About this Resource

Datasets (72 entries)

Brain Tumors  (4 entries)
Breast Cancer  (17 entries)
Bladder Cancer  (2 entries)
Cervical Cancer (1 entry)
Colon Cancer  (2 entries)
Esophageal Cancer  (2 entries)
Gastric Cancer  (5 entries)
Head and Neck Cancer (1 entry)
Kidney Cancer (5 entries)
Leukemia (2 entries)

Liver Cancer (7 entries)
Lymphoma (6 entries)
Lung Cancer (3 entries)
Melanoma (4 entries)

Meningioma (1 entry)

Mesothelioma (1 entry)

Oral Cancer  (2 entry)
Ovarian Cancer (4 entries)

Pancreatic Cancer (1 entry)

Prostate Cancer (6 entries)

Thyroid Cancer (1 entry)

Submit New Dataset

Credits
Tue Ngyuen, Matthew Hlobilek, Satish Patel, Soumyaroop Bhattacharya, James Lyons-Weiler

Entry 1:Khatua et. al (2003)

Overexpression of the EGFR/FKBP12/HIF-2alpha pathway identified in childhood astrocytomas by angiogenesis gene profiling.
Khatua S, Peterson KM, Brown KM, Lawlor C, Santi MR, LaFleur B, Dressman D, Stephan DA, MacDonald TJ.
Cancer Res. 2003 Apr 15;63(8):1865-70.
[Pubmed]
[Fulltext]
[Dataset Download Site]
[Group]

Entry 2:van der Boom et. al (2003)

Characterization of gene expression profiles associated with glioma progression using oligonucleotide-based microarray analysis and real-time reverse transcription-polymerase chain reaction.
van den Boom J, Wolter M, Kuick R, Misek DE, Youkilis AS, Wechsler DS, Sommer C, Reifenberger G, Hanash SM.
Am J Pathol. 2003 Sep;163(3):1033-43.
[PubMed]
[Full Text]
[Data Set Download Page]
[Group]

Entry 3
Kim S, Dougherty ER, Shmulevich L, Hess KR, Hamilton SR, Trent JM, Fuller GN, Zhang W. Identification of combination gene sets for glioma classification. Mol Cancer Ther.  2002 Nov;1(13):1229-36.

[Pubmed]

[Full Text]

[Data Set Download Page]

[Group]

Entry 4.

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 Sep 15;61(18):6885-91. 

[Pubmed]

[Full Text]

[Data Set Download Page]

[Group]

Top

Entry 1:Veer et. al (2002)

Gene expression profiling predicts clinical outcome of breast cancer
van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH.
Nature 2002 Jan 31;415(6871):530-6.
[Pubmed]
[Fulltext]
[Dataset Download Site]
[Group]

Entry 2:Perou et. al (2000)

Molecular portraits of human breast tumours.
Perou CM, Sorlie T, Eisen MB et al.
Nature 406 (2000) 747-752.
[PubMed]
[Full Text]
[Data Set Download Page1]
[Data Set Download Page2]
[Group]

Entry 3:Hedenfalk et. al (2001)

Gene-expression profiles in hereditary breast cancer.
Hedenfalk I, Duggan D, Chen Y, Radmacher M, Bittner M, Simon R,
Meltzer P, Gusterson B, Esteller M, Kallioniemi OP, Wilfond B, Borg A, Trent J.
N Engl J Med 2001 Feb 22;344(8):539-48
[PubMed]
[Full Text]
[Data Set Download Site]
[Project Web Site]

Entry 4:Huang et. al (2003)

Gene expression predictors of breast cancer outcomes.
Huang E, Cheng SH, Dressman H, Pittman J, Tsou MH, Horng CF, Bild A, Iversen ES, Liao M, Chen CM, West M, Nevins JR, Huang AT.
Lancet 2003 May 10;361(9369):1590-6.
[PubMed]
[Full Text]
[Data Set Download Site]

Entry 5:Perou et. al (1999)

Distinctive gene expression patterns in human mammary epithelial cells and breast cancers.
Perou CM, Jeffrey SS, van de Rijn M, Rees CA, Eisen MB, Ross DT, Pergamenschikov A, Williams CF, Zhu SX, Lee JC, Lashkari D, Shalon D, Brown PO, Botstein D.
Lancet Proc Natl Acad Sci USA 96,9212-7.
[PubMed]
[Full Text]
[Data Set Download Site]

Entry 6:Perou et. al (2000)

Molecular portraits of human breast tumours.
Perou, C.M., Sorlie T., Eisen, M.B., van de Rijn M., Jeffrey S.S., Rees C.A., Pollack J.R., Ross D.T., Johnsen H., Akslen L.A., Fluge O., Pergamenschikov A., Williams C., Zhu S.X., Lonning P.E., Borresen-Dale A.L., Brown P.O., and Botstein D.
Nature, 406, 747-752.

