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NIH, National Cancer Institute, Division of Cancer Treatment and Diagnosis (DCTD)
BRB-ArrayTools Data Archive for Human Cancer Gene Expression 

Expression array data and clinical descriptors are stored as BRB-ArrayTools project folders. To analyze a dataset, simply download and unzip the file and open the project worksheet in excel on a Microsoft Windows PC. BRB-ArrayTools must have been installed on the machine.

BRB-ArrayTools is a comprehensive state-of-the-art statistical analysis system for the analysis of microarray gene expression data. It is easily installed as an excel plug-in using its self installer. To download BRB-ArrayTools, go to Click here to download BRB-ArrayTools User's Manual.

To cite your use of BRB-ArrayTools Data Archive, please reference:
Zhao Y and Simon R. BRB ArrayTools Data Archive for Human Cancer Gene Expression: A Unique and Efficient Data Sharing Resource. Cancer Informatics 6:9-15, 2008.

Tumor Type Citation Paper Transformed Zip File Readme File
Bladder Cancer Dyrskjot et al. Nat Genet. (2003) 33:90-96 Identifying distinct classes of bladder carcinoma using microarrays zip4.3 MB
Bladder Cancer Dozmorov et al. (2003) Extracellular matrix-modulation of malignant phenotype in bladder zip0.1 MB
Brain Cancer Pomeroy et al. (2002) Nature 415:436-42 Prediction of central nervous system embryonal tumour outcome based on gene expression zip6.6 MB
Brain Cancer Liang et al. (2005) PNAS 102:5814-9 Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme zip18.1 MB
Brain Cancer Dong et al. (2005) J Neuropathol Exp Neurol. 64:948-55 Histology-based expression profiling yields novel prognostic markers in human glioblastoma zip8.4 MB
Brain Cancer Bredel et al. (2005) Cancer Cancer Res. 65:8679-89;

Bredel et al. (2006) J Clin Oncol. 24:274-87

Functional network analysis reveals extended gliomagenesis pathway maps and three novel MYC-interacting genes in human gliomas

Tumor necrosis factor-alpha-induced protein 3 as a putative regulator of nuclear factor-kappaB-mediated resistance to O6-alkylating agents in human glioblastomas

zip23.2 MB
Brain Cancer Ma et al. (2005) Cancer Res. 65:5523-34 Autocrine platelet-derived growth factor-dependent gene expression in glioblastoma cells is mediated largely by activation of the transcription factor sterol regulatory element binding protein and is associated with altered genotype and patient survival in human brain tumors zip5.2 MB
Brain Cancer Bredel et al. (2006)J Clin Oncol. 24:274-87 Tumor necrosis factor-alpha-induced protein3 as a putative regulator of nuclear factor-kappaB-mediated resistance to O6-alkylating agents in human glioblastomaszip8.5 MB
Brain Cancer Fine et al. (2006) Glioma-derived stem cell factor effect on angiogenesis in the brain zip121.7 MB
Breast Cancer Perou CM et al.(1999) PNAS 96:9212-7 Distinctive gene expression patterns in human mammary epithelial cells and breast cancers zip0.8 MB
Breast Cancer Perou CM et al.(2000) Nature 406:747-52 Molecular portraits of human breast tumours zip14.9 MB
Breast Cancer Sorlie et al.(2001) PNAS 98:10869-74 Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications 18.3 MB
Breast Cancer van't Veer et al.(2002) Nature 415:530-6 Gene expression profiling predicts clinical outcome of breast cancer 21.4 MB
Breast Cancer Sotiriou et al.(2003) PNAS 100:10393-8 Breast cancer classification and prognosis based on gene expression profiles from a population-based study 9.9 MB
Breast Cancer Sorlie et al.(2003) PNAS 100:8418-2398 Repeated observation of breast tumor subtypes in independent gene expression data sets 48.7 MB
Breast Cancer Chang et al. (2003) Lancet 362:362-9 Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer 7.1 MB
Breast Cancer Ma et al. (2004) Cancer Cell 5:607-16 A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen 14.3 MB

