A new framework for identifying differentially expressed genes

Pattern Recognition

Volumn 40, Issue 11, 2007, Pages 3249-3262

  Li, Jie ^a   Tang, Xianglong ^a   Zhao, Wei ^a   Huang, Jianhua ^a  

^a HARBIN INSTITUTE OF TECHNOLOGY   (China)

Author keywords

"Outlier" gene; Differentially expressed genes; KS test; Microarray data; Regression model; t Test; Wilcoxon rank sum test; Window of confidence level

Indexed keywords

ALGORITHMS; DISEASES; MICROARRAYS; MOLECULAR DYNAMICS; STATISTICAL TESTS; TUMORS;

DIFFERENTIALLY EXPRESSED GENES; MICROARRAY DATA; REGRESSION MODELS; WILCOXON RANK SUM TEST; WINDOW OF CONFIDENCE LEVELS;

GENE EXPRESSION;

EID: 34250877418     PISSN: 00313203     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.patcog.2007.01.032     Document Type: Article

References (29)

1. Alon U., Barkai N., Notterman D.A., Gish K., Ybarra S., Mack D., and Levine A.J. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed Oligonucleotide arrays. Proc. Natl. Acad. Sci. USA 96 (1999) 6745-6750
2. 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., Bloomfield C.D., and Lander E.S. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286 (1999) 531-537
3. Zhang H., Yu C., Singer B., and Xiong M. Recursive partitioning for tumor classification with gene expression microarray data. Proc. Natl. Acad. Sci. USA 98 (2001) 6730-6735
4. Li X., Rao S., Wang Y., and Gong B. Gene mining: a novel and powerful ensemble decision approach to hunting for disease genes using microarray expression profiling. Nucleic Acids Res. 32 (2004) 2685-2694
5. Li L., Darden T.A., Weinberg C.R., Levine A.J., and Lee G.P. Gene assessment and sample classification for gene expression data using a genetic algorithm/k-nearest neighbor method. Combinatorial Chem. High throughput Screening 4 (2001) 727-739
6. Li H., Zhang K., and Jiang T. Robust and accurate classification with gene expression profiling. Proceedings of the 4th IEEE Computational Systems Bioinformatics Conference (2005) 310-321
7. DeRisi J.L., Iyer V.R., and Brown P.O. Exploring the metabolic and genetic control of gene expression on a genomics scale. Science 278 (1997) 680-686
8. 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. 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 (2001) 1176-1181
9. Model F., Adorjan P., Olek A., and Piepenbrock C. Feature selection for DNA methylation based cancer classification. Bioinformatics 17 (2001) S157-S164
10. Ambroise C., and McLachlan G.J. Selection bias in gene extraction on the basis of microarray gene expression data. Proc. Natl. Acad. Sci. 99 (2002) 6562-6566
11. Berrar D., Bradbury I., and Dubitzky W. Avoiding model selection bias in small sample genomic datasets. Bioinformatics 22 (2006) 1245-1250
12. Singh D., Febbo P.G., Ross K., Jackson D.G., Manola J., Ladd C., Tamayo P., Renshaw A.A., et al. Gene expression correlates of clinical prostate cancer behavior. Cancer Cell 1 (2002) 203-209
13. Notterman D.A., Alon U., Sierk A.J., and Levine A.J. Transcriptional gene expression profiles of colorectal adenoma, adenocarcinoma, and normal tissue examined by oligonucleotide arrays. Cancer Res. 61 (2001) 3124-3130
14. Hippo Y., Taniguchi H., Tsutsumi S., Machida N., Chong J.M., Fukayama M., Kodama T., and Aburatani H. Global gene expression analysis of gastric cancer by oligonucleotide microarrays. Cancer Res. 62 (2002) 233-240
