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Home > programs > Cancer Program Data Sets Broad Institute Genome Data Analysis Center (GDAC) On behalf of The Cancer Genome Atlas, the Broad Genome Data Analysis Center designs and operates scientific data and analysis pipelines which pump terabyte-scale genomic datasets through scores of quantitative algorithms, in the hope of accelerating the understanding of cancer.   An RNA interference model of RPS19 deficiency in Diamond Blackfan Anemia recapitulates defective hematopoiesis and rescue by dexamethasone: identification of dexamethasone responsive genes by microarray   Manuscript Ebert,%20RPS19%20and%20dex%20in%20DBA,%20Blood%202005.pdf   Commentary in Blood RPS19 paper commentary, Blood 2005.pdf   Gene expression data: CEL files DBA_cel_files.zip   Supplementary Figure S1 Figure S1.pdf   Supplementary Table S1 TableS1.xls   Supplementary Table S2 TableS2.xls   Supplementary Table S3 TableS3.xls   Supplementary Table S4 TableS4.xls   Supplementary Table S5 TableS5.xls   Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9   Normal Progenitor And Leukemic Samples Normals_Leu.gct   MLL-AF9 Immediate Samples MLL_AF9.gct   HSC Signature compared to other normal progenitors.   Metric:SNR; # significant genes 1334 (FDR<=0.02) HSC_FDR002.gct   Leukemic GMP Signature. filtering:max-min=80;max/min=2.5   SNR;592 genes;p-value<=0.01;FDR<=0.023 leuGMP.gct   Self-renewal associated signature.   Filtering: max-min=80;max/min=2.5 Normals_Leu.threshold_FDR01.gct   Metric:SNR;420 significant probesets; p-value<=0.001, FDR <=0.01   Self-renewal associated signature - Down.   Filtering: max-min=80;max/min=2.5 300_HSCLeu_dn_0306.gct   Metric:SNR;302 significant probe sets; p-value<=0.001, FDR<=0.01   Zip of CEL Files nature.zip   Sample Key SampleKey.xls   Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays.   Manuscript Lindblad-Toh.pdf   Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL-1 and glucocorticoid resistance in leukemia   ALL Patient Samples Children_NE.gct   Rapamycin treated CEM-C1 cell line(24 hour). Rap24hour_Control.gct   Rapamycin treated CEM-C1 cell line(3 hour). Rap3hour_control.gct   Resistant/Sensitive Signatures.   Resistant Markers p-value <=0.0005 Res_p0005.gct   Sensitive Markers p-value <=0.0005 Sens_p0005.gct   Resistant Markers p-value <=0.001 Res_p001.gct   Sensitive Markers p-value <=0.001 Sens_p001.gct   Zip of all CEL files armstrong.zip   Lesional gene expression profiling in cutaneous T-cell lymphoma reveals natural clusters associated with disease outcome   Samples' Annotation SampleAnnotation.xls   RMA, un-log2 transformed data ('.res' format) ctl.rma2.res.gz   Raw '.CEL' files (1st 21 chips) RAWDATA01_21.zip   Raw '.CEL' files (2nd 21 chips) RAWDATA22_42.zip   Raw '.CEL' files (last 21 chips) RAWDATA43_63.zip   Expression-based Screening Identifies the Combination of Histone Deacetylase Inhibitors and Retinoids for Neuroblastoma Differentiation   Plain text file describing available supplementary information README.NB   Neuroblastoma microarray data NeuroCellLines_060628_ams.res   CEL files for neuroblastoma data Neuroblastoma_CelFiles_070924.zip   An erythroid differentiation signature predicts response to lenalidomide in Myelodysplastic Syndrome   Datasets files and prediction program (R script) Revlimid_files_and_program.zip   Sample annotation file journal.pmed.0050035.st001.xls   CEL files revlimid_files (1).zip   Sanger Cell Line Project   Sanger Cell Line Project Affymetrix Data Sanger_Cell_Line_Project_Affymetrix_QCed_Data_n798.gct   Sanger Cell Line Project Affymetrix Data Information Sanger_affy_n798_sample_info_published.xls   Instruction to obtain CEL files for Affymetrix Data How_to_obtain_CEL_files_for_SCLP_Affymetrix_data.doc   Sanger Cell Line Project miR Raw Data Sanger_miR_raw.zip   Sanger Cell Line Project miR Normalized Data Sanger_miR_data1.pn.cn.matlab2.res   Sanger Cell Line Project miR Sample Info Sanger800_miRNA.stl   MicroRNA Dynamics in the Stages of Tumorigenesis Correlate with Hallmark Capabilities of Cancer   Supplemental Table 1 OlsonSupTable1.xls   Supplemental Table 2 OlsonSupTable2.xls   Supplemental Table 3 OlsonSupTable3.doc   Supplemental Table 4 OlsonSupTable4.xls   COT drives resistance to RAF inhibition through MAP kinase pathway reactivation   DNA copy-number (segfile) of chromosome 10 in cell lines (CCLE) CCLE_Chrom10_MAP3K8_segfile.seg.txt   DNA copy-number of MAP3K8/COT in cell lines (CCLE) CCLE_MAP3K8_copy-number.txt   mRNA expression level of MAP3K8/COT in cell lines (CCLE) CCLE_MAP3K8_expressionAffy.txt   GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers   INSTALL.txt   LICENSE.txt   GISTIC_2_0_0.tar.gz   Nearest Template Prediction: A Single-Sample-Based Flexible Class Prediction with Confidence Assessment   Example datasets Ex_datasets.zip   Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1.   