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Study IDStudy Title Author (Published)DiseaseSubjectsPlatformDescriptionSourceDatatype DownloadScript
CCLECancer Cell-Line Encyclopedia
Cancers1070GPL570 modifiedCancer cell-line encyclopedia clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksCCLEload_all_EtriksCCLE.sh
GSK Cell LinesGlaxo SmithKline Cell Lines

(many)950GPL570Clinical data and gene expression data for cell line catalogeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSKCellLinesload_all_EtriksGSKCellLines.sh


Test Datasets V1.3 contributed by Sanofi for datatypes and serial data

These datasets are used for testing tranSMART releases. Data may be changed for testing purposes.

Study IDStudy Title Author  (Published)DiseaseSubjectsPlatformDescriptionSourceDatatypesDownloadScript
TEST_MANNHEIM_V13Test Mannheim with samplesTest dataDIabetes45-Serial Loading of data and analysis on longitudinal studiesSanoficlinicalSanofiV13Clinicalload_all_SanofiV13Clinical.sh
TESTLARGEV13Test diabetes largeTest dataDiabetes25422-Large number of patients, loaded as multiple input files.Sanofi 

clinical

SanofiV13ClinicalLargeload_all_SanofiV13ClinicalLarge.sh
 V13_MRNAMICROARRAYTest data for mRNA expressionTest dataMuscle tissue17GPL96Muscle tissue for expression data, survival similar for both sexesSanofi

clinical

ref_annotation

expression

SanofiV13Expressionload_all_SanofiV13Expression.sh
V1.3_PROTEOMICSTest mass spec proteomicsTest dataUnknown17PROTEOMICSTest mass spec proteomics dataSanofi

clinical

ref_annotation

msproteomics

SanofiV13Proteomicsload_all_SanofiV13Proteomics.sh
V1.3_QPCRMIRNATest data for miRNA qPCR GSE37425Rheumatoid arthritis8 GPL15467Test miRNA qPCR dataSanofi

clinical

ref_annotation

mirnaqpcr

SanofiV13Mirnaload_all_SanofiV13Mirna.sh
V1.3_MERGED_DATA_TYPESMultiple datatypes for the same subjects, from GSE4382Test dataBreast cancer17 GSE4382PDM
METABOLOMICS_ANNOT
PROTEIN_TO_PROTEIN
Fake survival data. Expression data is from breast tissue yet hald the patients are male. Apparently the same patients as the mass spec proteomics test studySanofi

clinical

ref_annotation

expression

metabolomics

msproteomics

SanofiiV13Mergedload_all_SanofiV13Merged.sh

Test Datasets (older v1.2 set) contributed by Sanofi for datatypes and serial data

These datasets are used for testing tranSMART releases. Data may be changed for testing purposes.

Study IDStudy Title Author  (Published)DiseaseSubjectsPlatformDescriptionSourceDatatypesDownloadScript
TEST_MANNHEIM

Test Mannheim with samples

Test data for serial clinical (low-dimensional) data

Test dataDiabetes30-Serial Loading of data and
Analysis
analysis on longitudinal studiesSanofi 

clinical

SanofiMannheimload_all_SanofiMannheim.sh
TEST_GSE18938

Data derived from GSE18938

Effect of EGF and/or HER2 on the growth of MCF10A cells on extracellular matrix: time course.

Pradeep (2012)Breast Cancer2GPL6244Serial Loading of expression data and analysis on longitudinal studiesSanofi

clinical

ref_annotation

expression

SanofiSerialHighdimload_all_SanofiSerialHighdim.sh
TEST_SERIAL_RICERCATest data for serial expression   GPL570Serial Loading of expression dataSanofi

clinical

ref_annotation

expression

SanofiSerialRicercaload_all_SanofiSerialRicerca.sh
 TEST_GSE37424

miRNA qPCR data derived from GSE37424

miRNAs expression in spinal cords of experimental autoimmune encephalomyelitis (EAE) mice