15. H Fox F., Whalen G.F., Sanders M.M., Burleson J.A., Jennings K., Kurtzman S., and Kreutzer D. Angiogenesis in normal tissue adjacent to colon cancer. J. Surg. Oncol. 69 (1998) 230-234
16. Toshina K., Hirata I., Maemura K., Sasaki S., Murano M., Nitta M., Yamauchi H., Nishikawa T., Hamamoto N., and Katsu K. Enprostil, a prostaglandin-E(2) analogue, inhibits interleukin-8 production of human colonic epithelial cell lines. Scand. J.Immunol. 52 (2000) 570-575
17. Inoue K., Perrotte P., Wood C.G., Slaton J.W., Sweeney P., and Dinney C.P. Gene therapy of human bladder cancer with adenovirus-mediated antisense basic fibroblast growth factor. Clin. Cancer Res. 6 (2000) 4422-4431
18. Kowalski J., and Denhardt D.T. Regulation of the mRNA for monocyte-derived neutrophil-activating peptide in differentiating HL60 promyelocytes. Mol. Cell Biol. 9 (1989) 1946-1957
19. Arumugam T., Simeone D.M., Van Golen K., and Logsdon C.D. S100P promotes pancreatic cancer growth, survival, and invasion. Clin. Cancer Res. 11 (2005) 5356-5364
20. Nambiar P.R., Giardina C., Guda K., Aizu W., Raja R., and Rosenberg D.W. Role of the alternating reading frame (P19)-53 pathway in an in vivo murine colon tumor model. Cancer Res. 62 (2002) 3667-3674
21. Li M., Lin Y., Hasegawa S., Shimokawa T., Murata K., Kameyama M., Ishikawa O., Katagiri T., Tsunoda T., Nakamura Y., and Furukawa Y. Genes associated with liver metastasis of colon cancer, identified by genome-wide cDNA microarray. Int. J. Oncol. 24 (2004) 305-312
22. Claeskens A., Ongenae N., Neefs J.M., Cheyns P., Kaijen P., Cools M., and Kutoh E. Hevin is down-regulated in many cancers and is a negative regulator of cell growth and proliferation. Br. J. Cancer 82 (2000) 1123-1130
23. Heikkila R., Schwab G., Wickstrom E., Loke S.L., Pluznik D.H., Watt R., and Neckers L.M. A c-myc antisense oligodeoxynucleotide inhibits entry into S phase but not progress from G0 to G1. Nature 328 (1987) 445-449
24. Qi Y., Gregory M.A., Li Z., Brousal J.P., West K., and Hann S.R. p19ARF directly and differentially controls the functions of c-Myc independently of p53. Nature 431 (2004) 712-717
25. Chen B., Campos E.I., Crawford R., Martinka M., and Li G. Analyses of the tumour suppressor ING1 expression and gene mutation in human basal cell carcinoma. Int. J. Oncol. 22 (2003) 927-931
26. Mylonas I., Makovitzky J., Shabani N., Richter D.U., Kuhn C., Jeschke U., Briese V., and Friese K. Leukaemia inhibitory factor LIF is immunohistochemically expressed in normal hyperplastic and malignant endometrial tissue. Eur. J. Obstet. Gynecol. Reprod. Biol. 118 (2005) 101-108
27. Ikoma H., Ichikawa D., Koike H., Ikoma D., Tani N., Okamoto K., Ochiai T., Ueda Y., Otsuji E., and Yamagishi H. Correlation between serum DNA methylation and prognosis in gastric cancer patients. Anticancer Res. 26 (2006) 2313-2316
28. Yasui W., Oue N., Ito R., Kuraoka K., and Nakayama H. Search for new biomarkers of gastric cancer through serial analysis of gene expression and its clinical implications. Cancer Sci. 95 (2004) 385-392
29. Ofuji S., Ikeda M., Tsujitani S., Ikeguchi M., Kaibara N., Yuasa I., Mitsuya K., Katoh M., and Ito H. Expression of MAGE-1, MAGE-2, and MAGE-3 genes in human gastric carcinomas; lack of evidence for cytotoxic effects in cases with simultaneous expression of MAGE-3 and HLA-A2. Anticancer Res. 18 (1998) 3639-3644