B-scores data file AchillesData19celllines.txt   B-scores data file description AchillesData19celllines File Description.doc   Integrative Transcriptome Analysis Reveals Common Molecular Subclasses of Human Hepatocellular Carcinoma   HCC subclass meta-analysis signature genes Hoshida_HCC_meta_analysis_3subclass_signature.txt   Identification of AML1-ETO Modulators by Chemical Genomics   Text file describing supplemental information contents README.AE   Supplementary Tables and Figures Corsello_SupplementaryTablesFigures.pdf   Supplementary Methods Corsello_SupplementaryMethods.pdf   Kasumi AML1-ETO Knockdown Data Kasumi_AML1-ETO_complete_200410.res   U937 AML1-ETO Induced Data U937_AMLeto_inducible_ams.res   Kasumi AML1-ETO Knockdown Data CEL Files Kasumi_AML1-ETO_CelFiles_080505.zip   U937 AML1-ETO Induced Data CEL Files U937_AML1-ETO_Induce_CelFiles_080505.zip   High-resolution mapping of copy-number alterations with massively parallel sequencing   Alignment positions of sequence reads (hg18) arachne_qltout_marks.tar.gz   Matlab files with alignable coordinates hg18_alignable_N36_D2.tar.gz   Matlab source code, SegSeq version 1.0.1 SegSeq_1.0.1.tar.gz   microRNA-mediated control of cell fate in megakaryocyte-erythrocyte progenitors   Supplemental Data in pdf Lu_Supplemental_Data_dev_cell.pdf   Table S1 Supplementary_Table1.xls   Table S2 Supplementary_Table2.xls   Table S3 Supplementary_Table3.xls   Table S4, normalized expression data megamiR_data.normalized.log2.th6.gct   Identification of RPS14 as a 5q- syndrome gene by RNA interference screen   Sample information and data matrix (Excel) 5q_shRNA_affy.xls   GCT gene expression dataset 5q_GCT_file.gct   RES gene expression dataset 5q_GCT_file.res   CEL files set 5q_CEL_files.zip   Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma   Manuscript GISTIC_071020.pdf   Supplemental Information GISTIC_Supplement_071020.pdf   Segmented Data segmented_data_080520.seg   Array List File for GISTIC Glioma_array_list_080423.txt   Copy-number Polymorphisms (100K SNP only) 100K_CNVs_080423.txt   Marker Positions 100K_markerpositions.hg16.txt   Sample information (txt format) Sample_info_070424.txt   Array List File for GISTICPreprocessing Gliomas_normals_array_list_080522.txt   GISTIC FAQ GISTIC FAQ_090320.htm   GISTICPreprocessing for 64-bit Linux PREPROCESSING.tar.gz   GISTIC for 64-bit Linux GISTIC_0_9_2.tar.gz   Characterizing the cancer genome in lung adenocarcinoma   Paper text Weir_Nature2007.doc   Figure 1 fig1.pdf   Figure 2 fig2.pdf   Figure 3 fig3.pdf   Full supplementary information Weir_supplement.pdf   Sample information file - TSP samples Newsampleinfo_TSP.xls   Sample information file - non-TSP samples sampleinfo_non-TSP.xls   Viewable file of GISTIC scores for high threshold TSP_highthresh_scores.txt   Viewable file of GISIC scores for low threshold TSP_lowthresh_scores.txt   Subclass Mapping: Identifying Common Subtypes in Independent Disease Data Sets   Breast-A: data set Breast_A.gct   Breast-A: class labels Breast_A.cls   Breast-B: data set Breast_B.gct   Breast-B: class labels Breast_B.cls   Multi-A: data set Multi_A.gct   Multi-A: class labels Multi_A.cls   Multi-B: data set Multi_B.gct   Multi-B: class labels Multi_B.cls   DLBCL-A: data set DLBCL_A.gct   DLBCL-A: class labels DLBCL_A.cls   DLBCL-B: data set DLBCL_B.gct   DLBCL-B: class labels DLBCL_B.cls   DLBCL-C: data set DLBCL_C.gct   DLBCL-C: class labels DLBCL_C.cls   DLBCL-D: dara set DLBCL_D.gct   DLBCL-D: class labels DLBCL_D.cls   HCclustid (generates .cls files from a clustering result) HCclustid.zip   Signature-Based Small Molecule Screening Identifies Cytosine Arabinoside as an EWS/FLI Modulator in Ewing Sarcoma   README README   Manuscript 10.1371_journal.pmed.0040122-L.pdf   Microsoft Excel sheet with supplementary tables Stegmaier_Supplementary_Tables.xls   Data file with compound treated cell lines HTA_Ewings_CmpdTest_060510_ams.res   Untreated control sample CEL files Ewings_Control_CELfiles_060510.zip   ARA-C treated samples CEL files Ewings_ARA-C_CELfiles_060510.zip   Doxorubicin treated samples CEL files Ewings_Dox_CELfiles_060510.zip   Puromycin treated samples CEL files Ewings_Puro_CELfiles_060510.zip   Supplementary Figure 1 Stegmaier_Supplementary_Figure1.pdf   Supplementary Figure 2 Stegmaier_Supplementary_Figure2.pdf   Supplementary Figure 3 Stegmaier_Supplementary_Figure3.pdf   Supplementary Figure 4 Stegmaier_Supplementary_Figure4.pdf   Supplementary Table 1 Stegmaier_Supplement.Table1.pdf   Supplementary Table 2 Stegmaier_Supplement.Table2.pdf   Supplementary Table 3 Stegmaier_Supplement.Table3.pdf   Supplementary Table 4 Stegmaier_Supplement.Table4.pdf   