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Study IDStudy Title Author (Published)DiseaseSubjectsPlatformDescriptionSourceDatatype Download LabelScript 
GSE10024Key Regulatory Molecules of Cartilage Destruction in Rheumatoid Arthritis: An in vitro StudyAndreas (2008)
Rheumatoid Arthritis6GPL96GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE10024 load_all_EtriksGSE10024.sh
GSE10220Gene expression profiling of human monocytes and monocyte-derived-macrophagesCambien (2008)Macrophage expression96GPL1946GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE10220load_all_EtriksGSE10220.sh
GSE10500Gene expression in rheumatoid arthritis synovial macrophagesYarilina (2008)
Rheumatoid Arthritis8GPL8300GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE10500load_all_EtriksGSE10500.sh
GSE10616Human colon expression in healthy controls, colon-only CD, ileo-colonic CD, and UCDenson (2008)Inflammatory Bowel Disease58GPL5760GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE10616load_all_EtriksGSE10616.sh
GSE10714Expression data from human colonic biopsy sampleSolymosi (2008)Inflammatory Bowel Disease33GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE10714load_all_EtriksGSE10714.sh
GSE11575Mutual Antagonistic Relationship Between Prostaglandin E2 and Interferon-(gamma): Implications for Rheumatoid ArthritisMathieu (2008)Rheumatoid Arthritis12GPL4372GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE11575load_all_EtriksGSE11575.sh
GSE11827Identification of markers of responsiveness in rheumatoid arthritis patientBansard (2011)Rheumatoid Arthritis49GPL5215GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE11827load_all_EtriksGSE11827.sh
GSE11886Gene expression analysis of macrophages from ankylosing spondylitis patients reveals interferon-gamma dysregulationBarnes (2008)Macrophage expression33GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE11886load_all_EtriksGSE11886.sh
GSE11903Effective treatment of psoriasis with etanercept is linked to suppression of IL17 signaling, not immediate response TNFSuarez-Farinas (2009)
Psoriasis89GPL571GEO Public Studies with clinical and gene expression dataThomson Reutersclinical

ref_annotation

expression

RanchoGSE11903load_all_RanchoGSE11903.sh
GSE11909A modular analysis framework for the discovery of biomarkers of Systemic Lupus ErythematosusChaussabel (2008)Systemic Lupus Erythematosus (SLE)175

GPL96

GPL97

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE11909load_all_EtriksGSE11909.sh
GSE11947Integrated Network and Microarray Analysis to Identify New Biomarkers in Ischemic Heart DiseaseDevaux (2008)Acute Myocardial Infarction (AMI)32GPL1947

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE11947load_all_EtriksGSE11947.sh
GSE12051Microarray predictor of response to infliximab in rheumatoid arthritis (RA) patientsJulia (2009)Rheumatoid Arthritis44GPL2507GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE12051load_all_EtriksGSE12051.sh
GSE12196Rat exposure to RDXDillman (2008)Epilepsy48GPL1355

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE12196load_all_EtriksGSE12196.sh
GSE12374Interactions of cytokines in peripheral blood cells from Systemic Lupus ErythematosusNishimoto (2008)Systemic Lupus Erythematosus (SLE)17GPL1291

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE12374load_all_EtriksGSE12374.sh
GSE12653Gene Expression Analysis in Peripheral Blood of Patients with Rheumatoid ArthritisNishimoto (2008)Rheumatoid Arthritis72GPL7220GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE12653load_all_EtriksGSE12653.sh
GSE13026Early and long-standing rheumatoid arthritis: molecular signatures identified by gene expression profiling in synoviumLequerre (2009)Rheumatoid Arthritis45GPL5215GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE13026load_all_EtriksGSE13026.sh
GSE13168Effects of glucocorticoids and Protein Kinase A on growth factor- and 1beta- regulated geneMisior (2009)Asthma54GPL96

GEO Public Studies with clinical and gene expression data

Asthma dataset which has fairly complex structure.

Used to test ETL procedures and time series workflow

Rancho

clinical

ref_annotation

expression

RanchoGSE13168load_all_RanchoGSE13168.sh
GSE13355Gene expression data of skin from psoriatic patients and normal controlsAbecasis (2008)Psoriasis180GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE13355load_all_EtriksGSE13355.sh
GSE13428Gene Expression Profiling of Rat Hippocampus Following Exposure to the Acetylcholinesterase Inhibitor SomanDillman (2008)Epilepsy38GPL1355

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE13428load_all_EtriksGSE13428.sh
GSE13732CIS (multiple sclerosis) (case-control) (time-series)Baranzini (2008)Multiple Sclerosis113GPL570GEO Public Studies with clinical and gene expression data  Rancho

clinical

ref_annotation

expression

 
RanchoGSE13732load_all_RanchoGSE13732.sh
GSE13887Activation of mTOR controls the loss of TCRζ in lupus T cells through HRES-1/Rab4-regulated lysosomal degradationMiddleton (2008)Systemic Lupus Erythematosus (SLE)27GPL570

