Example datasets | Ex_datasets.zip |
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 |
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 |
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 |
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 |
Manuscript | Bioinformatics manuscript.pdf |
Draft Manuscript | Sample_size_fin.pdf |
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 |
Paper (Word document) | multiclass.siam_final_March_12_2003.pdf |
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 |
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 |
Paper (PDF) | Bioinformatics_200107.pdf |
Experimental protocol (.html) | protocol.html |
Dataset description | Datasets_description.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 |
Dataset data_set_HL60_U937_NB4_Jurkat (Excel) | data_set_HL60_U937_NB4_Jurkat.tsv |
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 |
Paper | Nutt et al - revised manuscript with references.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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
Manuscript | Ebert, RPS19 and dex in DBA, Blood 2005.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 |
Supplementary information | endoglin.doc |
HCC subclass meta-analysis signature genes | Hoshida_HCC_meta_analysis_3subclass_signature.txt |
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 |
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 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 |
Normal Progenitor And Leukemic Samples | Normals_Leu.gct |
MLL-AF9 Immediate Samples | MLL_AF9.gct |
Metric:SNR; # significant genes 1334 (FDR<=0.02) | HSC_FDR002.gct |
SNR;592 genes;p-value<=0.01;FDR<=0.023 | leuGMP.gct |
Filtering: max-min=80;max/min=2.5 | Normals_Leu.threshold_FDR01.gct |
Filtering: max-min=80;max/min=2.5 | 300_HSCLeu_dn_0306.gct |
Zip of CEL Files | nature.zip |
Sample Key | SampleKey.xls |
AMKL dataset, raw CEL files | AMKL dataset.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 |
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 |
Paper (PDF) | Slonim_et_al_2000.pdf |
Paper (PS) | Slonim_et_al_2000.ps |
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 |
Raw data | CAN_6-15-04_Halmos.xls |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
Supplemental Table S1 | Supplemental Table S1.xls |
Supplemental Table S2 | Supplemental Table S2.xls |
Supplemental Table S3 | Supplemental Table S3.xls |
Supplemental Table S4 | Supplemental Table S4.xls |
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 |
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 |
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 |
B-scores data file | AchillesData19celllines.txt |
B-scores data file description | AchillesData19celllines File Description.doc |
Manuscript | Review Genomics of Heme Malig, Blood 2004.pdf |
Article | Microarray_data_mining_facing _the_challenges.pdf |
Paper | Lancet Commentary.pdf |
Paper (PDF) | Humana_final_Ch_06_23_2002 SR.pdf |
Review Article | JCO.pdf |
Paper (PDF) | Golub_2001.pdf |
paper (PDF) | LanderWeinberg.pdf |
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 |
Manuscript | LaFramboise.pdf |
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 |
Supplemental data | Zhao_2005_Suppl.pdf |
Manuscript | Zhao_2005.pdf |
Manuscript | Allinen.pdf |
Manuscript | Paez_NAR.pdf |
Manuscript | Zhao_2004.pdf |
Supplemental Figure 1 | Janne_s1.jpg |
Supplemental Tables | Janne_supp_tables.doc |
Manuscript | Janne.pdf |
Manuscript | Lin.pdf |
Manuscript | Wang.pdf |
Manuscript | Lieberfarb.pdf |
Supplementary Figure 1 | Lieberfarb_s1.pdf |
Supplementary Table 1 | Lieberfarb_s2.pdf |
LOH Data | LieberfarbSummary LOH data.txt |
Manuscript | Lindblad-Toh.pdf |
Manuscript | Smith et al.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 |
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 |
gene expression data | data.res |
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 |
Paper (PDF) | Johansen_et_al_2000.pdf |
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 |
Supplemental Table 1 | OlsonSupTable1.xls |
Supplemental Table 2 | OlsonSupTable2.xls |
Supplemental Table 3 | OlsonSupTable3.doc |
Supplemental Table 4 | OlsonSupTable4.xls |
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 |
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 |