14.2 MB

Breast Cancer Troester et al. (2004) Cancer Res. 64:4218-26 Cell-type-specific responses to chemotherapeutics in breast cancer 13.8 MB
Breast Cancer Acevedo et al. (2004) Mol Cell. 13:725-38 Selective recognition of distinct classes of coactivators by a ligand-inducible activation domain 7.2 MB
Breast Cancer Frasor et al. (2004) Cancer Res. 64:1522-33 Selective estrogen receptor modulators: discrimination of agonistic versus antagonistic activities by gene expression profiling in breast cancer cells 5.1 MB
Breast Cancer Yang et al.(2005) Clin Cancer Res 11:6226-32 Gene expression patterns and profile changes pre- and post-erlotinib treatment in patients with metastatic breast cancer 10.0 MB
Breast Cancer Moqqi et al. (2005) J Mol Endocrinol. 34:535-51 Anti-proliferative effect of estrogen in breast cancer cells that re-express ERalpha is mediated by aberrant regulation of cell cycle genes 7.6 MB
Breast Cancer Farmer et al. (2005) Oncogene 24:4660-71 Identification of molecular apocrine breast tumours by microarray analysis 15.2 MB
Cancer Cell Lines Ross et al. (2000) Nat Genet. 24:227-35 Systematic variation in gene expression patterns in human cancer cell lines 4.7 MB
Colon Cancer Alon et al. (1999) PNAS 96:6745-50 Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays 1.4 MB
Colon Cancer Fleet et al. (2003) Physiol Genomics. 13:57-68 Gene expression profiling of Caco-2 BBe cells suggests a role for specific signaling pathways during intestinal differentiation 4.2 MB
Colon Cancer Anderle et al. (2004) Intestinal epithelial cell immune response 10.0 MB
Colon Cancer Bandres et al. (2005) Gene signature for relapse prediction in DukesB colon cancer 4.9 MB
Colon Cancer Dommels et al. (2005) Folic acid deficiency effect on colon cancer cells 2.8 MB
Colon Cancer West et al. (2005) Chem Res Toxicol. 18:1642-53 Alterations in gene expression induced by the lipid peroxidation product, 4-hydroxy-2-nonenal 24.8 MB
Colon Cancer Yang et al. (2005) Transgenic Kruppel-like factor 4 induction: time course 7.8 MB
Colon Cancer Koinuma et al. (2006) Oncogene 25:139-46 pigenetic silencing of AXIN2 in colorectal carcinoma with microsatellite instability 8.2 MB

7.7 MB

Cervical Cancer Wong et al. (2003) Clin Cancer Res. 9:5486-92 Molecular Classification and Prediction of Radiotherapy Response by DNA Microarray 4.8 MB
Embryonal Cancer Skotheim et al. (2005) Cancer Res. 65:5588-98 Differentiation of human embryonal carcinomas in vitro and in vivo reveals expression profiles relevant to normal development 3.5 MB
Endometrial Cancer Wu et al. (2005) Nature 438:981-7 Hypomethylation-linked activation of PAX2 mediates tamoxifen-stimulated endometrial carcinogenesis 4.7 MB
Esophageal Cancer Kimchi et al. (2005) Cancer Res. 65:3146-54 Progression of Barrett's metaplasia to adenocarcinoma is associated with the suppression of the transcriptional programs of epidermal differentiation 10.6 MB
Ewing Family Tumor Staege et al. (2004) Cancer Res. 64:8213-21 DNA microarrays reveal relationship of Ewing family tumors to both endothelial and fetal neural crest-derived cells and define novel targets 7.1 MB
Gastric Cancer Hippo et al.(2002) Cancer Res. 62:233-40 Global gene expression analysis of gastric cancer by oligonucleotide microarrays 3.7 MB
Gastric Cancer Chen et al.(2003) Mol Biol Cell 14:3208-15 Variation in gene expression patterns in human gastric cancers 112.6 MB
Gastric Cancer Subramanian et al.(2004) Oncogene 23:7780-90 Gastrointestinal stromal tumors (GISTs) with KIT and PDGFRA mutations have distinct gene expression profiles 22.3 MB
Head and Neck Cancer Chung et al. (2004) Cancer Cell 5:489-500 Molecular classification of head and neck squamous cell carcinomas using patterns of gene expression 8.6 MB
Head and Neck Cancer Cromer et al. (2004) Oncogene 23:2484-98 Identification of genes associated with tumorigenesis and metastatic potential of hypopharyngeal cancer by microarray analysis 7.3 MB
Head and Neck Cancer O'Donnell et al. (2005) Oncogene 24:1244-51 Gene expression signature predicts lymphatic metastasis in squamous cell carcinoma of the oral cavity 10.4 MB
Leukemia Cheok et al. (2003) Nat Genet. 34:85-90 Treatment-specific changes in gene expression discriminate in vivo drug response in human leukemia cells 22.0 MB
Leukemia Yaqi et al. (2003) Blood 102:1849-56 Identification of a gene expression signature associated with pediatric AML prognosis 9.2 MB
Leukemia Addya et al. (2004) Physiol Genomics. 19:117-30 Erythroid-induced commitment of K562 cells results in clusters of differentially expressed genes enriched for specific transcription regulatory elements 7.2 MB
Leukemia Raetz et al. (2006) Pediatr Blood Cancer 47:130-40 Gene expression profiling reveals intrinsic differences between T-cell acute lymphoblastic leukemia and T-cell lymphoblastic lymphoma 10.8 MB
Leukemia Steqmaier et al. (2004) Nat Genet. 36:257-63 Gene expressionbased high-throughput screening(GE-HTS) and application to leukemia differentiation 3.7 MB
Leukemia Steqmaier et al. (2004) Nat Genet. 36:257-63 Gene expressionbased high-throughput screening(GE-HTS) and application to leukemia differentiation 22.5 MB