Type: Classification
[PubMed]
[Full Text]
[Data Set Download Site]

Entry 7:West et. al (2001)

Predicting the clinical status of human breast cancer by using gene expression profiles.
West M, Blanchette C, Dressman H, Huang E, Ishida S, Spang R, Zuzan H, Olson JA Jr, Marks JR, Nevins JR.
Proc Natl Acad Sci U S A 2001 Sep 25;98(20):11462-7
[PubMed]
[Full Text]
[Data Set Download Site]

Entry 8:Martin et. al., 2000

Linking gene expression patterns to therapeutic groups in breast cancer.
Martin KJ, Kritzman BM, Price LM, Koh B, Kwan CP, Zhang X, Mackay A, O'Hare MJ, Kaelin CM, Mutter GL, Pardee AB, Sager R.
Cancer Res. 2000 Apr 15;60(8):2232-8.
[PubMed]
[Full Text]
[Data Set Download Site]

Entry 9:Berns et. al., 2000

Molecular profiles of BRCA1-mutated and matched sporadic breast tumours: relation with clinico-pathological features.
Berns EM, van Staveren IL, Verhoog L, van de Ouweland AM, Meijer-van Gelder M, Meijers-Heijboer H, Portengen H, Foekens JA, Dorssers LC, Klijn JG.
Br J Cancer. 2001 Aug 17;85(4):538-45.
[PubMed]
[Full Text]
[Data Set Download Site]

Entry 10:LaCroix et. al., 2002

A low-density DNA microarray for analysis of markers in breast cancer.
Lacroix M, Zammatteo N, Remacle J, Leclercq G.
Int J Biol Markers. 2002 Jan-Mar;17(1):5-23.
[PubMed]
[Full Text]
[Data Set Download Site] Data set release pending

Entry 11:Buccholz et. al., 2002

Global gene expression changes during neoadjuvant chemotherapy for human breast cancer.
Buchholz TA, Stivers DN, Stec J, Ayers M, Clark E, Bolt A, Sahin AA,Symmans WF, Hess KR, Kuerer HM, Valero V, Hortobagyi GN, Pusztai L.
Cancer J. 2002 Nov-Dec;8(6):461-8.
[PubMed]
[Full Text]
[Data Set Download Site]

Entry 12: 

Porter D, Lahti-Domenici J, Keshaviah A, Bae YK, Argani P, Marks J, Richardson A, Cooper A, Strausberg R, Riggins GJ, Schnitt S, Gabrielson E, Gelman R, Polyak K. Molecular markers in ductal carcinoma in situ of the breast. Mol Cancer Res.  2003 Mar;1(5):362-75. 

Type: Diagnosis

[PubMed]
[Full Text]
[Data Set Download Site]

Entry 13: 

Glinsky GV, Higashiyama T, Glinskii AB. Classification of human breast cancer using gene expression profiling as a component of the survival predictor algorithm. Clin Cancer Res.  2004 Apr 1;10(7):2272-83.

Type: Survivorship

[PubMed]
[Full Text]
[Data Set Download Site]

Entry 14:

Woelfle U, Cloos J, Sauter G, Riethdorf L, Janicke F, van Diest P, Brakenhoff R, Pantel K. Molecular signature associated with bone marrow micrometastasis in human breast cancer. Cancer Res.  2003 Sep 15;63(18):5679-84. 

Type: Metastasis

[PubMed]
[Full Text]
[Data Set Download Site]

Entry 15.

Kang Y, Siegel PM, Shu W, Drobnjak M, Kakonen SM, Cordon-Cardo C, Guise TA, Massague J. A multigenic program mediating breast cancer metastasis to bone. Cancer Cell.  2003 Jun;3(6):537-49. 

Type: Metastasis

[PubMed]
[Full Text]
[Data Set Download Site]

Entry 16.

Wang ZC, Lin M, Wei LJ, Li C, Miron A, Lodeiro G, Harris L, Ramaswamy S, Tanenbaum DM, Meyerson M, Iglehart JD, Richardson A. Loss of heterozygosity and its correlation with expression profiles in subclasses of invasive breast cancers. Cancer Res.  2004 Jan 1;64(1):64-71.

Type: Metastasis

[PubMed]
[Full Text]
[Data Set Download Site]

Entry 17.

Bertucci F, Borie N, Ginestier C, Groulet A, Charafe-Jauffret E, Adelaide J, Geneix J, Bachelart L, Finetti P, Koki A, Hermitte F, Hassoun J, Debono S, Viens P, Fert V, Jacquemier J, Birnbaum D. Identification and validation of an ERBB2 gene expression signature in breast cancers. Oncogene.  2004 Apr 1;23(14):2564-75.

