ArraySolver: An algorithm for colour-coded graphical display and Wilcoxon signed-rank statistics for comparing microarray gene expression data

Comparative and Functional Genomics

Volumn 5, Issue 1, 2004, Pages 39-47

  Khan, Haseeb Ahmad ^a  

^a The General Directorate of Armed Forces Health Services   (Saudi Arabia)

Author keywords

Colour coded display; Gene expression; Microarray; Software; Statistical comparison; Wilcoxon signed rank test

Indexed keywords

ACCURACY; ARTICLE; COMPUTER GRAPHICS; COMPUTER PROGRAM; DATA ANALYSIS; DISPLAY SYSTEM; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE NUMBER; GENETIC ALGORITHM; GENETIC ANALYSIS; INTERMETHOD COMPARISON; PRIORITY JOURNAL; STATISTICAL ANALYSIS; WILCOXON SIGNED RANKS TEST;

EID: 2942623967     PISSN: 15316912     EISSN: None     Source Type: Journal    
DOI: 10.1002/cfg.369     Document Type: Article

References (47)

1. Ahr A, Karn T, Solbach C, et al. 2002. Identification of high-risk breast-cancer patients by gene expression profiling. Lancet 359: 131-132.
2. Alizadeh AA, Eisen MB, Davis RE, et al. 2000. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403: 503-511.
3. Beenken SW, Hockett R Jr, Grizzle W, et al. 2002. Transforming growth factor-α: a surrogate endpoint biomarker. J Am Coll Surg 195: 149-158.
4. Bouras T, Southey MC, Chang AC, et al. 2002. Stanniocalcin 2 is an estrogen-responsive gene coexpressed with the estrogen receptor in human breast cancer. Cancer Res 62: 1289-1295.
5. Bradbury AW, Carter DC, Miller WR, Cho-Chung YS, Clair T. 1994. Protein kinase A (PK-A) regulatory subunit expression in colorectal cancer and related mucosa. Br J Cancer 69: 738-742.
6. Bull JH, Ellison G. Patel A, et al. 2001. Identification of potential diagnostic markers of prostate cancer and prostatic intraepithelial neoplasia using cDNA microarray. Br J Cancer 84: 1512-1519.
7. Bushel PR, Hamadeh HK, Bennett L, et al. 2002. Computational selection of distinct class- and subclass-specific gene expression signatures. J Biomed Inform 35: 160-170.
8. Campbell MJ, Machin D. 1996. Medical Statistics. Wiley: Chichester; 83.
9. Conway T, Kraus B, Tucker DL, et al. 2002. DNA array analysis in a Microsoft windows environment. Biotechniques 110: 112-119.
10. Efron B, Tibshirani R. 2002. Empirical Bayes methods and false discovery rates for microarrays. Genet Epidemiol 23: 70-86.
11. Gaasterland T, Bekiranov S. 2000. Making the most of microarray data. Nature Genet 24: 204-206.
12. Golub TR, Slonim DK, Tamayo P, et al. 1999. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 285: 531-537.
13. Gutgemann A, Golob M, Muller S, Buettner R, Bosserhoff AK. 2001. Isolation of invasion-associated cDNAs in melanoma. Arch Dermatol Res 293: 283-290.
14. Han GM, Chen SL, Shen N, Ye S, Bao CD, Gu YY. 2003. Analysis of gene expression profiles in human systemic lupus erythematosus using oligonucleotide microarray. Genes Immun 4: 177-186.
15. Hoffmann R, Seidl T, Dugas M. 2002. Profound effect of normalization on detection of differentially expressed genes in oligonuclectide microarray data analysis. Genome Biol 3: 0033.1-0033.11.
16. Johnston SR, Saccani-Jotti G, Smith IE, et al. 1995. Changes in estrogen receptor, progesterone receptor, and pS2 expression in tamoxifen-resistant human breast cancer. Cancer Res 55: 3331-3338.
17. Kihara C, Tsunoda T, Tanaka T, et al. 2001. Prediction of sensitivity of esophageal tumors to adjuvant chemotherapy by cDNA microarray analysis of gene-expression profiles. Cancer Res 61: 6474-6479.
18. Ladanyi M, Chan WC, Triche TJ, Gerald WL. 2001. Expression profiling of human tumors: the end of surgical pathology. J Mol Diagn 3: 92-97.
19. Leygue E, Dotzlaw H, Watson PH, Murphy LC. 2000. Altered expression of estrogen receptor-α variant messenger RNAs between adjacent normal breast and breast tumor tissues. Breast Cancer Res 2: 64-72.
20. Liu WM, Mei R, Di X, et al. 2002. Analysis of high density expression with signed-rank call algorithms. Bioinformatics 18: 1593-1599.
21. Mariadason JM, Arango D, Corner GS, et al. 2002. A gene expression profile that defines colon cell maturation in vitro. Cancer Res 62: 4791-4804.
22. Maxwell DT, Jacobson JD, King A, Chan PJ. 2002. Effect of pentoxifylline on tumor suppressor and proto-oncogene apoptosis in sperm. J Assist Reprod Genet 19: 279-283.