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE13887load_all_EtriksGSE13887.sh
GSE1432Transcriptional Response of Human Microglial Cells to Interferon-gammaRock (2004)Macrophage expression24GPL96GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE1432load_all_EtriksGSE1432.sh
GSE14468Gene expression profiling of CEBPA double and single mutant and CEBPA wild type AMLVerhaak (2009)Acute Myeloid Leukemia526

GPL570

GEO Public Studies with clinical and gene expression data Elevadaclinical

ref_annotation

expression

ElevadaGSE14468  load_all_ElevadaGSE14668.sh
GSE1456Gene expression of breast cancer tissue in a large population-based cohort of Swedish patientsPawitan (2005)Breast Cancer159

GPL96

GPL97

GEO Public Studies with clinical and gene expression data  Ranchoclinical

ref_annotation

expression

RanchoGSE1456 load_all_RanchoGSE1456.sh
GSE14763Whole transcriptome analysis of the hippocampus: toward a molecular portrait of epileptogenesisOkamoto (2009)Epilepsy18GPL2896

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE14763load_all_EtriksGSE14763.sh
GSE14769Time course of bone marrow-derived macrophages simulated with LPSMarzoff (2009)Macrophage expression24GPL1261GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE14769load_all_EtriksGSE14769.sh
GSE14905Type I Interferon: Potential Therapeutic Target for Psoriasis?Higgs (2009)Psoriasis82GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE14905load_all_EtriksGSE14905.sh
GSE15245Prediction of acute multiple sclerosis relapses by transcription levels of peripheral blood cells Gurevich (2009)Multiple Sclerosis94

GPL96

GPL571

GEO Public Studies with clinical and gene expression data eTRIKS (University of Luxembourg)clinical

ref_annotation

expression

RanchoGSE15245

EtriksGSE15245

 

load_all_RanchoGSE15245.sh

load_all_EtriksGSE15245.sh

GSE15258Whole blood transcript profiling of rheumatoid arthritis patients Bienkowska Rheumatoid Arthritis86GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)clinical

ref_annotation

expression

RanchoGSE15258

EtriksGSE15258

 

load_all_RanchoGSE15258.sh

load_all_EtriksGSE15258.sh

GSE15316Differential expression of rituximab responders vs. non responders on 3 different blood cell typesJulia (2009)Rheumatoid Arthritis23GPL2507GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE15316load_all_EtriksGSE15316.sh
GSE15573Immunity and Defense Genes in Peripheral Blood Mononuclear Cells of Rheumatoid Arthritis patientsTeixeira (2009)Rheumatoid Arthritis33GPL6102GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE15573load_all_EtriksGSE15573.sh
GSE15602Differential gene expression in RA synovial biopsies from responders versus non-responders to adalimumab therapyBadot (2009)Rheumatoid Arthritis11GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE15602load_all_EtriksGSE15602.sh
GSE15615Differential effects of TNFalpha and IL1beta on FLS global gene expression profileBadot (2009)Rheumatoid Arthritis6GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE15615load_all_EtriksGSE15615.sh
GSE15907Immunological Genome Project data Phase 1Gopalan (2009)Macrophage expression653GPL6246GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE15907load_all_EtriksGSE15907.sh
GSE16385Expression data from human macrophagesSzanto (2009)Macrophage expression38GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE16385load_all_EtriksGSE16385.sh
GSE1643Normal Variance of Gene Expression in the Human LungColdren (2004)Epilepsy40GPL570

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE1643load_all_EtriksGSE1643.sh
GSE16879Mucosal expression profiling in patients with inflammatory bowel disease before and after first infliximab treatmentArijs (2009)Inflammatory Bowel Disease73GPL570GEO Public Studies with clinical and gene expression data eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

RanchoGSE16879

EtriksGSE16879

 

load_all_RanchoGSE16879.sh

load_all_EtriksGSE16879.sh

GSE16969Gene expression analysis of TSC-tubers reveals increased expression of adhesion and inflammatory factorsWittink (2009)Epilepsy10GPL570

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE16969load_all_EtriksGSE16969.sh
GSE17755Human peripheral blood cells: autoimmune diseases vs. healthy individuals Nishimoto (2011)Autoimmune Diseases244GPL1291GEO Public Studies with clinical and gene expression data  Rancho

clinical

ref_annotation

expression

RanchoGSE17755 load_all_RanchoGSE17755.sh
GSE17761The type of phagocytic receptor modulates gene expression and phagosome functions in macrophagesHoffman (2009)Macrophage expression29GPL9079GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE17761load_all_EtriksGSE17761.sh
GSE18275Macrophages heterogeneity in human atherosclerotic plaquesMaouche (2009)Macrophage expression18GPL1946GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE18275load_all_EtriksGSE18275.sh
GSE19821Rheumatoid arthritis and anti-TNF treatmentvan Baarsen (2010)Rheumatoid Arthritis30