Type: Therapy Response

[PubMed]
[Full Text]
[Data Set Download Site]

The Breast Cancer Research Foundation - make a donation today!

Top

Entry 1:Dyrskjot et. al (2003)
Identifying distinct classes of bladder carcinoma using microarrays
Dyrskjot L, Thykjaer T, Kruhoffer M, Jensen JL, Marcussen N, Hamilton-Dutoit S, Wolf H, Orntoft TF.
Nat Genet 2003 Jan;33(1):90-6
[Pubmed]
[Full text]
[Data Download Site]
[Group]

Entry 2:Nocito et. al (2001)
Microarrays of bladder cancer tissue are highly representative of proliferation index and histological grade.
Nocito A, Bubendorf L, Maria Tinner E, Suess K, Wagner U, Forster T, Kononen J, Fijan A, Bruderer J, Schmid U, Ackermann D, Maurer R, Alund G, Knonagel H, Rist M, Anabitarte M, Hering F, Hardmeier T, Schoenenberger AJ, Flury R, Jager P, Luc Fehr J, Schraml P, Moch H, Mihatsch MJ, Gasser T, Sauter G.
J Pathol 194,349-57.
[Pubmed]
[Full text]
[Data Download Site]

Top

Entry 1:

Wong YF, Selvanayagam ZE, Wei N, Porter J, Vittal R, Hu R, Lin Y, Liao J, Shih JW, Cheung TH, Lo KW, Yim SF, Yip SK, Ngong DT, Siu N, Chan LK, Chan CS, Kong T, Kutlina E, McKinnon RD, Denhardt DT, Chin KV, Chung TK. Expression genomics of cervical cancer: molecular classification and prediction of radiotherapy response by DNA microarray. Clin Cancer Res.  2003 Nov 15;9(15):5486-92. 

[Pubmed]
[Full text]
[Data Download Site]

Entry 1: Alon et al., 1999.
Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays
Alon U, Barkai N, Notterman DA, Gish, K, Ybarra, S. Mack, D and Levine, AJ.
Proc. Natl. Acad. Sci. USA. 96 (1999) 6745-6750.
[PubMed Entry]
[Fulltext]
[Data Set Download Sites (Links provided by D. Notterman)

• MatLab file
• Text and Excel files]

[Group]

Entry 2:

Wang Y, Jatkoe T, Zhang Y, Mutch MG, Talantov D, Jiang J, McLeod HL, Atkins D. Gene Expression Profiles and Molecular Markers To Predict Recurrence of Dukes' B Colon Cancer. J Clin Oncol. 2004 Mar 29   [Epub ahead of print]

Type: Diagnosis.

[Pubmed]
[Fulltext]
[Data Download Site]

[Group]

Top

Entry 1: Selaru et al., 2002
Global gene expression profiling in Barrett's esophagus and esophageal cancer: a comparative analysis using cDNA microarrays
Selaru FM, Zou T, Xu Y, Shustova V, Yin J, Mori Y, Sato F, Wang S, Olaru A, Shibata D, Greenwald BD, Krasna MJ, Abraham JM, Meltzer SJ.
Oncogene 2002 Jan 17;21(3):475-8.
[Pubmed]
[Fulltext]
[Data Download Site]

[Group]

Entry 2: Kihara et al., 2001
Prediction of sensitivity of esophageal tumors to adjuvant chemotherapy by cDNA microarray analysis of gene-expression profiles.
Kihara C, Tsunoda T, Tanaka T, Yamana H, Furukawa Y, Ono K, Kitahara O, Zembutsu H, Yanagawa R, Hirata K, Takagi T, Nakamura Y.
Oncogene 2002 Jan 17;21(3):475-8.
[Pubmed]
[Fulltext]
[Data Download Site]

Top

Entry 2. Hasegawa et. al., 2002
Genome-wide analysis of gene expression in intestinal-type gastric cancers using a complementary DNA microarray representing 23,040 Genes.
Hasegawa S, Furukawa Y, Li M, Satoh S, Kato T, Watanabe T, Katagiri T, Tsunoda T, Yamaoka Y, Nakamura Y. 2002.
Cancer Res 2002 Dec 1;62(23),7012-7017.
[PubMed Entry]
[Data Set Download Site]
[Full text]

Entry 3. Inoue et. al., 2002
Prognostic score of gastric cancer determined by cDNA microarray.
Inoue H, Matsuyama A, Mimori K, Ueo H, Mori M. 2002.
Clin Cancer Res 8,3475-9.
[PubMed Entry]
[Data Set Download Site]
[Full text]

Entry 5. Boussioutas et. al., 2003
Distinctive patterns of gene expression in premalignant gastric mucosa and gastric cancer.
Boussioutas A, Li H, Liu J, Waring P, Lade S, Holloway AJ, Taupin D, Gorringe K, Haviv I, Desmond PV, Bowtell DD.
Cancer Res. 2003 May 15;63(10):2569-77.
[PubMed]
[Data Set Download Site]
[Full text]

Entry 6.