Supplementary Table 5 Stegmaier_Supplement.Table5.pdf   Metagene projection for cross platform, cross species characterization of global transcriptional states   Readme file with instructions about how to run the code readme.txt   Leukemia 1 example: R code and datasets MP_leukemia1_example_R_code_and_datasets.zip   Leukemia 2 example: R code and datasets MP_leukemia2_example_R_code_and_datasets.zip   Lung example: R code and datasets MP_lung_example_R_code_and_datasets.zip   Expression profiling of EWS/FLI identifies NKX2.2 as a critical target gene in Ewing's sarcoma   Manuscript Smith%20et%20al.pdf   Preview article Cancer Cell preview.pdf   CEL file descriptions Smith_et_al_CEL_file_list.xls   CEL files for knockdown samples Smith_etal_knockdown_CEL_files.zip   CEL files for inducible samples Smith_etal_inducible_CEL_files.zip   Supplemental appendix 1 Smith, et al., supplemental appendix 1.doc   Supplemental appendix 2 Smith, et al., supplemental appendix 2.xls   Supplemental appendix 3 Smith, et al., supplemental appendix 3.xls   Identification of distinct molecular phenotypes in acute megakaryoblastic leukemia by gene expression profiling   AMKL dataset, raw CEL files AMKL%20dataset.zip   AMKL dataset, sample information file Sample Information AMKL dataset.xls   consensus clustering of non-DS AMKL Consensus_Clustering_nonDS_AMKL.xls   marker selection by SAM: DS-TMD vs. DS-AMKL Marker_selection_SAM_DS_versus_TMD.xls   marker selection by SAM: DS-AMKL vs. non-DS-AMKL Marker_selection_SAM_DS_vs_NDS.xls   predictor of DS-AMKL vs. non-DS-AMKL PredictiionResults_d.xls   PDF copy of preprint bourquin_pnas_2006.pdf   Allele-specific amplification in cancer revealed by SNP array analysis.   Manuscript LaFramboise.pdf   Gefitinib (Iressa) induces myeloid differentiation of acute myeloid leukemia   Plain text file describing available supplementary information README   Manuscript blank.pdf   Microsoft Excel sheet with supplementary information StegmaierSupplementalData050516.xls   Gefitinib treated HL-60 cell line data Iressa_HL60_MeansScaling.res   Gefitinib treated Kasumi cell line data Iressa_Kasumi_041201_ams.res   Patient 1 (M3-AML) sample data Iressa_Patient1_ams.gct   Patient 2 (M5-AML) sample data Iressa_Patient2_ams.res   Patient 7 (M4-AML) sample data Iressa_Patient7_ams.res   Primary patient AML cells sample data Myeloid_Screen1_newData_021203_ams.AML_poly_mono.gct   Gefitinib treated HL-60 cell line data CEL files Iressa_HL60_CEL_files.zip   Gefitinib treated Kasumi cell line data CEL files Iressa_Kasumi_CEL_files.zip   Patient 1 (M3-AML) sample data CEL files Iressa_Patient1_CEL_files.zip   Patient 2 (M5-AML) sample data CEL files Iressa_Patient2_CEL_files.zip   Patient 7 (M4-AML) sample data CEL files Iressa_Patient7_CEL_files.zip   Primary patient AML cells sample data CEL files Primary_Patient_AML_CEL_files.zip   Manuscript Figure 1 Stegmaier_Fig1_Final.pdf   Manuscript Figure 2 Stegmaier_Fig2_Final.pdf   Manuscript Figure 3 Stegmaier_Fig3_Final.pdf   Manuscript Figure 4 Stegmaier_Fig4_Final.pdf   Manuscript Figure 5 Stegmaier_Fig5_Final.pdf   Manuscript Figure 6 Stegmaier_Fig6_Final.pdf   A zebrafish bmyb mutation causes genome instability and increased cancer susceptibility   MAGE formatted zebra fish crb mutant expression dataset bmyb.zip   Whitehead gct formatted zebra fish crb mutant expression dataset crash_and_burn.gct   Class labels for the zebra fish expression dataset crash_and_burn.cls   Global Cancer Map (GCM) dataset GCM_All.gct   Acute Lymphoblastic Leukemia (Golub et al) ALL_vs_AML_U95_test.res   Adenocarcinoma with p53 mutation status (Beer et al) beer_lung_for_p53.gct   Anaplastic Oligodendroglioma (Nutt et al) glioma_classic_hist.gct   Classic Glioblastoma (Nutt et al) glioma_classic_hist.gct   Glioblastoma Survival (Nutt et al) glioma_nutt_combo.gct   Hepatic Carcinoma (Iizuka et al) hep_japan.gct   Lung Adenocarcinoma Outcome (Beer et al) lung_annarbor_outcome_only.gct   Lung Cancer Outcome (Bhatacharjee et al) lung_datasetB_outcome.gct   Lymph Node Metastatic Gastric Adenocarcinoma (Chen et al) gastric_full_from_smad.paired_14.f1.5_g0.6.pcl   Medulloblastoma (McDonald et al) med_macdonald_from_childrens.gct   Medulloblastoma (Pomeroy et al) medullo_datasetC_outcome.gct   Metastatic Tumors (Ramawamy et al) met.gct   References to published datasets used in this analysis references_and_URLS_of_datasets.html   Bmyb signature -- with expression levels (Table S1 full) bymb_signature_genes.htm   Bmyb signature -- list of unique human genes bmyb_crb_plus_signature_genes.html   Zebra fish p53 mutant and wild type CEL files zebrafish_p53_cel_files.zip   Zebra fish HU, Aph and control CEL files zebrafish_HU_APH_and_control_sphase_cel_files.zip   Zebra fish 8g and MO treatment CEL files