Large-scale integration of cancer microarray data identifies a robust common cancer signature

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Xu, Lei ^a   Geman, Donald ^a   Winslow, Raimond L ^a  

^a Johns Hopkins University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CANCER DATA SETS; CANCER DIAGNOSIS; DIAGNOSTIC TESTS; EXPRESSION PROFILE; GENE EXPRESSION SIGNATURES; MICROARRAY GENE EXPRESSION; MOLECULAR DIAGNOSTICS; TRAINING DATA SETS;

BIOASSAY; BIOCHIPS; GENE EXPRESSION; HISTOLOGY; TISSUE;

DISEASES;

DNA; TUMOR MARKER; TUMOR PROTEIN;

ARTICLE; CANCER; CANCER DIAGNOSIS; CANCER TISSUE; CLASSIFIER; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; HUMAN; MICROARRAY ANALYSIS; NUCLEOTIDE SEQUENCE; STATISTICAL ANALYSIS; ARTIFICIAL INTELLIGENCE; CLASSIFICATION; COMPUTER ASSISTED DIAGNOSIS; DATA BASE; INFORMATION RETRIEVAL; METABOLISM; METHODOLOGY; NEOPLASM; PROTEIN DATABASE; SYSTEM ANALYSIS;

ARTIFICIAL INTELLIGENCE; DATABASE MANAGEMENT SYSTEMS; DATABASES, PROTEIN; DIAGNOSIS, COMPUTER-ASSISTED; GENE EXPRESSION PROFILING; HUMANS; INFORMATION STORAGE AND RETRIEVAL; NEOPLASM PROTEINS; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SYSTEMS INTEGRATION; TUMOR MARKERS, BIOLOGICAL;

EID: 34548127285     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-275     Document Type: Article

References (55)