Boussioutas A, Li H, Liu J, Waring P, Lade S, Holloway AJ, Taupin D, Gorringe K, Haviv I, Desmond PV, Bowtell DD. Distinctive patterns of gene expression in premalignant gastric mucosa and gastric cancer. Cancer Res.  2003 May 15;63(10):2569-77.

Type: Diagnosis

[PubMed]
[Data Set Download Site]
[Full text]

Entry 7.

Meireles SI, Cristo EB, Carvalho AF, Hirata R Jr, Pelosof A, Gomes LI, Martins WK, Begnami MD, Zitron C, Montagnini AL, Soares FA, Neves EJ, Reis LF. Molecular classifiers for gastric cancer and nonmalignant diseases of the gastric mucosa. Cancer Res.  2004 Feb 15;64(4):1255-65. 

[PubMed]
[Data Set Download Site]
[Full text]

Top

Entry 1:

Ginos MA, Page GP, Michalowicz BS, Patel KJ, Volker SE, Pambuccian SE, Ondrey FG, Adams GL, Gaffney PM. Identification of a gene expression signature associated with recurrent disease in squamous cell carcinoma of the head and neck. Cancer Res.  2004 Jan 1;64(1):55-63. 

[PubMed]
[Data Set Download Site]
[Full text]

• Renal Cell Carcinoma

Entry 1: Boer et. al.,2001
Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31,500-element cDNA array.
Boer JM, Huber WK, Sultmann H, Wilmer F, von Heydebreck A, Haas S, Korn B, Gunawan B, Vente A, Fuzesi L, Vingron M, Poustka A.
Genome Res. 2001 Nov;11(11):1861-70.
[Pub med]
[Full text]
[Data Download Site]
[Group]

Entry 2: Moch et. al.
High-throughput tissue microarray analysis to evaluate genes uncovered by cDNA microarray screening in renal cell carcinoma.
Moch H, Schraml P, Bubendorf L, Mirlacher M, Kononen J, Gasser T, Mihatsch MJ, Kallioniemi OP, Sauter G.
Am J Pathol 154,981-6.
[Pub med]
[Full text]
[Data Download Site]

Entry 3:Yamazaki et. al. 2003
Overexpression of KIT in chromophobe renal cell carcinoma.
Yamazaki K, Sakamoto M, Ohta T, Kanai Y, Ohki M, Hirohashi S.
Oncogene. 2003 Feb 13;22(6):847-52.
[Pubmed]
[Full text]
[Data Download Site]

Entry 4. 

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: potential clinical relevance. Cancer.  2004 Mar 1;100(5):976-85. 

[PubMed]
[Fulltext]
[Data]
[Group]

• Wilm's Tumor

Entry 5 : Li CM, Guo M, Borczuk A, Powell CA, Wei M, Thaker HM, Friedman R, Klein U, Tycko B. Gene expression in Wilms' tumor mimics the earliest committed stage in the metanephric mesenchymal-epithelial transition. Am J Pathol.  2002 Jun;160(6):2181-90. 

Type: Diagnosis

[PubMed]
[Fulltext]
[Data]
[Group]

Top

Entry 1: Golub et al., 1999
Molecular classification of cancer: class discovery and class prediction by gene expression monitoring
Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES.
Science 1999 286:531-537.
[PubMed]
[Fulltext]
[Data Set Download Site]
[Group]

Entry 2: Virtaneva et. al., 2001
Expression profiling reveals fundamental biological  differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogenetics
Virtaneva, K, Wright, FA,  Tanner, SM, Yuan, B, Lemon, WJ, Caligiuri, MA, Bloomfield, CD, A. de la Chapelle, and R. Krahe
Proc. Natl. Acad. Sci. USA, 2001;98 1124-1129.
Paper (PNAS)
Data Set Download Site

Additional Sites on Leukemia
 

Schiller, G. High-Dose Consolidation Chemotherapy V Bone Marrow
Transplantation as Postremission Therapy in Adult Acute
Myeloid Leukemia. http://www.meds.com/leukemia/trends/mon_pt2.html

Top

Entry 1:Chung et al., 2002
Gene expression profile analysis in human hepatocellular carcinoma by cDNA microarray.
Chung EJ, Sung YK, Farooq M, Kim Y, Im S, Tak WY, Hwang YJ, Kim YI, Han HS, Kim JC, Kim MK.
Mol Cells. 2002 Dec 31;14(3):382-7.
[PubMed]
[Fulltext]
[Data Set Download Site]
[Group]

