Expression profiling of human tumors: The end of surgical pathology?

The Journal of molecular diagnostics : JMD

Volumn 3, Issue 3, 2001, Pages 92-97

  Ladanyi, Marc ^a   Chan, Wing C ^b   Triche, Timothy J ^c   Gerald, William L ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

^c UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CARCINOMA; GENETICS; HUMAN; LYMPHOMA; NEOPLASM; PATHOLOGY; SARCOMA;

CARCINOMA; HUMANS; LYMPHOMA; NEOPLASMS; SARCOMA;

EID: 0035432509     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1525-1578(10)60657-5     Document Type: Article

References (49)

1. L Liotta E Petricoin Molecular profiling of human cancer Nat Rev Genet 1 2000 48 56
2. AM Snijders GA Meijer RH Brakenhoff AJC van den Brule PJ van Diest Microarray techniques in pathology: tool or toy? J Clin Pathol Mol Pathol 53 2000 289 294
3. M Bittner P Meltzer Y Chen Y Jiang E Seftor M Hendrix M Radmacher R Simon Z Yakhini A Ben-Dor N Sampas E Dougherty E Wang F Marincola C Gooden J Lueders A Glatfelter P Pollock J Carpten E Gillanders D Leja K Dietrich C Beaudry M Berens D Alberts V Sondak Molecular classification of cutaneous malignant melanoma by gene expression profiling Nature 406 2000 536 540
4. J Khan R Simon M Bittner Y Chen SB Leighton T Pohida PD Smith Y Jiang GC Gooden JM Trent PS Meltzer Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays Cancer Res 58 1998 5009 5013
5. TR Golub DK Slonim P Tamayo C Huard M Gaasenbeek JP Mesirov H Coller ML Loh JR Downing MA Caligiuri CD Bloomfield ES Lander Molecular classification of cancer: class discovery and class prediction by gene expression monitoring Science 286 1999 531 537
6. AA Alizadeh MB Eisen RE Davis C Ma IS Lossos A Rosenwald JC Boldrick H Sabet T Tran X Yu JI Powell L Yang GE Marti T Moore JJ Hudson L Lu DB Lewis R Tibshirani G Sherlock WC Chan TC Greiner DD Weisenburger JO Armitage R Warnke LM Staudt Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling Nature 403 2000 503 511
7. CM Perou T Sorlie MB Eisen M van de Rijn SS Jeffrey CA Rees JR Pollack DT Ross H Johnsen LA Akslen O Fluge A Pergamenschikov C Williams SX Zhu PE Lonning AL Borresen-Dale PO Brown D Botstein Molecular portraits of human breast tumours Nature 406 2000 747 752
8. J Khan JS Wei M Ringnér LH Saal M Ladanyi F Westermann F Berthold M Schwab CR Antonescu C Peterson PS Meltzer Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks Nat Med 7 2001 673 679
9. MJ Becich The role of the pathologist as tissue refiner and data miner: the impact of functional genomics on the modern pathology laboratory and the critical roles of pathology informatics and bioinformatics Mol Diagn 5 2000 287 299
10. PL Pearson RB Van der Luijit The genetic analysis of cancer J Intern Med 243 1998 413 417
11. DJ Lockhart H Dong MC Byrne MT Follettie MV Gallo MS Chee M Mittmann C Wang M Kobayashi H Horton EL Brown Expression monitoring by hybridization to high-density oligonucleotide arrays Nature Biotechnol 14 1996 1675 1680
12. JL DeRisi VR Iyer PO Brown Exploring the metabolic and genetic control of gene expression on a genomic scale Science 278 1997 680 686
13. MB Eisen PT Spellman PO Brown D Botstein Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci USA 95 1998 14863 14868
14. JZ Huang WG Sanger DL Pickering TC Greiner LM Staudt JC Lynch DD Weisenburger JO Armitage WC Chan CD10, BCL-2, and BCL-6 protein expression and t(14;18)(q32;q21) in two subtypes of diffuse large B-cell lymphoma defined by gene expression profiles Lab Invest 81 2001 167A
15. JL DeRisi VR Iyer Genomics and array technology Curr Opin Oncol 11 1999 76 79
16. J Marx DNA arrays reveal cancer in its many forms Science 289 2000 1670 1672
17. WC Chan Cellular origin of nodular lymphocyte-predominant Hodgkin's lymphoma: immunophenotypic and molecular studies Semin Hematol 36 1999 242 252
18. MB Eisen PO Brown DNA arrays for analysis of gene expression Methods Enzymol 303 1999 179 205
19. RJ Lipshutz SP Fodoe TR Gingeras DJ Lockhart High density synthetic oligonucleotide arrays Nat Genet 21 Suppl 1 1999 20 24
20. RA Young Biomedical discovery with DNA arrays Cell 102 2000 9 15
21. TJ Triche DS Schofield J Buckley DNA microarrays in pediatric cancer Cancer Journal 7 2001 2 15
22. T Werner Cluster analysis and promoter modelling as bioinformatics tools for the identification of target genes from expression array data Pharmacogenomics 2 2001 25 36