1. Liotta L Petricoin E Molecular Profiling Of Human Cancer Nature Reviews Genetics 2000 1 48-56 10.1038/35049567 11262874
2. Bast RC Jr. Lilja H Urban N Rimm DL Fritsche H Gray J Veltri R Klee G Allen A Kim N Gutman S Rubin MA Hruszkewycz A Translational Crossroads for Biomarkers Clin Cancer Res 2005 11 17 6103-6108 10.1158/ 1078-0432.CCR-04-2213 16144908
3. Dhanasekaran SM Barrette TR Ghosh D Shah R Varambally S Kurachi K Pienta KJ Rubin MA Chinnaiyan AM Delineation of prognostic biomarkers in prostate cancer Nature 2001 412 822-826 10.1038/35090585 11518967
4. Chen X Cheung ST So S Fan ST Barry C Higgins J Lai KM Ji J Dudoit S Ng IOL van de Rijn M Botstein D Brown PO Gene Expression Patterns in Human Liver Cancers Mol Biol Cell 2002 13 6 1929-1939 117615 12058060 10.1091/ mbc.02-02-0023.
5. Su AI Welsh JB Sapinoso LM Kern SG Dimitrov P Lapp H Schultz PG Powell SM Moskaluk CA Frierson HF Jr. Hampton GM Molecular Classification of Human Carcinomas by Use of Gene Expression Signatures Cancer Res 2001 61 20 7388-7393 11606367
6. Luo J Duggan DJ Chen Y Sauvageot J Ewing C Bittner ML Trent JM Isaacs WB Human prostate cancer and benign prostatic hyperplasia: Molecular dissection by gene expression profiling Cancer Research 2001 61 4683-4688 11406537
7. Yagi T Morimoto A Eguchi M Hibi S Sako M Ishii E Mizutani S Imashuku S Ohki M Ichikawa H Identification of a gene expression signature associated with pediatric AML prognosis Blood 2003 102 5 1849-1856 10.1182/blood-2003-02-0578 12738660
8. Iacobuzio-Donahue CA Maitra A Olsen M Lowe AW Van Heek NT Rosty C Walter K Sato N Parker A Ashfaq R Jaffee E Ryu B Jones J Eshleman JR Yeo CJ Cameron JL Kern SE Hruban RH Brown PO Goggins M Exploration of Global Gene Expression Patterns in Pancreatic Adenocarcinoma Using cDNA Microarrays Am J Pathol 2003 162 4 1151-1162 1851213 12651607
9. Watson MA Gutmann DH Peterson K Chicoine MR Kleinschmidt-DeMasters BK Brown HG Perry A Molecular Characterization of Human Meningiomas by Gene Expression Profiling Using High-Density Oligonucleotide Microarrays Am J Pathol 2002 161 2 665-672 1850745 12163391
10. Higgins JPT Shinghal R Gill H Reese JH Terris M Cohen RJ Fero M Pollack JR van de Rijn M Brooks JD Gene Expression Patterns in Renal Cell Carcinoma Assessed by Complementary DNA Microarray Am J Pathol 2003 162 3 925-932 1868114 12598325
11. Bittner M Meltzer P Chen Y Jiang Y Seftor E Hendrix M Radmacher M Simon R Yakhini Z Ben-Dor A Sampas N Dougherty E Wang E Marincola F Gooden C Lueders J Glatfelter A Pollock P Carpten J Gillanders E Leja D Dietrich K Beaudry C Berens M Alberts D Sondak V Hayward N Trent J Molecular classification of cutaneous malignant melanoma by gene expression profiling Nature 2000 406 6795 536-540 10.1038/35020115 10952317
12. Golub TR Slonim DK Tamayo P Huard C Gaasenbeek M Mesirov JP Coller H Loh ML Downing JR Caligiuri MA Bloomfield CD Lander ES Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring Science 1999 286 5439 531-537 10.1126/ science.286.5439.531 10521349
13. Geman D d'Avignon C Naiman DQ Winslow RL Classifying gene expression profiles from pairwise mRNA comparison Statistical Applications in Genetics and Molecular Biology 2004 3 1 19 10.2202/1544-6115.1071
14. Xu L Tan AC Naiman DQ Geman D Winslow RL Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data Bioinformatics 2005 21 20 3905-3911 10.1093/bioinformatics/bti647 16131522
15. Tan AC Naiman DQ Xu L Winslow RL Geman D Simple decision rules for classifying human cancers from gene expression profiles Bioinformatics 2005 21 20 3896-3904 10.1093/bioinformatics/bti631 16105897
16. Yang X Bentink S Spang R Detecting Common Gene Expression Patterns in Multiple Cancer Outcome Entities Biomedical Microdevices 2005 7 3 247-251 10.1007/s10544-005-3032-7 16133813
17. Rhodes DR Yu J Shanker K Deshpande N Varambally R Ghosh D Barrette T Pandey A Chinnaiyan AM Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression PNAS 2004 101 25 9309-9314 438973 15184677 10.1073/pnas.0401994101
18. Segal E Friedman N Koller D Regev A A module map showing conditional activity of expression modules in cancer Nat Genet 2004 36 10 1090 15448693
19. Price ND Trent J El-Naggar AK Cogdell D Taylor E Hunt KK Pollock RE Hood L Shmulevich I Zhang W Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas PNAS 2007 104 9 3414-3419 10.1073/pnas.0611373104 17360660