Entry 2:Chen et al., 2002
Gene expression patterns in human liver cancers.
Chen X, Cheung ST, So S, Fan ST, Barry C, Higgins J, Lai KM, Ji J, Dudoit S, Ng IO, Van De Rijn M, Botstein D, Brown PO.
Mol Biol Cell 13(6):1929-39.
[PubMed]
[Fulltext]
[Data Set Download Site]
[Group]

Entry 3:Li et al., 2002
Discovery and analysis of hepatocellular carcinoma genes using cDNA microarrays.
Li Y, Li Y, Tang R, Xu H, Qiu M, Chen Q, Chen J, Fu Z, Ying K, Xie Y, Mao Y.
J Cancer Res Clin Oncol. 2002 Jul;128(7):369-79. Epub 2002 Jun 20.
[PubMed]
[Fulltext]
[Data Set Download Site]
[Group]

Entry 4:

Kim JW, Ye Q, Forgues M, Chen Y, Budhu A, Sime J, Hofseth LJ, Kaul R, Wang XW. Cancer-associated molecular signature in the tissue samples of patients with cirrhosis. Hepatology.  2004 Feb;39(2):518-27. 

[PubMed]
[Fulltext]
[Data Set Download Site]
[Group]

Entry 5:

Goldenberg D, Ayesh S, Schneider T, Pappo O, Jurim O, Eid A, Fellig Y, Dadon T, Ariel I, de Groot N, Hochberg A, Galun E. Analysis of differentially expressed genes in hepatocellular carcinoma using cDNA arrays. Mol Carcinog.  2002 Feb;33(2):113-24.

[PubMed]
[Fulltext]
[Data Set Download Site]
[Group]

  Entry 6:

Chuma M, Sakamoto M, Yamazaki K, Ohta T, Ohki M, Asaka M, Hirohashi S. Expression profiling in multistage hepatocarcinogenesis: identification of HSP70 as a molecular marker of early hepatocellular carcinoma. Hepatology.  2003 Jan;37(1):198-207. 

[PubMed]
[Fulltext]
[Data Set Download Site]
[Group]

  Entry 7:

Ye QH, Qin LX, Forgues M, He P, Kim JW, Peng AC, Simon R, Li Y, Robles AI, Chen Y, Ma ZC, Wu ZQ, Ye SL, Liu YK, Tang ZY, Wang XW. Predicting hepatitis B virus-positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning. Nat Med.  2003 Apr;9(4):416-23. Epub 2003 Mar 17.

[PubMed]
[Fulltext]
[Data Set Download Site]
[Group]

Top

Entry 1: Garber et al., 2001
Diversity of gene expression in adenocarcinoma of the lung
Mitchell E. Garber, Olga G. Troyanskaya, Karsten Schluens, Simone Petersen, Zsuzsanna Thaesler, Manuela Pacyna-Gengelbach, Matt van de Rijn, Glenn D. Rosen, Charles M. Perou, Richard I. Whyte, Russ B. Altman, Patrick O. Brown, David Botstein, and Iver Petersen
Proc. Natl. Acad. Sci. USA, Vol. 98, Issue 24, 13784-13789, November 20, 2001
[PubMed Entry]
[Data Set Download Site]
[Full text]
[Group]

Entry 2: Heighway et al., 2002
Expression profiling of primary non-small cell lung cancer for target identification.
Heighway J, Knapp T, Boyce L, Brennand S, Field JK, Betticher DC, Ratschiller D, Gugger M, Donovan M, Lasek A, Rickert P.
Oncogene 21,7749-63.
[PubMed Entry]
[Data Set Download Site] Propietary Data
[Full text]

Entry 3: Virtanen et al., 2002
Integrated classification of lung tumors and cell lines by expression profiling.
Virtanen C, Ishikawa Y, Honjoh D, Kimura M, Shimane M, Miyoshi T, Nomura H, Jones MH.
Proc Natl Acad Sci USA 99,12357-62.
[PubMed Entry]
[Data Set Download Site]
[Full text]

Top

Entry 1: Alizadeh et al., 2000.
Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling
Alizadeh AA, Eisen MB, Davis RE, et al. (2000)
Nature 403 (2000) 503-11.
[Pub Med ]
[Full Text]
[Data set download site]
[Group: Lymphoma/Leukemia Molecular Profiling Project]

Entry 2: Chan et al., 2001
Gene expression analysis in aggressive NHL
Chan WC, Huang JZ.
Ann Hematol 2001;80 Suppl 3:B38-41.
[Pub med]
[Fulltext]
[Data Download Site]

Entry 3: Shipp et al., 2002
Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning
Shipp MA, Ross KN, Tamayo P, Weng AP, Kutok JL, Aguiar RC, Gaasenbeek M, Angelo M, Reich M, Pinkus GS, Ray TS, Koval MA, Last KW, Norton A, Lister TA, Mesirov J, Neuberg DS, Lander ES, Aster JC, Golub TR.
Nat Med 2002 Jan;8(1):68-74.
[Pub med]
[Fulltext]
[Data Download Site]

Entry 4: De Vos et al., 2002
Comparison of gene expression profiling between malignant and normal plasma cells with oligonucleotide arrays.