3.7 MB

Leukemia Scandura et al. (2004) Proc Natl Acad Sci U S A. 101:15231-6 Transforming growth factor beta-induced cell cycle arrest of human hematopoietic cells requires p57KIP2 up-regulation 7.1 MB
Leukemia Haslinger et al. (2004) J Clin Oncol. 22:3937-49 Microarray gene expression profiling of B-cell chronic lymphocytic leukemia subgroups defined by genomic aberrations and VH mutation status 22.9 MB
Leukemia Neumann et al. (2005) Leukemia 19:458-60 Gene expression profiling of Philadelphia chromosome (Ph)-negative CD34+ hematopoietic stem and progenitor cells of patients with Ph-positive CML in major molecular remission during therapy with imatinib 3.2 MB
Leukemia Gutierrez et al. (2005) Leukemia19:402-9 Gene expression profile reveals deregulation of genes with relevant functions in the different subclasses of acute myeloid leukemia 13.4 MB
Leukemia Crossman et al. (2005) Haematologica 90:459-64 In chronic myeloid leukemia white cells from cytogenetic responders and non-responders to imatinib have very similar gene expression signatures 6.4 MB
Leukemia De Pitta et al. (2005) Haematologica 90:890-8 A leukemia-enriched cDNA microarray platform identifies new transcripts with relevance to the biology of pediatric acute lymphoblastic leukemia 2.9 MB
Leukemia Dik et al. (2005) Leukemia 19:1948-57 CALM-AF10+ T-ALL expression profiles are characterized by overexpression of HOXA and BMI1 oncogenes 11.7 MB
Leukemia Falt et al. (2005) Exp Hematol. 33:883-93 Identification of progression markers in B-CLL by gene expression profiling 5.3 MB
Liver Cancer Ye et al. (2003) Nat Med. 9:416-423 Predicting hepatitis B viruspositive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning 4.5 MB
Lung Cancer Bhattacharjee et al. (2001) PNAS 98:13790-5 Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses 24.8 MB
Lung Cancer Beer et al. (2002) Nat Med 8:816-24 Gene-expression profiles predict survival of patients with lung adenocarcinoma 8.2 MB
Lung Cancer Garber et al. (2001) PNAS 98:13784-9 Diversity of gene expression in adenocarcinoma of the lung 32.1 MB
Lung Cancer Gordon et al. (2002) Cancer Research 62:4963-7 Translation of microarray data into clinically relevant cancer diagnostic tests using gene expression ratios in lung cancer and mesothelioma 23.1 MB
Lung Cancer Michael et al. (2004) Two prognostically significant subtypes of high-grade lung neuroendocrine tumors independent of small-cell and large-cell neuroendocrine carcinomas identified by gene expression profiles 26.4 MB
Lung Cancer Magda et al. (2005) Lung cancer cell line response to motexafin gadolinium 8.0 MB
Lung Cancer Washi et al. (2005) Squamous Lung Cancer, Paired Samples 6.7 MB
Lung Cancer Gemma et al. (2006) Anticancer drug clustering in lung cancer based on gene expression profiles and sensitivity database 11.8 MB
Lymphoma Rosenwald et al. (2002) NEJM 346:1937-47 The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma 33.3 MB
Lymphoma Shipp et al. (2002) Nat Med 8:68-74 Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning 8.3 MB
Lymphoma Rosenwald et al. (2003) Cancer Cell 3:185-97 The proliferation gene expression signature is a quantitative integrator of oncogenic events that predicts survival in mantle cell lymphoma 12.2 MB
Lymphoma Dave et al. (2004) NEJM 351:2159-69 Prediction of survival in follicular lymphoma based on molecular features of tumor-infiltrating immune cells 103.5 MB
Lymphoma Fan et al. (2005) Gene Expression Profile of Primary Effusion Lymphoma 9.4 MB
Medulloblastoma MacDonald et al. (2001) 29:143-52 Expression profiling of medulloblastoma: PDGFRA and the RAS/MAPK pathway as therapeutic targets for metastatic disease 1.0 MB
Melanoma Bittner et al. (2000) Nature 406:536-40 Molecular classification of cutaneous malignant melanoma by gene expression profiling 2.3 MB
Melanoma Smith et al. (2005) Cancer Biol Ther. 4:1018-29 Whole-genome expression profiling of the melanoma progression pathway reveals marked molecular differences between nevi/melanoma in situ and advanced-stage melanomas 19.1 MB
Melanoma Talantov et al. (2005) Clin Cancer Res. 11:7234-42 Novel genes associated with malignant melanoma but not benign melanocytic lesions 22.8 MB
Melanoma Winnepenninckx et al. (2006) J Natl Cancer Inst. 98(7):472-82. Gene expression profiling of primary cutaneous melanoma and clinical outcome 42.9 MB
10.1 MB
Mesothelioma Gordon et al. (2005) Malignant pleural mesothelioma 15.7 MB
Myeloma Tian et al. (2003) N Engl J Med. 349:2483-94 The role of the Wnt-signaling antagonist DKK1 in the development of osteolytic lesions in multiple myeloma 30.6 MB
Myeloma Mattioli et al. (2005) Oncogene 24:2461-2473 Gene expression profiling of plasma cell dyscrasias reveals molecular patterns associated with distinct IGH translocations in multiple myeloma 15.3 MB
Osteosarcoma Stossi et al. (2004) Endocrinology 145:3473-86 Transcriptional profiling of estrogen-regulated gene expression via estrogen receptor (ER) alpha or ERbeta in human osteosarcoma cells: distinct and common target genes for these receptors 5.9 MB
Osteosarcoma Monroe et al. (2005) Mol Endocrinol. 19:1555-68 Estrogen receptor alpha and beta heterodimers exert unique effects on estrogen- and tamoxifen-dependent gene expression in human U2OS osteosarcoma cells 7.2 MB
Ovarian Cancer Peters et al. (2004) Carboplatin Sensitivity in Ovarian Carcinoma 6.1 MB
Pancreatic Cancer Mano et al. (2005) Expression profile of pancreatic ductal cells 26.8 MB