20. Barrett T Troup DB Wilhite SE Ledoux P Rudnev D Evangelista C Kim IF Soboleva A Tomashevsky M Edgar R NCBI GEO: Mining tens of millions of expression profiles - database and tools update Nucl Acids Res 2007 35 suppl 1 D760-765 10.1093/nar/gkl887
21. Rhodes DR Yu J Shanker K Deshpande N Varambally R Ghosh D Barrette T Pandey A Chinnaiyan AM ONCOMINE: A Cancer Microarray Database and Integrated Data-Mining Platform Neoplasia 2004 6 1 1635162 15068665
22. Basil CF Zhao Y Zavaglia K Jin P Panelli MC Voiculescu S Mandruzzato S Lee HM Seliger B Freedman RS Taylor PR Hu N Zanovello P Marincola FM Wang E Common Cancer Biomarkers Cancer Res 2006 66 6 2953-2961 10.1158/ 0008-5472.CAN-05-3433 16540643
23. Michiels S Koscielny S Hill C Prediction of canceroutcome with microarrays: A multiple random validation strategy Lancet 2005 365 9458 488-492 10.1016/S0140-6736(05)17866-0 15705458
24. Pavlidis P Noble WS Matrix2png: A utility for visualizing matrix data Bioinformatics 2003 19 2 295-296 10.1093/bioinformatics/19.2.295 12538257
25. Beer DG Kardia SLR Huang CC Giordano TJ Levin AM Misek DE Lin L Chen G Gharib TG Thomas DG Lizyness M Kuick R Hayasaka S Taylor JMG Iannettoni MD Orringer MB Hanash SM Gene-expression profiles predict survival of patients with lung adenocarcinoma Nature Medicine 2002 8 8 816-824 12118244
26. Dyrskjot L Thykjaer T Kruhoffer M Jensen JL Marcussen N Hamilton-Dutoit S Wolf H Orntoft TF Identifying distinct classes of bladder carcinoma using microarrays Nature Genetics 2003 33 90-96 10.1038/ng1061 12469123
27. Hippo Y Taniguchi H Tsutsumi S Machida N Chong JM Fukayama M Kodama T Aburatani H Global Gene Expression Analysis of Gastric Cancer by Oligonucleotide Microarrays Cancer Res 2002 62 1 233-240 11782383
28. Hsiao LL Dangond F Yoshida T Hong R Jensen RV Misra J Dillon W Lee KF Clark KE Haverty P Weng Z Mutter GL Frosch MP Macdonald ME Milford EL Crum CP Bueno R Pratt RE Mahadevappa M Warrington JA Stephanopoulos G Stephanopoulos G Gullans SR A compendium of gene expression in normal human tissues Physiol Genomics 2001 7 2 97-104 11773596
29. Lancaster JM Dressman HK Whitaker RS Havrilesky L Gray J Marks JR Nevins JR Berchuck A Gene expression patterns that characterize advanced stage serous ovarian cancers Journal of the Society for Gynecologic Investigation 2004 11 1 51-59 10.1016/j.jsgi.2003.07.004 14706684
30. Logsdon CD Simeone DM Binkley C Arumugam T Greenson JK Giordano TJ Misek DE Hanash S Molecular Profiling of Pancreatic Adenocarcinoma and Chronic Pancreatitis Identifies Multiple Genes Differentially Regulated in Pancreatic Cancer Cancer Res 2003 63 10 2649-2657 12750293
31. Pomeroy SL Tamayo P Gaasenbeek M Sturla LM Angelo M McLaughlin ME Kim JYH Goumnerova LC Black PM Lau C Allen JC Zagzag D Olson JM Curran T Wetmore C Biegel JA Poggio T Mukherjee S Rifkin R Califano A Stolovitzky G Louis DN Mesirov JP Lander ES Golub TR Prediction of central nervous system embryonal tumour outcome based on gene expression Nature 2002 415 436-442 10.1038/415436a 11807556
32. Quade BJ Mutter GL Morton CC Comparision of Gene expression in Uterine Smooth Muscle Tumors Gene Expression Omnibus: GSE764 2003
33. Ramaswamy S Tamayo P Rifkin R Mukherjee S Yeang CH Angelo M Ladd C Reich M Latulippe E Mesirov JP Poggio T Gerald W Loda M Lander ES Golub TR Multiclass cancer diagnosis using tumor gene expression signatures PNAS 2001 98 26 15149-15154 64998 11742071 10.1073/pnas.211566398
34. Rickman DS Bobek MP Misek DE Kuick R Blaivas M Kurnit DM Taylor J Hanash SM Distinctive Molecular Profiles of High-Grade and Low-Grade Gliomas Based on Oligonucleotide Microarray Analysis Cancer Res 2001 61 18 6885-6891 11559565
35. Welsh JB Zarrinkar PP Sapinoso LM Kern SG Behling CA Monk BJ Lockhart DJ Burger RA Hampton GM Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer PNAS 2001 98 3 1176-1181 14728 11158614 10.1073/pnas.98.3.1176
36. Zhan F Hardin J Kordsmeier B Bumm K Zheng M Tian E Sanderson R Yang Y Wilson C Zangari M Anaissie E Morris C Muwalla F van Rhee F Fassas A Crowley J Tricot G Barlogie B Shaughnessy J Jr. Global gene expression profiling of multiple myeloma, monoclonal gammopathy of undetermined significance, and normal bone marrow plasma cells Blood 2002 99 5 1745-1757 10.1182/blood.V99.5.1745 11861292