zebrafish_8g_and_mo_CEL_files.zip   Zebra fish bmyb crb, mo and control CEL files zebrafish_bmyb_crb_mo_and_control_CEL_files.zip   Zebra fish cyclin WT and mutant CEL files zebrafish_cyclin_wt_and_mutant_CEL_files.zip   README for a description of zebrafish datasets used README_FOR_INFO_ON_ZF_DATASETS.html   NFkB activity, function and target gene signatures in primary mediastinal large B-cell lymphoma and diffuse large B-cell lymphoma subtypes   Manuscript FF_NFKB_manuscr_revised.pdf   Supplementary Information FF_NFKB_suppl_revised.pdf   ASH '04 slides ASH04_friedrich.pdf   Super-repressor expression data (RMA) super.rma.res.gz   Super-repressor expression data (MAS5) super.mas5.res.gz   Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma.   Supplementary Figure S1 Garraway-s1.pdf   Supplementary Figure S2 Garraway-s2.pdf   Supplementary Figure S3 Garraway-s3.pdf   Supplementary Figure S4 Garraway-s4.pdf   Supplementary Figure S5 Garraway-s5.pdf   Supplementary Figure Legends Garraway-s6.doc   Supplementary Methods Garraway-s7.doc   Supplementary Table S1 Garraway-s8.doc   Supplementary Table S2 Garraway-s9.doc   Supplementary Table S3 Garraway-s10.doc   Supplementary Notes Garraway-s11.doc   Manuscript Garraway.pdf   Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis.   Supplemental data Zhao_2005_Suppl.pdf   Manuscript Zhao_2005.pdf   MicroRNA Expression Profiles Classify Human Cancers   Supplementary Table 1, probe information supplementary_table_1.xls   Supplementary Table 2, sample information supplementary_table_2.xls   Supplementary Table 3, N vs T predition result supplementary_table_3.xls   Suppl. Table 4, poorly differentiated tumor prediction result supplementary_table_4.xls   microRNA data, miGCM_218 collection miGCM_218.gct   microRNA data, acute lymphoblastic leukemia ALL.gct   microRNA data, for samples with both miRNA and mRNA data Common_miRNA.gct   microRNA data, mouse lung samples mLung.gct   microRNA data, poorly differentiated tumors PDT_miRNA.gct   microRNA data, HL-60 differentiation HL60.gct   microRNA data, erythroid differentiation Erythroid.gct   mRNA data, for samples with both miRNA and mRNA data Common_Affy.zip   mRNA data, poorly differentiated tumors PDT_Affy.zip   microRNA data, raw data miRNA_raw.zip   Expression data in MAGE-ML format Expression_Data_MAGE_ML.zip   Raw data in MAGE-ML format miRNA_raw_MAGE_ML.zip   Frequently Asked Questions FAQ_miGCM.html   Paper Nature_miR_classify_cancer.pdf   Supplementary Notes Supplementary_Notes.pdf   Molecular profiling of diffuse large B-cell lymphoma reveals a novel disease subtype with brisk host inflammatory response and distinct genetic features   Manuscript DLBCL_manuscript.pdf   Figures DLBCL_manuscript.ppt   References DLBCL_manuscript.enl   Supplementary Information DLBCL_supplement.pdf   Raw data (mean scaled, see supplement) LF_ms_dlbcl_new_womedia.res.gz   Raw data (unscaled) LF_dlbcl_new_womedia.res.gz   Sample annotation sample_annotation.xls   2118 genes (Top 5% by F statistic) genelist.50mean.fstat95.txt   4246 genes (Top 10% by F statistic) genelist.50mean.fstat90.txt   ASH meeting presentation (slides) ASH04.pdf   ASH meeting presentation (handouts) ASH04handouts.pdf   UNIGENE and GenBank annotation of Affymetrix Affy2UnigeneGenBank.xls   UNIGENE and GenBank annotation of Lymphochip Lymphochip2UnigeneGenBank.xls   Lymphochip 2 Affymetrix mapping Lymphochip2Affy.xls   Consensus Clusters' Markers LF_ms_dlbcl_new_womedia_fstat95.DB2.unique.xls   An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis   All datasets in a single zipped file DATASETS.RAR   All figures and tables in a single zipped file figuresandtables.rar   All gene sets in a single zipped file GENESETS.RAR   Supplementary methods and description (ms doc) 4679_3_supp_0_1100271809.doc   Genomic Approaches to Hematologic Malignancies   Manuscript Review%20Genomics%20of%20Heme%20Malig,%20Blood%202004.pdf   Molecular characterization of the tumor microenvironment in breast cancer.   Manuscript Allinen.pdf   A Transcriptional Profiling Study of CAAT/Enhancer Binding Protein Targets Identifies Hepatocyte Nuclear Factor 3beta as a Novel Tumor Suppressor in Lung Cancer   Raw data CAN_6-15-04_Halmos.xls   Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification.   Manuscript Paez_NAR.pdf   An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays.   Manuscript Zhao_2004.pdf   The Six1 Homeoprotein Stimulates Tumorigenesis via Reactivation of Cyclin A1   gene expression data data.res   Erra and Gabpa/b specify PGC-1a-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle   PGC-1-alpha timecourse (scaled expression data) Scaled_Expression_Data.xls   Mouse promoters refGene_mm3_PERI_TSS_1000   Mouse:human masked promoters mm3_1k_1k_70_10_mouse   Gene list for Figure 1 correlogram 5034_Genes_Correlogram_Figure_1.xls   High-resolution single-nucleotide polymorphism array and clustering analysis of loss of heterozygosity in human lung cancer cell lines.   