Shen Autoimmune Diseases  Test all HD Analysis  for qPCR miRNA data type; Sample IDs can be viewed in Grid view; Biomarker search based on miRNA id from miRBaseSanofi

clinical

ref_annotation

mirnaqpcr

SanofiMirnaGSE37424load_all_SanofiMirnaGSE37424.sh
 TEST_GSE37425

miRNA qPCR data derived from GSE37425

miRNAs expression in synovial tissues of rheumatoid arthritis (RA) individuals

ShenRheumatoid Arthritis  Test all HD Analysis  for qPCR miRNA data type; Sample IDs can be viewed in Grid view; Biomarker search based on miRNA id from miRBaseSanofi

clinical

ref_annotation

mirnaqpcr

SanofiMirnaGSE37425load_all_SanofiMirnaGSE37425.sh
 TEST_GSE42468

miRNA qPCR data derived from GSE42468

Differentially expressed miRNAs in MDA-MB-231 over-expressing GATA3 

Chou Breast Cancer  Test all HD Analysis  for qPCR miRNA data type; Sample IDs can be viewed in Grid view; Biomarker search based on miRNA id from miRBaseSanofi

clinical

ref_annotation

mirnaqpcr

SanofiMirnaGSE42468load_all_SanofiMirnaGSE42468.sh
TEST_GSE49520

miRNA qPCR data derived from GSE49520

microRNA Dysregulation in Human Prostate Cancer Cell Model (M12 and P69)

Budd Prostate Cancer  Test all HD Analysis  for qPCR miRNA data type; Sample IDs can be viewed in Grid view; Biomarker search based on miRNA id from miRBaseSanofi

ref_annotation

mirnaqpcr

(no clinical)

SanofiMirnaGSE49520load_all_SanofiMirnaGSE49520.sh
TEST_WITTEN_2010miRNAseq test dataWitten (2010)Test Data31

WITTEN

(test data)

Test all HD Analysis  for sequence based miRNA data type; Sample IDs can be viewed in Grid view; Biomarker search based on miRNA id from miRBaseSanofi

clinical

ref_annotation

mirnaseq

SanofiMirnaseqWittenload_all_SanofiMirnaseqWitten.sh
TEST_GSE48213

RNAseq test data derived from GSE48213

Transcriptional profiling of a breast cancer cell line panel using RNAseq technology

Heiser (2013)Breast Cancer56GPL10999Test all Analysis  for rnaseq data type; Sample IDs can be viewed in Grid view; Biomarker search based on transcript IDs/Gene Symbol from Ensembl and RefseqSanofi

clinical

ref_annotation

rnaseq

SanofiRnaseqGSE48213load_all_SanofiRnaseqGSE48213.sh
TEST_METABOLOMICSMetabolomics test dataTest dataTest Data24

METABOLOMICS_ANNOT

(test data)

Test all Analysis  for metabolomics data type; Sample IDs can be viewed in Grid view; Biomarker search based on  pathway name and super pathway namesSanofi

clinical

ref_annotation

metabolomics

SanofiMetabolomicsload_all_SanofiMetabolomics.sh

TEST_MASS_

SPEC_PROTEOMICS

Mass-spec proteomics test dataTest dataTest Data17

PROTEOMICS

(test data)

Test all Analysis  for Proteomics data type; Sample IDs can be viewed in Grid view; Biomarker search based on Uniprot ID, Uniprot name and Gene SymbolSanofi

clinical

ref_annotation

msproteomics

SanofiProteomicsload_all_SanofiProteomics.sh
TEST_RBM_ADNIRBM proteomics test dataAlzheimers DiseaseTest Data158

DISCOVERY_MAP

(test  data)

Test all Analysis  for RBM data type; Sample IDs can be viewed in Grid view; Biomarker search based on Uniprot ID, Uniprot name, Gene symbol and analyte nameSanofi

clinical

ref_annotation

rbm

SanofiRbmAdniload_all_SanofiRbmAdni.sh

TEST_GSE4382_INC

Test data derived from GSE4382

Repeated observation of breast tumor subtypes in independent gene expression data sets

Breast CancerTest Data143 + 22-

Clinical test data loaded in 4 incremental steps:

  • Initial data load
  • adding new nodes
  • replace data for the new nodes
  • adding new 22 subjects
Sanofi

clinical

clinical

clinical

clinical

SanofiGSE4382Inc

SanofiGSE4382Inc2

SanofiGSE4382Inc3

SanofiGSE4382Inc4

load_all_SanofiGSE4382Inc.sh

Other Test Datasets

These datasets are used for testing tranSMART releases. Data may be changed for testing purposes.

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