13.8 MB

Prostate Cancer Dhanasekaran et al.(2001) Nature 412:822-6 Delineation of prognostic biomarkers in prostate cancer 5.3 MB
Prostate Cancer Singh et al. (2002) Cancer Cell 1:203-9 Gene expression correlates of clinical prostate cancer behavior 10.0 MB
Prostate Cancer Buchsbaum et al. (2003) Prostate adenocarcinoma and ionizing radiation 3.8 MB
Prostate Cancer Lapointe et al. (2004) PNAS 101:811-6 Gene expression profiling identifies clinically rele vant subtypes of prostate cancer 86.9 MB
Prostate Cancer Chen et al. (2004) Nat Med. 10:33-9 Molecular determinants of resistance to antiandrogen therapy 4.6 MB

9.5 MB

Prostate Cancer Best et al. (2005) Clin Cancer Res. 11:6823-34 Molecular alterations in primary prostate cancer after androgen ablation therapy 9.7 MB
Prostate Cancer Varambally et al. (2005) Cancer Cell. 8:393-406 Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression 24.5 MB
Prostate Cancer Nanni et al. (2006) Mol Cancer Res. 4:79-92 Epithelial-restricted gene profile of primary cultures from human prostate tumors: a molecular approach to predict clinical behavior of prostate cancer 11.3 MB
Pediatric sarcoma Baer et al. (2005) Pediatric sarcoma: rhabdomyosarcoma & Ewing's sarcoma 5.8 MB
Renal Cancer Vasselli et al. (2003) PNAS 100:6958-63 Predicting survival in patients with metastatic kidney cancer by gene-expression profiling in the primary tumor 9.7 MB
Renal Cancer Boer et al. (2001) Genome Research 11:1861-1870 Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31,500-element cDNA array 61.7 MB

61.7 MB

Renal Cancer Lenburg et al. (2003) BMC Cancer3:31 Previously unidentified changes in renal cell carcinoma gene expression identified by parametric analysis of microarray data 8.9 MB

8.8 MB

Renal Cancer Boni et al. (2005) Clin Pharm Ther. 77:76-89 Population pharmacokinetics of CCI-779: Correlations to safety and pharmacogenomic responses in patients with advanced renal cancer 17.9 MB
Renal Cancer Tsui et al. (2005) Clear cell sarcoma of the kidney 14.9 MB
Renal Cancer Yang et al. (2005) Cancer Res. 65:5628-37 A molecular classification of papillary renal cell carcinoma 27.9 MB
Soft Tissue Sarcoma West et al. (2005) PLoS Biol 3:e187 Determination of stromal signatures in breast carcinoma 47.2 MB
Soft Tissue Sarcoma Yoon et al. (2005) Gene expression of human soft tissue sarcoma 18.3 MB
Thyroid Cancer Reyes et al. (2005) Papillary thyroid cancer versus paired normal thyroid tissue 20.7 MB
Uterine Leiomyoma Hoffman et al. (2003) Uterine Fibroid and Normal Myometrial Expression Profiles 6.7 MB
Uterine Leiomyoma Quade et al. (2003) Comparison of Gene Expression in Uterine Smooth Muscle Tumors zip file3.1 MB

Updated on Sept. 26, 2014