Features

 unsupervised hierarchical clustering
 multidimensional scaling
 permutation testing
 comparison of significantly expressed genes within a pair

References

 Tumor Analysis Best Practices Working Group. Expression profiling--best practices for data generation and interpretation in clinical trials. Nat Rev Genet. 2004 Mar;5(3):229-37. PMID: #14970825#

 Yang XJ, Sugimura J, Tretiakova MS, Furge K, Zagaja G, Sokoloff M, Pins M, Bergan R, Grignon DJ, Stadler WM, Vogelzang NJ, Teh BT. Gene expression profiling of renal medullary carcinoma. Cancer. 2004 Mar 1;100(5):976-85. PMID: #14983493#

 Bertucci F, Salas S, Eysteries S, Nasser V, Finetti P, Ginestier C, Charafe-Jauffret E, Loriod B, Bachelart L, Montfort J, Victorero G, Viret F, Ollendorff V, Fert V, Giovaninni M, Delpero JR, Nguyen C, Viens P, Monges G, Birnbaum D, Houlgatte R. Gene expression profiling of colon cancer by DNA microarrays and correlation with histoclinical parameters. Oncogene. 2004 Feb 19;23(7):1377-91. PMID: #14973550#

 Lapointe J, Li C, Higgins JP, van de Rijn M, Bair E, Montgomery K, Ferrari M, Egevad L, Rayford W, Bergerheim U, Ekman P, DeMarzo AM, Tibshirani R, Botstein D, Brown PO, Brooks JD, Pollack JR. Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci U S A. 2004 Jan 20;101(3):811-6. PMID: #14711987#

 Bloom G, Yang IV, Boulware D, Kwong KY, Coppola D, Eschrich S, Quackenbush J, Yeatman TJ. Multi-platform, multi-site, microarray-based human tumor classification. Am J Pathol. 2004 Jan;164(1):9-16. PMID: 14695313

 Hiyama E, Hiyama K, Yamaoka H, Sueda T, Reynolds CP, Yokoyama T. Expression profiling of favorable and unfavorable neuroblastomas. Pediatr Surg Int. 2003 Dec 23 PMID: #14691637#

 Kim B, Bang S, Lee S, Kim S, Jung Y, Lee C, Choi K, Lee SG, Lee K, Lee Y, Kim SS, Yeom YI, Kim YS, Yoo HS, Song K, Lee I. Expression profiling and subtype-specific expression of stomach cancer. Cancer Res. 2003 Dec 1;63(23):8248-55. PMID: #14678982#

 Martinez N, Camacho FI, Algara P, Rodriguez A, Dopazo A, Ruiz-Ballesteros E, Martin P, Martinez-Climent JA, Garcia-Conde J, Menarguez J, Solano F, Mollejo M, Piris MA. The molecular signature of mantle cell lymphoma reveals multiple signals favoring cell survival. Cancer Res. 2003 Dec 1;63(23):8226-32. PMID: #14678979#

 Liang P, Pardee AB. Analysing differential gene expression in cancer. Nat Rev Cancer. 2003 Nov;3(11):869-76. PMID: #14668817#

 Lee Y, Miller HL, Jensen P, Hernan R, Connelly M, Wetmore C, Zindy F, Roussel MF, Curran T, Gilbertson RJ, McKinnon PJ. A molecular fingerprint for medulloblastoma. Cancer Res. 2003 Sep 1;63(17):5428-37. PMID: #14500378#

 Hampton GM, Frierson HF. Classifying human cancer by analysis of gene expression. Trends Mol Med. 2003 Jan;9(1):5-10. PMID: #12524204#

 Chung CH, Bernard PS, Perou CM. Molecular portraits and the family tree of cancer. Nat Genet. 2002 Dec;32 Suppl:533-40. PMID: #12454650#

 Ramsay M. Gene expression profiling to predict lymphoma outcome. Trends Mol Med. 2002 Apr;8(4):159. PMID: #11927271#

 Astolfi A, De Giovanni C, Landuzzi L, Nicoletti G, Ricci C, Croci S, Scopece L, Nanni P, Lollini PL. Identification of new genes related to the myogenic differentiation arrest of human rhabdomyosarcoma cells. Gene. 2001 Aug 22;274(1-2):139-49. PMID: #11675006#

 Takano T, Hasegawa Y, Matsuzuka F, Miyauchi A, Yoshida H, Higashiyama T, Kuma K, Amino N. Gene expression profiles in thyroid carcinomas. Br J Cancer. 2000 Dec;83(11):1495-502. PMID: #11076659#

 Liotta L, Petricoin E. Molecular profiling of human cancer. Nat Rev Genet. 2000 Oct ;1(1):48-56. PMID : #11262874#

 Wooster R. Cancer classification with DNA microarrays is less more ? Trends Genet. 2000 Aug ;16(8):327-9. PMID : #10904257#