23. LM Jakt L Cao KS Cheah DK Smith Assessing clusters and motifs from gene expression data Genome Res 11 2001 112 123
24. M Xiong L Jin W Li E Boerwinkle Computational methods for gene expression-based tumor classification Biotechniques 29 2000 1264 1270
25. PJ Woolf Y Wang A fuzzy logic approach to analyzing gene expression data Physiol Genomics 3 2000 9 15
26. G Sherlock Analysis of large-scale gene expression data Curr Opin Immunol 12 2000 201 205
27. R Sharan R Shamir CLICK: a clustering algorithm with applications to gene expression analysis Proc Int Conf Intell Syst Mol Biol 8 2000 307 316
28. DB Searls Using bioinformatics in gene and drug discovery Drug Discov Today 5 2000 135 143
29. M Larsson S Stahl M Uhlen A Wennborg Expression profile viewer (ExProView): a software tool for transcriptome analysis Genomics 63 2000 341 353
30. N Kaminski Bioinformatics. A user's perspective Am J Respir Cell Mol Biol 23 2000 705 711
31. T Hastie R Tibshirani MB Eisen A Alizadeh R Levy L Staudt WC Chan D Botstein P Brown ‘Gene shaving’ as a method for identifying distinct sets of genes with similar expression patterns Genome Biol 1 2000 RESEARCH0003
32. G Getz E Levine E Domany Coupled two-way clustering analysis of gene microarray data Proc Natl Acad Sci USA 97 2000 12079 12084
33. N Friedman M Linial I Nachman D Pe'er Using Bayesian networks to analyze expression data J Comput Biol 7 2000 601 620
34. Y Cheng GM Church Biclustering of expression data Proc Int Conf Intell Syst Mol Biol 8 2000 93 103
35. A Califano G Stolovitzky Y Tu Analysis of gene expression microarrays for phenotype classification Proc Int Conf Intell Syst Mol Biol 8 2000 75 85
36. HB Burke Discovering patterns in microarray data Mol Diagn 5 2000 349 357
37. MP Brown WN Grundy D Lin N Cristianini CW Sugnet TS Furey M Ares Jr D Haussler Knowledge-based analysis of microarray gene expression data by using support vector machines Proc Natl Acad Sci USA 97 2000 262 267
38. CM Bouton J Pevsner DRAGON: Database Referencing of Array Genes Online Bioinformatics 16 2000 1038 1039
39. T Akutsu S Miyano S Kuhara Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function J Comput Biol 7 2000 331 343
40. M Vingron J Hoheisel Computational aspects of expression data J Mol Med 77 1999 3 7
41. RH Valdivia Regulatory network analysis Trends Microbiol 7 1999 398 399
42. P Tamayo D Slonim J Mesirov Q Zhu S Kitareewan E Dmitrovsky ES Lander TR Golub Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation Proc Natl Acad Sci USA 96 1999 2907 2912
43. Z Szallasi Genetic network analysis in light of massively parallel biological data acquisition Pac Symp Biocomput 1999 5 16
44. MR Emmert-Buck RL Strausberg DB Krizman MF Bonaldo RF Bonner DG Bostwick MR Brown KH Buetow RF Chuaqui KA Cole PH Duray CR Englert JW Gillespie S Greenhut L Grouse LW Hillier KS Katz RD Klausner V Kuznetzov AE Lash G Lennon WM Linehan LA Liotta MA Marra PJ Munson DK Ornstein VV Prabhu C Prang GD Schuler MB Soares CM Tolstoshev CD Vocke RH Waterston Molecular profiling of clinical tissue specimens: feasibility and applications J Mol Diagn 2 2000 60 66
45. DT Ross U Scherf MB Eisen CM Perou C Rees P Spellman V Iyer SS Jeffrey M Van de Rijn M Waltham A Pergamenschikov JC Lee D Lashkari D Shalon TG Myers JN Weinstein D Botstein PO Brown Systemic variation in gene expression patterns in human cancer cell lines Nat Genet 24 2000 227 235
46. CM Perou SS Jeffrey M van de Rijn CA Rees MB Eisen DT Ross A Pergamenschikov CF Williams SX Zhu JC Lee D Lashkari D Shalon PO Brown D Botstein Distinctive gene expression patterns in human mammary epithelial cells and breast cancers Genetics 96 1999 9212 9217
47. U Alon N Barkai DA Notterman K Gish S Ybarra D Mack AJ Levine Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays Proc Natl Acad Sci USA 96 1999 6745 6750
48. L Amler D Agus C LeDuc ML Sapinoso WD Fox S Kern D Lee V Wang M Leysens B Higgins J Martin W Gerald N Dracopoli C Cordon-Cardo HI Scher GM Hampton Dysregulated expression of androgen-responsive and nonresponsive genes in the androgen-independent prostate cancer xenograft model CWR22–R1 Cancer Res 60 2000 6134 6141
49. EA Clark TR Golub ES Lander RO Hynes Genomic analysis of metastasis reveals an essential role for RhoC Nature 406 2000 532 535