Supplemental Figure 1 Janne_s1.jpg   Supplemental Tables Janne_supp_tables.doc   Manuscript Janne.pdf   Metagenes and molecular pattern discovery using matrix factorization   ALL-AML gene expression data ALL_AML_data.txt   ALL-AML samples ALL_AML_samples.txt   ALL-AML genes ALL_AML_genes.txt   Medulloblastomas gene expression data Medulloblastoma_data.txt   Medulloblastomas samples Medulloblastomas_samples.txt   Medulloblastomas genes Medulloblastoma_genes.txt   Matlab M-file for NMF nmf.m   Matlab M-file for reordering NMF consensus matrices nmforderconsensus.m   supplemental information NMF_final_supplement.pdf   Matlab M-file for NMF (model selection) nmfconsensus.m   Some papers making use of NMF codes (as of 8/07) NMF_code_used_8_07.doc   NMF codes FAQ NMF_codes_FAQ.doc   GeneCluster 2.0: An advanced toolset for bioarray analysis   Manuscript Bioinformatics%20manuscript.pdf   dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data.   Manuscript Lin.pdf   Gene Expression-Based High Throughput Screening (GE-HTS) and Application to Leukemia Differentiation   Text file describing supplemental information contents README   Manuscript ng1305.pdf   Manuscript Figure 1 Fig1_edited.pdf   Manuscript Figure 2 Fig2_edited.pdf   Manuscript Figure 3 Fig3_edited.pdf   Manuscript Figure 4 Fig4_edited.pdf   Manuscript Figure 5 Fig5_edited.pdf   Supplemental Information Document Stegmaier_SupplementaryMethodsFiguresTables.pdf   Supplemental Information Excel Worksheets Stegmaier_SupplementaryData.xls   Initial Myeloid Primary Cell Data Myeloid_primarycells.res   Initial HL-60 Cell Data HL60_undiff_PMA_ATRA.res   Compound Treated HL-60 Cell Data Myeloid_Screen_Compound_Eval.res   Primary Patient APL Cell Data Myeloid_APL_compound_eval.res   Initial Myeloid Primary Cell Data CEL Files Myeloid_primarycells_CELfiles.tar.gz   Initial HL-60 Cell Data CEL Files HL60_undiff_PMA_ATRA_CELfiles.tar.gz   Compound Treated HL-60 Cell Data CEL Files Myeloid_Screen_Compound_Eval_CELfiles.tar.gz   Primary Patient APL Cell Data CEL Files Myeloid_APL_compound_eval_CELfiles.tar.gz   Nature Genetics GE-HTS News and Views GE-HTS_NandV.pdf   Loss of heterozygosity and its correlation with expression profiles in subclasses of invasive breast cancers.   Manuscript Wang.pdf   Microarray Data Mining: Facing the Challenges   Article Microarray_data_mining_facing%20_the_challenges.pdf   Integrated Analysis of Protein Composition, Tissue Diversity, and Gene Regulation in Mouse Mitochondria   Supplemental Table S1 Supplemental%20Table%20S1.xls   Supplemental Table S2 Supplemental Table S2.xls   Supplemental Table S3 Supplemental Table S3.xls   Supplemental Table S4 Supplemental Table S4.xls   The molecular signature of mediastinal large B-cell lymphoma differs from that of other diffuse large B-cell lymphomas and shares features with classical Hodgkin lymphoma   Raw (unormalized) data ('.res' format) gzip compressed Mediastinal.res.gz   Class membership (DLBCL or MLBCL?) Mediastinal.txt   Supplementary Information SupplementaryInfo.pdf   CEL files (A chip) DLBCLwMLBCL.chipA.zip   CEL files (B chip) DLBCLwMLBCL.chipB.zip   Chip-to-sample mapping scan2sample.txt   Genome-wide loss of heterozygosity analysis from laser capture microdissected prostate cancer using single nucleotide polymorphic allele (SNP) arrays and a novel bioinformatics platform dChipSNP.   Manuscript Lieberfarb.pdf   Supplementary Figure 1 Lieberfarb_s1.pdf   Supplementary Table 1 Lieberfarb_s2.pdf   LOH Data LieberfarbSummary LOH data.txt   A Mechanism of Cyclin D1 Action Encoded in the Patterns of Gene Expression in Human Cancer   Supplementary Information 1 (cyclin D1 nearest neighbors) SI1.txt   Supplementary Information 2 (GCM KSS) SI2.txt   Supplementary Information 3 (prostate KSS) SI3.txt   Supplementary Information 4 (lung KSS) SI4.txt   Supplementary Information 5 (brain KSS) SI5.txt   Supplementary Information 6 (NCI60 KSS) SI6.txt   Supplementary Information 7 (chromosome coordinates) SI7.pdf   Supplementary Information 8 (competitor oligonucleotides) SI8.pdf   Supplementary Information 9 (additional panels for Figure 6D) SI9.pdf   Supplementary Information 10 (additional panels for Figure 6E) SI10.pdf   raw gene expression data raw_data.res   PGC-1a Responsive Genes Involved in Oxidative Phosphorylation are Coordinately Downregulated in Human Diabetes   Human diabetes expression data reannotate_select_cal.eis.gz   Phenotype data Phenotype_Data.xls   Probe sets corresponding to gene sets all_pathways.tar.gz   GSEA results for NGT versus DM2 GSEA_results_NGT_vs_DM2.xls   OXPHOS homolog expression in mouse