23. Mycko MP, Papoian R, Boschert U, Raine CS, Selmaj KW. 2003. cDNA microarray analysis in multiple sclerosis lesions: detection of genes associated with disease activity. Brain 126: 1048-1057.
24. Notterman DA, Alon U, Sierk AJ, Levine AJ. 2001. Transcriptional gene expression profiles of colorectal adenoma, adenocarcinoma, and normal tissue examined by oligonucleotide arrays. Cancer Res 61: 3124-3130.
25. Okabe S, Fujimoto N, Sueoka N, Suganuma M, Fujiki H. 2001. Modulation of gene expression by (-) -epigallocatechin gallate in PC-9 cells using a cDNA expression array. Biol Pharm Bull 24: 883-886.
26. Pfaffl MW, Wittmann SL, Meyer HHD, Bruckmaier RM. 2003. Gene expression of immunologically important factors in blood cells, milk cells and mammary tissue of cows. J Dairy Sci 86: 538-545.
27. Ramaswamy S, Ross KN, Lander ES, Golub TR. 2003. A molecular signature of metastasis in primary solid tumors. Nature Genet 33: 49-54.
28. Robinson P, White AC, Lewis DE, et al. 2002. Sequential expression of the neuropeptides substance P and somatostatin in granulomas associated with murine cysticercosis. Infect Immun 70: 4534-4538.
29. Rus V, Atamas SP, Shustova V, et al. 2002. Expression of cytokine- and chemokine-related genes in peripheral blood mononuclear cells from lupus patients by cDNA array. Clin Immunol 102: 283-290.
30. Schageman JJ, Basit M, Gallardo TD, Garner HR, Shohet RV. 2002. MarC-V: a spreadsheet-based tool for analysis, normalization and visualization of single cDNA microarray experiments. Biotechniques 32: 338-344.
31. Siegel S. 1956. Non-parametric Statistics for Behavioral Scientists. McGraw-Hill: Maidenhead; 75-83.
32. Smid-Koopman E, Blok LJ, Chadha-Ajwani S, et al. 2000. Gene expression profiles of human endometrial cancer samples using a cDNA-expression array technique: assessment of an analysis method. Br J Cancer 83: 246-251.
33. SPSS for Windows, SPSS Inc., Chicago, IL, USA.
34. Su AI, Welsh JB, Sapinoso LM, et al. 2001. Molecular classification of human carcinomas by use of gene expression signatures. Cancer Res 61: 7388-7393.
35. Tamayo P, Slonim D, Mesirov J, et al. 1999. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 96: 2907-2912.
36. Tanaka TS, Jaradat SA, Lim MK, et al. 2000. Genome-wide expression profiling of mid-gestation placenta and embryo using a 15 000 mouse developmental cDNA microarray. Proc Natl Acad Sci USA 97: 9127-9132.
37. Thomas JG, Olson JM, Tapscott SJ, Zhao LP. 2001. An efficient and robust statistical modeling approach to discover differentially expressed genes using genomic expression profiles. Genome Res 11: 1227-1236.
38. Troyanskaya OG, Garber ME, Brown PO, Botstein D, Altman RB. 2002. Non-parametric methods for identifying differentially expressed genes in microarray data. Bioinformatics 18: 1454- 1461.
39. Tusher VG, Tibshirani R, Chu G. 2001. Significance analysis of microarrays applied to the ionizing radiation purpose. Proc Natl Acad Sci USA 98: 5116-5121.
40. Wang K, Gan L, Jeffery E, et al. 1999. Monitoring gene expression profile changes in ovarian carcinomas using cDNA microarray. Gene 229: 101-108.
41. Wang W, Marsh S, Cassidy J, McLeod HL. 2001. Pharmacogenomic dissection of resistance to thymidylate synthase inhibitors. Cancer Res 61: 5505 -5510.
42. Wilcoxon F. 1945. Individual comparisons by ranking methods. Biometric Bull 1: 80-83.
43. Wilcoxon F. 1947. Probability tables for individual comparisons by ranking methods. Biometrics 3: 119-122.
44. Xu Y, Selaru FM, Yin J, et al. 2002. Artificial neural networks and gene filtering distinguish between global gene expression profiles of Barrett's esophagus and esophageal cancer. Cancer Res 62: 3493-3497.
45. Yu CL, Sun KH, Tsai CY, Hsieh SC, Yu HS. 2001. Anti-dsDNA antibody upregulates interleukin 6, but not cycleoxygenase, gene expression in glomerular mesangial cells: a marker of immune-mediated renal damage. Inflamm Res 50: 12-18.
46. Zhao Y, Pan W. 2003. Modified non-parametric approaches to detecting differentially expressed genes in replicated microarray experiments. Bioinformatics 19: 1046-1054.
47. Zhou X, Tan FK, Xiong M, et al. 2001. Systemic sclerosis (scleroderma): specific autoantigen genes are selectively overexpressed in scleroderma fibroblasts. J Immunol 167: 7126-7133.