GPL9869

GPL9870

GPL9871

GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE19821load_all_EtriksGSE19821.sh
GSE19236Expression analysis of dendritic cells, macrophages and monocytesKlug (2009)Macrophage expression48

GPL6480

GPL6848

GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE19236load_all_EtriksGSE19236.sh
GSE19976Gene expression analysis of lung biopsies from patients with two different forms of pulmonary sarcoidosis Ho (2010)Lung Cancer15GPL6244GEO Public Studies with clinical and gene expression data Sanofi

clinical

ref_annotation

expression

SanofiGSE19976load_all_SanofiGSE19976.sh
GSE20141Expression analysis of laser-dissected SNpc neurons in Parkinson's diseaseZheng (2010)Parkinsons Disease18GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE20141load_all_EtriksGSE20141.sh
GSE20146Expression analysis of dissected GPi in Parkinson's diseaseMiddleton (2010)Parkinsons Disease20GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE20146load_all_EtriksGSE20146.sh
GSE20153Expression analysis of lymphoblast cells lines in Parkinson's diseaseZheng (2010)Parkinsons Disease16GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE20153load_all_EtriksGSE20153.sh
GSE20163Systematic meta-analysis and replication of genome-wide expression studies of Parkinson's disease: 2Zheng (2010)Parkinsons Disease12GPL96GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE20163load_all_EtriksGSE20163.sh
GSE20164Systematic meta-analysis and replication of genome-wide expression studies of Parkinson's disease: 3Zheng (2010)Parkinsons Disease11GPL96GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE20164load_all_EtriksGSE20164.sh
GSE20168Transcriptional analysis of prefrontal area 9 in Parkinson's diseaseZhang (2005)Parkinsons Disease29GPL96GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE20168load_all_EtriksGSE20168.sh
GSE20194MAQC-II Project: human breast cancer (BR) data set Popovici (2010)Breast Cancer278GPL96GEO Public Studies with clinical and gene expression data Rancho

clinical

ref_annotation

expression

RanchoGSE20194 load_all_EtriksGSE20194.sh
GSE20291Transcriptional analysis of putamen in Parkinson's diseaseZhang (2005)Parkinsons Disease35GPL96GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE20291load_all_EtriksGSE20291.sh
GSE20292Transcriptional analysis of whole substantia nigra in Parkinson's diseaseZhang (2005)Parkinsons Disease29GPL96GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE20292load_all_EtriksGSE20292.sh
GSE20295Transcriptional analysis of multiple brain regions in Parkinson's diseaseZhang (2005)Parkinsons Disease93GPL96GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE20295load_all_EtriksGSE20295.sh
GSE20314Systematic meta-analysis and replication of genome-wide expression studies of Parkinson’s disease: 4Zheng (2010)Parkinsons Disease8GPL96GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE20314

load_all_EtriksGSE20314.sh
GSE20333Gene expression profiling of parkinsonian substantia nigraEdnaParkinsons Disease12GPL201GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE20333

load_all_EtriksGSE20333.sh
GSE20690Efficacy of anti-TNF biologic agent, infliximab, for RA patients using transcriptome analysis of white blood cells Takeuchi (2009)Rheumatoid Arthritis68GPL4133GEO Public Studies with clinical and gene expression data

Thomson Reuters

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

RanchoGSE20690

EtriksGSE20690

 

load_all_RanchoGSE20690.sh

load_all_EtriksGSE20690.sh
GSE20864Human peripheral blood cells: systemic lupus erythematosus vs healthy individual.Nishimoto (2010)Systemic Lupus Erythematosus (SLE)66GPL1291

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE20864load_all_EtriksGSE20864.sh
GSE20881Colon biopsies from Crohns patients and healthy controlsAbbas (2010)Inflammatory Bowel Disease172GPL1708GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE20881load_all_EtriksGSE20881.sh
GSE2125isolated alveolar macrophagesWoodruff (2005)Asthma45GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE2125

load_all_EtriksGSE2125.sh
GSE21537The relationship between the gene expression profile in the synovium of RA patients at baseline and the clinical response to infliximab treatmentLindberg (2010)Rheumatoid Arthritis62GPL7768GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE21537

load_all_EtriksGSE21537.sh
GSE21548Gene Expression Profiles of RAW264.7 Macrophages Stimulated with Two Commonly Used Preparations of LPSYang (2010)Macrophage expression46GPL891GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE21548load_all_EtriksGSE21548.sh
GSE21959Transcriptional response to hypoxia of normal and rheumatoid arthritis synovial fibroblastsDel Rey (2010)Rheumatoid Arthritis36GPL4133GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE21959

