats fed a high-salt diet. Hypertension, 42, 189-194.