mouse_expression.tar.gz   DNA Microarrays in Cancer: Realising the Promise of Personalised Medicine   Paper Lancet%20Commentary.pdf   Gene expression-based classification of malignant gliomas correlates better with survival than histological classification   Paper Nutt%20et%20al%20-%20revised%20manuscript%20with%20references.doc   Figures Figures 1, 2 and 3.ppt   Supplement Supplementary Information - Cancer Research.doc   Classics Res File Brain_Classics.res   Classics Class File Brain_Classics.cls   NonClassics Res File Brain_NonClassics.res   NonClassics Class File Brain_NonClassics.cls   CEL Files Glioma CEL Files.zip   Cancer Genomics and Molecular Pattern Recognition   Paper (PDF) Humana_final_Ch_06_23_2002%20SR.pdf   Estimating Dataset Size Requirements for Classifying DNA Microarray Data   Draft Manuscript Sample_size_fin.pdf   An Analytical Method For Multi-class Molecular Cancer Classification   Paper (Word document) multiclass.siam_final_March_12_2003.pdf   Consensus Clustering: A resampling-based method for class discovery and visualization of gene expression microarray data   Technical Report consensus4pdflatex.pdf   Leukemia data ALB_ALT_AML.1000genes.res   Leukemia class template ALB_ALT_AML.cls   Novartis multi-tissue data Novartis_BPLC.top1000.gct   Novartis multi-tissue class template Novartis_BPLC.cls   St. Jude Leukemia data leukemia.top1000.gct   St. Jude Leukemia class template leukemia.cls   Lung cancer data LungA_1000genes.gct   Lung cancer class template LungA_local.cls   CNS tumors data brain_morpho.1000genes.res   CNS tumors class template brain_morpho.cls   Normal tissues data cGCM_9_15000_nml_90.top100.res   Normal tissues class template cGCM_9_15000_nml_90.cls   Uniform1 uniform1.gct.gz   Gaussian1 gaussian1.gct.gz   Gaussian3 gaussian3.gct.gz   Gaussian3 class template gaussian3.cls   Gaussian4 gaussian4.gct.gz   Gaussian4 class template gaussian4.cls   Gaussian5.delta2 gaussian5.delta2.gct.gz   Gaussian5.delta3 gaussian5.delta3.gct.gz   Gaussia5 class template gaussian5.cls   Simulated6 artificial_dataset1.gct.gz   Simulated6 class template artificial_dataset1.cls   Evidence for a Molecular Signature of Metastasis in Primary Solid Tumors   Manuscript Metastases_Nature_Genetics_030131_ng1060.pdf   Supplement Mets_Supplement_Revised_Final_110802_SR.pdf   Supplemental Information Mets_Supplement_Information_041110_KR.xls   Dataset A - Global Cancer Map Tumor vs. Met. DatasetA_Tum_vs_Met.res   Dataset B - Lung Outcome DatasetB_Lung_outcome.res   Dataset C - Rosetta Breast Outcome DatasetC_Rosetta_breast_outcome.res   Dataset D - Prostate Outcome DatasetD_prostate_outcome.res   Dataset E - Medulloblastoma Outcome DatasetE_medulloblastoma_outcome.res   Dataset F - LBC Lymphoma Outcome DatasetF_lymphoma_outcome.res   Table of Contents Table_of_Contents.pdf   Identification of endoglin as a functional marker that defines long-term repopulating hematopoietic stem cells   Supplementary information endoglin.doc   A Strategy for Oligonucleotide Microarray Probe Reduction   Description of these files AboutTheseFiles.doc   Paper in pdf format Antipova_et_al_2002.pdf   Raw feature data for all the genes on the chips RawFeatureData.tar.gz   Unscaled Delta(h), random Deltas, and Average Difference UnscaledResFiles.tar.gz   Scaled Delta(h), random Deltas, and Average Difference ScaledResFiles.tar.gz   Cls files, idealized expression vectors for class assignments ClsFiles.tar.gz   Expanded Figure 2 Fig2Features.xls   Expanded Table 1, includes classification parameters Table1Features.xls   List of selected Delta(h) probes ListOfDeltaHprobes.xls   The Ewing's Sarcoma Oncoprotein EWS/FLI Induces a p53-Dependent Growth Arrest in Primary Human Fibroblasts   Manuscript (PDF) CCELL.1_4_393.56.pdf   Appendix 1: Overview of appendices and methods (MS Word) Appendix 1.doc   Appendix 1: Overview of appendices and methods (PDF) Appendix 1.pdf   Appendix 2: Expression data from the tet-EF cell expt (Excel) Appendix_2.xls   Appendix 3: cls file for tet-EF cell knn analysis from fig. 2 Appendix_3.cls   Appendix 4a: cls file for Ewing's sarcoma Appendix_4a.cls   Appendix 4b: cls file for Burkitt's lymphoma Appendix_4b.cls   Appendix 4c: cls file for neuroblastoma Appendix_4c.cls   Appendix 4d: cls file for rhabdomyosarcoma Appendix_4d.cls   Appendix 5: limited tet-EF dataset (Excel) from fig. 2 Appendix_5.xls   Appendix 6: Limited SRCT dataset (Excel) from fig. 2 Appendix_6.xls   Appendix 7a: Ewing's-specific genes (Excel) Appendix_7a.xls   Appendix 7b: Burkitt's-specific genes (Excel) Appendix_7b.xls   Appendix 7c: neuroblastoma-specific genes (Excel) Appendix_7c.xls   Appendix 7d: rhabdomyosarcoma-specific genes (Excel) Appendix_7d.xls   Appendix 8: tet-EF cell upregulated genes (Excel) Appendix_8.xls   Appendix 9: SOM clusters