De Vos J, Thykjaer T, Tarte K, Ensslen M, Raynaud P, Requirand G, Pellet F, Pantesco V, Reme T, Jourdan M, Rossi JF, Orntoft T, Klein B.

Oncogene 2002 Oct 3;21(44):6848-57.
[Pub med]
[Fulltext]
[Data Download Site]

[Group]

Entry 5: Ando et al., 2002
Fuzzy neural network applied to gene expression profiling for predicting the prognosis of diffuse large B-cell lymphoma.
Ando T, Suguro M, Hanai T, Kobayashi T, Honda H, Seto M.
Jpn J Cancer Res. 93,1207-12
[Pub med]
[Fulltext]
[Data Download Site]

Entry 6: Li et al., 2001
Comparative genome-scale analysis of gene expression profiles in T cell lymphoma cells during malignant progression using a complementary DNA microarray.
Li S, Ross DT, Kadin ME, Brown PO, Wasik MA.
Am J Pathol 158,1231-7.
[Pub med]
[Fulltext]
[Data Download Site]

Top

Entry 1: Bittner et al., 2000.
Molecular classification of cutaneous malignant melanoma by gene expression profiling.
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
Nature. 406 (2000) 536-40.
[Pub Med ]
[Data Download Site(ftp)]
[Full Text]
[Group]
OncoLink Entry on Melanoma

Entry 2: Yakhini et al., 2000.
Molecular classification of cutaneous malignant melanoma by gene expression profiling.
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.
Nature. 406,536-40.
[Pub Med ]
[Data Download Site]
[Full Text]

Entry 3: Clark et al., 2000.
Genomic analysis of metastasis reveals an essential role for RhoC.
Clark EA, Golub TR, Lander ES, Hynes RO.
Nature. 2000 Aug 3;406(6795):532-5.
[Pub Med ]
[Data Download Site]
[Full Text]

Entry 4: de Wit et al., 2002.
Differentially expressed genes identified in human melanoma cell lines with different metastatic behaviour using high density oligonucleotide arrays.
de Wit NJ, Burtscher HJ, Weidle UH, Ruiter DJ, van Muijen GN.
Melanoma Res. 2002 Feb;12(1):57-69.
[Pub Med]
[Data Download Site]
[Full Text]

Top

Entry 1: Watson et al., 2002.
Molecular characterization of human meningiomas by gene expression profiling using high-density oligonucleotide microarrays.
Watson MA, Gutmann DH, Peterson K, Chicoine MR, Kleinschmidt-DeMasters BK, Brown HG, Perry A.
Am J Pathol. 2002 Aug;161(2):665-72.
[Pub Med]
[Data Download Site]
[Full Text]
[Group]

Top

Entry 1: Rihn et al., 2000.
Differential gene expression in mesothelioma.
Rihn BH, Mohr S, McDowell SA, Binet S, Loubinoux J, Galateau F, Keith G, Leikauf GD.
FEBS Lett. 2000 Sep 1;480(2-3):95-100.
[Pub Med ]
[Data Download Site]
[Full Text]
[Group]

Mesothelioma Web

Top

Entry 2. Hwang et. al., 2003
Genomic dissection for characterization of cancerous oral epithelium tissues using transcription profiling.
Hwang D, Alevizos I, Schmitt WA, Misra J, Ohyama H, Todd R, Mahadevappa M, Warrington JA, Stephanopoulos G, Wong DT, Stephanopoulos G.
Oral Oncol. 2003 Apr;39(3):259-68
[PubMed]
[Data Set Download Site]
[Full text]
[Group]

Top

Entry 1: Welsh et al., 2001.
Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer.
Welsh JB, Zarrinkar PP, Sapinoso LM, Kern SG, Behling CA, Monk BJ, Lockhart DJ, Burger RA, Hampton GM. 2001.
Proc. Natl. Acad. Sci. USA, Vol. 98, Issue 3, 1176-1181
[Pub Med]
[Full Text at PNAS]
[Data Set Download Site]

Entry 2: Smith, 2002.
Transcriptional profiling develops molecular signatures for ovarian tumors.
Smith DI.
Cytometry 2002 Jan 1;47(1):60-2.
[Pubmed]
[Fulltext]
[Data Download Site]
[Group]