37. Bhattacharjee A Richards WG Staunton J Li C Monti S Vasa P Ladd C Beheshti J Bueno R Gillette M Loda M Weber G Mark EJ Lander ES Wong W Johnson BE Golub TR Sugarbaker DJ Meyerson M Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses PNAS 2001 98 24 13790-13795 61120 11707567 10.1073/pnas.191502998
38. Cromer A Carles A Millon R Ganguli G Chalmel F Lemaire F Young J Dembele D Thibault C Muller D Poch O Abecassis J AWasylyk B Idenfification of genes associated with tumorigenesis and metastatic potential of hypopharyngeal cancer by microarray analysis Oncogene 2003 23 14 2484-2498 10.1038/sj.onc.1207345
39. Dehan E Kaminski N Non Small Cell Lung Cancer Gene Expression Onmibus: GSE1987 2004
40. Frierson HF Jr. El-Naggar AK Welsh JB Sapinoso LM Su AI Cheng J Saku T Moskaluk CA Hampton GM Large Scale Molecular Analysis Identifies Genes with Altered Expression in Salivary Adenoid Cystic Carcinoma Am J Pathol 2002 161 4 1315-1323 1867312 12368205
41. Giordano TJ Thomas DG Kuick R Lizyness M Misek DE Smith AL Sanders D Aljundi RT Gauger PG Thompson NW Taylor JMG Hanash SM Distinct Transcriptional Profiles of Adrenocortical Tumors Uncovered by DNA Microarray Analysis Am J Pathol 2003 162 2 521-531 1851158 12547710
42. Gutmann DH Hedrick NM Li J Nagarajan R Perry A Watson MA Comparative Gene Expression Profile Analysis of Neurofibromatosis 1-associated and Sporadic Pilocytic Astrocytomas Cancer Res 2002 62 7 2085-2091 11929829
43. Huang Y Prasad M Lemon WJ Hampel H Wright FA Kornacker K LiVolsi V Frankel W Kloos RT Eng C Pellegata NS de la Chapelle A Gene expression in papillary thyroid carcinoma reveals highly consistent profiles PNAS 2001 98 26 15044-15049 64980 11752453 10.1073/pnas.251547398
44. Shai R Shi T Kremen TJ Horvath S Liau LM Cloughesy TF Mischel PS Nelson SF Gene expression profiling identifies molecular subtypes of gliomas Oncogene 2003 22 31 4918-4923 10.1038/sj.onc.1206753 12894235
45. Stearman RS Dwyer-Nield L Zerbe L Blaine SA Chan Z Bunn PA Jr. Johnson GL Hirsch FR Merrick DT Franklin WA Baron AE Keith RL Nemenoff RA Malkinson AM Geraci MW Analysis of Orthologous Gene Expression between Human Pulmonary Adenocarcinoma and a Carcinogen-Induced Murine Model Am J Pathol 2005 167 6 1763-1775 1613183 16314486
46. Su AI Cooke MP Ching KA Hakak Y Walker JR Wiltshire T Orth AP Vega RG Sapinoso LM Moqrich A Patapoutian A Hampton GM Schultz PG Hogenesch JB Large-scale analysis of the human and mouse transcriptomes PNAS 2002 99 7 4465-4470 123671 11904358 10.1073/pnas.012025199
47. Welle S Brooks A Thornton C Computational method for reducing variance with Affymetrix microarrays BMC Bioinformatics 2002 3 1 23 126253 12204100 10.1186/1471-2105-3-23
48. Yanai I Benjamin H Shmoish M Chalifa-Caspi V Shklar M Ophir R Bar-Even A Horn-Saban S Safran M Domany E Lancet D Shmueli O Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification Bioinformatics 2005 21 5 650-659 10.1093/ bioinformatics/bti042 15388519
49. Yu YP Landsittel D Jing L Nelson J Ren B Liu L McDonald C Thomas R Dhir R Finkelstein S Michalopoulos G Becich M Luo JH Gene Expression Alterations in Prostate Cancer Predicting Tumor Aggression and Preceding Development of Malignancy J Clin Oncol 2004 22 14 2790-2799 10.1200/ JCO.2004.05.158 15254046
50. Gordon GJ Malignant pleural mesothelioma Gene Expression Omnibus: GSE2549 2005
51. Hoffman PJ Milliken DB Davis RP Gregg JP Uterine Fibroid and Normal Myometrial Expression Profiles Gene Expression Omnibus: GSE593 2003
52. Lenburg M Liou L Gerry N Frampton G Cohen H Christman M Previously unidentified changes in renal cell carcinoma gene expression identified by parametric analysis of microarray data BMC Cancer 2003 3 1 31 317310 14641932 10.1186/1471-2407-3-31
53. Talantov D Mazumder A Yu JX Briggs T Jiang Y Backus J Atkins D Wang Y Novel Genes Associated with Malignant Melanoma but not Benign Melanocytic Lesions Clin Cancer Res %R 101158/1078-0432CCR-05-0683 2005 11 20 7234-7242 10.1158/1078-0432.CCR-05-0683
54. Wachi S Yoneda K Wu R Squamous Lung Cancer Gene Expression Omnibus: GSE3268 2005
55. Yoon SS Segal NH W. RS Detwiller KY D'Amore PA Fernando NT Gene expression of human soft tissue sarcoma Gene Expression Onmibus: GSE2719 2005