from tet-EF cells (Excel) Appendix_9.xls   CEL files 1/2 (zip file, 15 MB) run1.tar.gz   CEL files 2/2 (zip file, 14 MB) run2.tar.gz   Sample descriptions for CEL files run_samples.txt   DNA Microarrays in Clinical Oncology   Review Article JCO.pdf   Gene Expression Correlates of Clinical Prostate Cancer Behavior   Prostate tumor and normal samples Prostate_TN_final0701_allmeanScale.res   Prostate tumor samples Prostate_T_allmeansquare.res   Prostate capsular penetration samples Prostate_CapPen_061901_allmeanscale.res   Prostate surgical margin samples Prostate_Margin_allmeanscale.res   Prostate outcome samples Prostate_nonrecur_vs_recur_scaled.res   Document describing each of the downloadable files. Readme   Prostate Normal Sample CEL files (N01 - N31) (65M) prostate_normal_N01-N31.CEL.tar.gz   Prostate Normal Sample CEL Files (N32 - N62) (65M) prostate_normal_N32-N62.CEL.tar.gz   Prostate Tumor Sample CEL files (T01 - T30) (66M) prostate_tumor_T01-T30.CEL.tar.gz   Prostate Tumor Sample CEL files (T31 - T62) (66M) prostate_tumor_T31-T62.CEL.tar.gz   Supplementary Information (pdf) SuppInfo_CCv3.pdf   Figure 1, 2 and 3 from paper (pdf) Figure1_2and3.pdf   Table 1 from paper (pdf). Table1v2.pdf   Supplementary Figure 1 (pdf) Supplemental_Figure1.pdf   Supplementary Figures 2 and 3 (pdf) Supplemental_Figure2and3.pdf   Supplementary Figure 4 (pdf) Supplemental_Figure4.pdf   Supplementary Figure 5 (pdf) Supplemental_Figure5.pdf   Supplementary Figure Legends (pdf) SupplementalFigureLegendsRv1.pdf   Gene Expression-Based Classification and Outcome Prediction of Central Nervous System Embryonal Tumors   Manuscript (PDF) Brain_Nature.pdf   Supplementary Information document (MS Word) Pomeroy_et_al_0G04850_11142001_suppl_info.doc   Figures (MS Power Point) Pomeroy_et_al_0G04850_11142001_figures.ppt   Datasets and clinical table (ZIP, 13 Mbytes) Pomeroy_et_al_0G04850_11142001_datasets.zip   Sample list CNS_samples_CEL_files_list.xls   Raw data 1/4 (57 MB) scans_pt1.tar.gz   Raw data 2/4 (57 MB) scans_pt2.tar.gz   Raw data 3/4 (58 MB) scans_pt3.tar.gz   Raw data 4/4 (58 MB) scans_pt4.tar.gz   Dataset C (gene expression) RES file format Dataset_C_MD_outcome.res   Dataset C (class labels) CLS file format Dataset_C_MD_outcome.cls   Dataset C (clinical table) ASCII file format Brain_4_MD_outcome_2.survival.tex   Diffuse Large B-Cell Lymphoma Outcome Prediction by Gene Expression Profiling and Supervised Machine Learning   Supplemental Information (Microsoft Word) Shipp_et_al_Supplementary_Information_v5.doc   Supplemental Information (pdf) Shipp_et_al_Supplementary_Information_v5.pdf   DLBCL vs. FL morphology res file lymphoma_8_lbc_fscc2_rn.res   DLBCL vs. FL morphology cls file lymphoma_8_lbc_fscc2.cls   DLBCL outcome res file lymphoma_8_lbc_outcome_rn.res   DLBCL outcome cls file lymphoma_8_lbc_outcome.cls   Clinical Data Table lymphoma_clinical_011127.xls   Validation Marker Mapping - UniGene Mapping lymphoma_common_unigene.xls   DLBCL CEL files (DLBC1 - DLBC29) (66M) Lymph_LBC_1-29.CEL.tar.gz   DLBCL CEL files (DLBC30 - DLBC58) (66M) Lymph_LBC_30-58.CEL.tar.gz   FSCC CEL files (FSCC1 - FSCC19) (43M) Lymph_FSCC_1-19.CEL.tar.gz   Expanded Figure 5 from paper Lymphoma_Shipp_et_al_Fig5.xls   README describing downloadable files Readme   Paper (PDF) Shipp_et_al_2002.pdf   Multi-Class Cancer Diagnosis Using Tumor Gene Expression Signatures   Manuscript (PDF) GCM.pdf   Supplementary Information (PDF) PNAS_Supplementary_Information.pdf   SAMPLES (XLS) SAMPLES.xls   GCM_Training.res GCM_Training.res   GCM_Training.cls GCM_Training.cls   GCM_Test.res GCM_Test.res   GCM_Test.cls GCM_Test.cls   GCM_PD.res GCM_PD.res   GCM_PD.cls GCM_PD.cls   GCM_Total.res GCM_Total.res   GCM_Total.cls GCM_Total.cls   OVA MARKERS (XLS) OVA_MARKERS.xls   TUMOR NORMAL MARKERS (XLS) TUMOR_NORMAL_MARKERS.xls   MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia   File info MLL_supplemental_file_info.txt   Scan ids, scaling factors and figure key scaling_factors_and_fig_key.txt   Expression data, scaled (Affymetrix expression_data.txt   Expression data as above, with Affymetrix A/P calls expression_data_plus_APcalls.txt   Raw data (CEL files) ALL scans part 1 (40MB) mll_scans_ALL1.tar.gz   Raw data (CEL files) ALL scans part 2 (41MB) mll_scans_ALL2.tar.gz   Raw data (CEL files) MLL scans part 1 (47MB) mll_scans_MLL1.tar.gz   Raw data (CEL files) MLL scans part 2 (47MB) mll_scans_MLL2.tar.gz   Raw data (CEL files) AML scans part 1 (33MB) mll_scans_AML1.tar.gz   Raw data (CEL files) AML scans part 2 (34MB) mll_scans_AML2.tar.gz   Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes   Key to scan names datasetA_scans.txt   Raw data (CEL files) ADENOS part 1 (~53MB) LUNG_scans_ADENO_part1.tar.gz   Raw data (CEL files) ADENOS part 2 (~53MB) LUNG_scans_ADENO_part2.tar.gz   