Entry 3: Martoglio et. al.,2000.
Changes in tumorigenesis- and angiogenesis-related gene transcript abundance profiles in ovarian cancer detected by tailored high density cDNA arrays.
Martoglio AM, Tom BD, Starkey M, Corps AN, Charnock-Jones DS, Smith SK.
Mol Med. 2000 Sep;6(9):750-65
[Pubmed]
[Fulltext]
[Data Download Site]
[Group]

Entry 4: Tonin et. al.,2001.
Microarray analysis of gene expression mirrors the biology of an ovarian cancer model.
Tonin PN, Hudson TJ, Rodier F, Bossolasco M, Lee PD, Novak J, Manderson EN, Provencher D, Mes-Masson AM.
Oncogene. 2001 Oct 4;20(45):6617-26.
[Pubmed]
[Fulltext]
[Data Download Site]
[Group]

Entry 4. 

Schwartz DR, Kardia SL, Shedden KA, Kuick R, Michailidis G, Taylor JM, Misek DE, Wu R, Zhai Y, Darrah DM, Reed H, Ellenson LH, Giordano TJ, Fearon ER, Hanash SM, Cho KR. Gene expression in ovarian cancer reflects both morphology and biological behavior, distinguishing clear cell from other poor-prognosis ovarian carcinomas. Cancer Res.  2002 Aug 15;62(16):4722-9.

[Pubmed]
[Fulltext]
[Data Download Site]
[Group]

Top

Pancreatic Cancer

Entry 1:

Friess H, Ding J, Kleeff J, Liao Q, Berberat PO, Hammer J, Buchler MW. Identification of disease-specific genes in chronic pancreatitis using DNA array technology. Ann Surg.  2001 Dec;234(6):769-78; discussion 778-9. 

Type: Diagnosis

[Pubmed]
[Fulltext]
[Data Download Site]
[Group]

Entry 1: Singh et al., 2002.
Gene expression correlates of clinical prostate cancer behavior.
Singh D, Febbo PG, Ross K, Jackson DG, Manola J, Ladd C, Tamayo P, Renshaw AA, D'Amico AV, Richie JP, Lander ES, Loda M, Kantoff PW, Golub TR, Sellers WR.
Cancer Cell 2002 Mar;1(2):203-9
[Pub Med]
[Full Text]

[Data Set Download Site]

Entry 2: Lou, 2002.
Gene expression alterations in human prostate cancer.
Luo JH.
Drugs Today (Barc) 2002 Oct;38(10):713-9
[Pub med]
[Full text]
[Data Download Site]
[Group]

Entry 3: Dhanasekaran et al., 2001.
Delineation of prognostic biomarkers in prostate cancer.
Dhanasekaran SM, Barrette TR, Ghosh D, Shah R, Varambally S, Kurachi K, Pienta KJ, Rubin MA, Chinnaiyan AM.
Nature 2001 Aug 23;412(6849):822-6
[Pub Med]
[Full Text]

[Data Set Download Site]

Entry 4: Welsh  et al., 2001.
Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer.
Welsh JB, Sapinoso LM, Su AI, Kern SG, Wang-Rodriguez J, Moskaluk CA, Frierson HF Jr, Hampton GM.
Cancer Res 2001 Aug 15;61(16):5974-8
[Pub Med]
[Full Text]

[Data Set Download Site]

Entry 5: Ernst  et al., 2002.
Decrease and gain of gene expression are equally discriminatory markers for prostate carcinoma, a gene expression analysis on total and microdissected prostate tissue.
Ernst T, Hergenhahn M, Kenzelmann M, Cohen CD, Bonrouhi M, Weninger A, Klaren R, Grone EF, Wiesel M, Gudemann C, Kuster J, Schott W, Staehler G, Kretzler M, Hollstein M, Grone HJ.
Am J Pathol 160,2169-80.
[Pub Med]
[Full Text]

[Data Set Download Site]

Entry 6: Rhodes  et al., 2002.
Meta-analysis of microarrays, interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer.
Rhodes DR, Barrette TR, Rubin MA, Ghosh D, Chinnaiyan AM.
Cancer Res 62,4427-33.
[Pub Med]
[Full Text]

[Data Set Download Site]

Entry 7: 

Huppi K, Chandramouli GV. Molecular profiling of prostate cancer. Curr Urol Rep.  2004 Feb;5(1):45-51. 

Type: Preclinical (Diagnosis)

[Pub Med]
[Full Text]

[Data Set Download Site] 

Entry 8: 

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 Aug 23;412(6849):822-6. 

Type: Preclinical (Prognosis)

[Pub Med]
[Full Text]

[Data Set Download Site]

Entry 9:

Latil A, Bieche I, Chene L, Laurendeau I, Berthon P, Cussenot O, Vidaud M. Gene expression profiling in clinically localized prostate cancer: a four-gene expression model predicts clinical behavior. Clin Cancer Res.  2003 Nov 15;9(15):5477-85. 

[Pub Med]
[Full Text]

[Data Set Download Site]

Reviews

Top

Thyroid Cancer

Entry 1: 

Barden CB, Shister KW, Zhu B, Guiter G, Greenblatt DY, Zeiger MA, Fahey TJ 3rd. Classification of follicular thyroid tumors by molecular signature: results of gene profiling. Clin Cancer Res.  2003 May;9(5):1792-800. 

Top

Data Sets Demonstrating or Validating Correlation of Putative Biomarkers with Survivorship

Beer DG, Kardia SL, Huang CC, Giordano TJ, Levin AM, Misek DE, Lin L, Chen G, Gharib TG, Thomas DG, Lizyness ML, Kuick R, Hayasaka S, Taylor JM, Iannettoni MD, Orringer MB, Hanash S 2002. Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med  2002 Aug;8(8):816-24
[Pubmed]
[Fulltext]
[Dataset Download Site]
[Group]

Hoshida Y, Moriyama M, Otsuka M, Kato N, Goto T, Taniguchi H, Shiratori Y, Seki N, Omata M. Identification of genes associated with sensitivity to 5-fluorouracil and cisplatin in hepatoma cells. J Gastroenterol  2002 Nov;37 Suppl 14:92-5
[Pubmed]
[Fulltext]
[Dataset Download Site]
[Group]

Nutt CL, Mani DR, Betensky RA, Tamayo P, Cairncross JG, Ladd C, Pohl U, Hartmann C, McLaughlin ME, Batchelor TT, Black PM, von Deimling A, Pomeroy SL, Golub TR, Louis DN. Gene expression-based classification of malignant gliomas correlates better with survival than histological classification. Cancer Res  2003 Apr 1;63(7):1602-7
[Pubmed]
[Fulltext]
[Dataset Download Site]
[Group]

Raetz E, Perkins S, Davenport V, Cairo MS. B large-cell lymphoma in children and adolescents. Cancer Treat Rev  2003 Apr;29(2):91-8
[Pubmed]
[Fulltext]
[Dataset Download Site]
[Group]

Ramaswamy S, Ross KN, Lander ES, Golub TR. 2003. A molecular signature of metastasis in  primary solid tumors. Nat Genet  2003 Jan;33(1):49-54
[Pubmed]
[Fulltext]
[Dataset Download Site]
[Group]

Saramaki O, Willi N, Bratt O, Gasser TC, Koivisto P, Nupponen NN, Bubendorf L, Visakorpi T. 2001. Amplification of EIF3S3 gene is associated with advanced stage in prostate cancer.Am J Pathol  2001 Dec;159(6):2089-94
[Pubmed]
[Fulltext]
[Dataset Download Site]
[Group]

Tan Y, Li G, Zhao C, Wang J, Zhao H, Xue Y, Han M, Yang C. Expression of sorcin predicts poor outcome in acute myeloid leukemia. Leuk Res  2003 Feb;27(2):125-31
[Pubmed]
[Fulltext]
[Dataset Download Site]
[Group]

Tolgay Ocal I, Dolled-Filhart M, D'Aquila TG, Camp RL, Rimm DL. Tissue microarray-based studies of patients with lymph node negative breast carcinoma show that met expression is associated with worse outcome but is not correlated with epidermal growth factor family receptors. Cancer  2003 Apr 15;97(8):1841-8.
[Pubmed]
[Fulltext]
[Dataset Download Site]
[Group]

van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, Parrish M, Atsma D, Witteveen A, Glas A, Delahaye L, van der Velde T, Bartelink H, Rodenhuis S, Rutgers ET, Friend SH, Bernards R. 2002. A gene-expression signature as a predictor of survival in breast cancer.  N Engl J Med Dec 19;347(25):1999-2009
[NEJM]
[Fulltext]
[Dataset Download Site]
[Group]

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 prognosis of pediatric AML.Blood  2003 May 8; [epub ahead of print]
[Pubmed]
[Fulltext]
[Dataset Download Site]
[Group]

Top

About this Resource

This list of papers and published microarray data sets is designed to facilitate the re-analysis of published data sets of global expression patterns in cancer in ways that will lead to meaningful clinical translation through repeated study validation.  In the near future, the list of links will be replaced by a database, organized by cancer type, with the following subsections:

Classification (Molecular Subtyping) , Diagnosis , Therapy Response , Survivorship , Recurrence , Reviews.

This list of entries is occasionally updated by curators.  If you would like to curate the entries for a specific cancer type, please email us.  As you can see, we haven't activated all of the links.  If you found any dead links, or if you locate a link we should add, please let us know.  Additional suggestions are also welcome.

This page was last modified on 4/19/2003 by JLW