Raw data (CEL files) ADENOS part 3 (~53MB) LUNG_scans_ADENO_part3.tar.gz   Raw data (CEL files) ADENOS part 4 (~54MB) LUNG_scans_ADENO_part4.tar.gz   Raw data (CEL files) ADENOS part 5 (~53MB) LUNG_scans_ADENO_part5.tar.gz   Raw data (CEL files) ADENOS part 6 (~53MB) LUNG_scans_ADENO_part6.tar.gz   Raw data (CEL files) ADENOS part 7 (~54MB) LUNG_scans_ADENO_part7.tar.gz   Raw data (CEL files) ADENOS part 8 (~55MB) LUNG_scans_ADENO_part8.tar.gz   Raw data (CEL files) ADENOS part 9 (~55MB) LUNG_scans_ADENO_part9.tar.gz   Raw data (CEL files) ADENOS part 10 (~53MB) LUNG_scans_ADENO_part10.tar.gz   Raw data (CEL files) Normal Lung (~48MB) LUNG_scans_NORM.tar.gz   Raw data (CEL files) Small Cell (~17MB) LUNG_scans_SMC.tar.gz   Raw data (CEL files) Squamous (~61MB) LUNG_scans_SQ.tar.gz   Raw data (CEL files) Carcinoids (~56MB) LUNG_scans_COID.tar.gz   DatasetA, all genes, rank-inv. scaled, averaged DatasetA_12600gene.txt.gz   All scans, raw AFFY av.diff and A/P vals Lung_DATASETA_scans_noscale.res.gz   Variable genes used to cluster DatasetA DatasetA_3312genesetdescription_sd50.txt   DatasetB, all genes, rank inv. scaled, av'd DatasetB_12600gene_Fig2order.txt.gz   DatasetB, 675 genes DatasetB_675gene.txt.gz   Chemosensitivity Prediction by Transcriptional Profiling   Scaled expression data w/A_P calls NCI60_aug99_resfile.txt   Drug sensitivity GI50 raw GI50_RAW.txt.gz   List of scan names samples_for_nci60paper.txt   Raw CEL files, part 1 (20 scans, ~44MB) nci60_scans_part1.tar.gz   Raw CEL files, part 2 (20 scans, ~44MB) nci60_scans_part2.tar.gz   Raw CEL files, part 3 (20 scans, ~44MB) nci60_scans_part3.tar.gz   Paper (PDF) Staunton_et_al_2001.pdf   Molecular Classification of Multiple Tumor Types   Paper (PDF) Bioinformatics_200107.pdf   Genome-Wide Views of Cancer   Paper (PDF) Golub_2001.pdf   Genomic analysis of metastasis reveals an essential role for RhoC   Paper (PDF) Clark_et_al_2000.pdf   Human A375 Table I (Excel) Human_data_set_A375_table_I.xls   Human A375 Table II (Excel) Human_data_set_A375_table_II.xls   Mouse B16 Table I (Excel) Mouse_data_set_B16_table_I.xls   Human A375 Table I (Textl) Human_data_set_A375_raw1.txt   Human A375 Table II (Text) Human_data_set_A375_raw2.txt   Mouse B16 Table I (Text) Mouse_data_set_B16_raw.txt   c-Myc is a critical target for c/EBPalpha in granulopoiesis.   Paper (PDF) Johansen_et_al_2000.pdf   Class prediction and discovery using gene expression data   Paper (PDF) Slonim_et_al_2000.pdf   Paper (PS) Slonim_et_al_2000.ps   Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling, and adhesion   Supplementary datasets and tables data_set_myc_genes.html   Supplementary figures figures_myc_genes.html   MYC genes dataset: ASCII data_set_myc_genes.txt   MYC genes dataset: Excel data_set_myc_genes.xls   Paper (PDF) Coller_et_all_2000.pdf   GENOMICS: Journey to the Center of Biology   paper (PDF) LanderWeinberg.pdf   Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression   Paper (PDF) Golub_et_al_1999.pdf   Files description Files_descriptions.txt   Experimental protocol protocol.html   Rescaling factors table_ALL_AML_rfactors.txt   Samples table (Word) table_ALL_AML_samples.rtf   Samples table (text) table_ALL_AML_samples.txt   Train dataset (Excel) data_set_ALL_AML_train.tsv   Train dataset (text) data_set_ALL_AML_train.txt   Test datset (Excel) data_set_ALL_AML_independent.tsv   Test dataset (text) data_set_ALL_AML_independent.txt   Prediction results (Word) table_ALL_AML_predic.rtf   Prediction results (text) table_ALL_AML_predic.txt   Original and supplemental figures (Powerpoint) Figures_original_plus_suppl.ppt   Train dataset in WI format ALL_vs_AML_train_set_38_sorted.res   Train dataset class vector in WI format ALL_vs_AML_train_set_38_sorted.cls   Test dataset in WI format Leuk_ALL_AML.test.res   Test dataset class vector in WI format Leuk_ALL_AML.test.cls   Interpreting patterns of gene expression with self-organizing maps   Experimental protocol protocol.html   Dataset description Datasets_description.txt   Dataset data_set_HL60 (text) data_set_HL60.txt   Dataset data_set_HL60 (Excel) data_set_HL60.tsv   Dataset data_set_HL60_U937_NB4_Jurkat (text) data_set_HL60_U937_NB4_Jurkat.txt   Dataset data_set_HL60_U937_NB4_Jurkat (Excel) data_set_HL60_U937_NB4_Jurkat.tsv What is Broad Our Approach Areas of Focus Who is Broad Collaboration Blog News and Publications News & Multimedia Scientific Publications For Journalists For the Scientific Community Science Data Software History & Leadership History Founders Board of Directors Board of Scientific Counselors Leadership Education Diversity Initiatives High School Educational Outreach DNAtrium Glossary Contribute Careers Contact Us Copyright © 2010 Broad Institute. 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