load_all_EtriksGSE21959.sh
GSE22138Expression Data from Uveal Melanoma primary tumorsLaurent (2010)Melanoma Uveal63GPL570GEO Public Studies with clinical and gene expression dataPfizer

clinical

ref_annotation

expression

PfizerGSE22138load_all_PfizerGSE22138.sh
GSE22324Mapping of disease-associated expression polymorphisms in primary peripheral blood CD4+ lymphocytesRaby (2010)Asthma200GPL6104GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE22324load_all_EtriksGSE22324.sh
GSE23076Gene Expression Profiles in a Rabbit Model of Systemic Lupus ErythematosusLempicki (2010)Systemic Lupus Erythematosus (SLE)66GPL8300

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE23076load_all_EtriksGS23076E.sh
GSE23611Lung biopsies from asthmatics pre- and post- steroid treatment and from healthy controlChoy (2011)Asthma62GPL6480GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE23611load_all_EtriksGSE23611.sh
GSE23622Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response GenesBenner (2010)Macrophage expression55

GPL6100

GPL7202

GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE23622load_all_EtriksGSE23622.sh
GSE23676Expression data from advanced Parkinson's disease (PD) patients leukocytes - prior to and following deep brain stimulation (DBS) treatment in on and off stimulation conditions, and matched healthy control (HC) subjectsSoreq (2012)Parkinsons Disease27GPL5188

GEO Public Studies with clinical and expression data.

Very large platform with 40 million probes. ETL can stall on smaller systems.

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE23676load_all_EtriksGSE23676.sh
GSE24060Peripheral Blood Cells Gene Expression Profiles from Discordant Monozygotic Twins with Systemic Autoimmune disease (SAIDs) O'Hanlon (2011)Autoimmune Diseases80GPL7264GEO Public Studies with clinical and gene expression dataRancho

clinical

ref_annotation

expression

RanchoGSE24060 load_all_RanchoGSE24060.sh
GSE24780Peritoneal and testicular macrophage mrna expression after exposure to UPEC CFT073Geisler (2010)Macrophage expression24GPL11067GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE24780load_all_EtriksGSE24780.sh
GSE25066Genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancerHatzis (2011)Breast Cancer508GPL96GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

RanchoGSE25066

EtriksGSE25066

load_all_RanchoGSE25066.sh

load_all_EtriksGSE25066.sh
GSE25160Combination of peripheral blood gene expression profiles and clinical parameters predicts response for tocilizumab (anti-IL6) treatment in rheumatoid arthritisMesko (2012)Rheumatoid Arthritis26GPL6244GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE25160

load_all_EtriksGSE25160.sh
GSE26246Polyglutamine Atrophin provokes neurodegeneration in DrosophilaBlanc (2010)Epilepsy36GPL1322

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE26246load_all_EtriksGSE26246.sh
GSE26952Expression data for human epithelium from subjects with atopic dermatitis, psoriasis and nonatopic controlsBerger (2011)Psoriasis16GPL2700GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE26952load_all_EtriksGSE26952.sh
GSE27015Rat model of MTLE: Animals with epilepsy vs animals without epilepsyWinden (2011)Epilepsy20GPL2882

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE27015load_all_EtriksGSE27015.sh
GSE27045Expression data from macrophages isolated from lupus NZB/W mouse kidneys prenephritic, nephritic or after complete remission.Berthier (2011)

Systemic Lupus Erythematosus (SLE)

17GPL7546

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE27045load_all_EtriksGSE27045.sh
GSE27268Rat model of MTLE: Animals with epilepsy vs animals without epilepsyWinden (2011)Epilepsy44GPL2882 GPL2896

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE27268load_all_EtriksGSE27268.sh
GSE27390Human bone marrow-derived mononuclear cells (BMMC): rheumatoid arthritis vs. osteoarthritisLee (2011)Rheumatoid Arthritis19GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE27390

load_all_EtriksGSE27390.sh
GSE27628Expression data from affected skin from psoriasis mouse models and normal skin from control miceSwindell (2011)Psoriasis34GPL1261GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE27628load_all_EtriksGSE27628.sh
GSE27831 Syntenin-1 is expressed in uveal melanoma and correlates with metastatic progression Gangemi (2012)Melanoma Uveal29GPL570

GEO Public Studies with clinical and gene expression data.

General oncology set to test main functionality

Rancho

clinical

ref_annotation

expression

RanchoGSE27831 load_all_EtriksGSE27831.sh
GSE27887Reversal of Atopic Dermatitis with Narrow-Band UVB Phototherapy and Biomarkers for Therapeutic ResponseSuarez-Farinas (2011)Psoriasis35GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE27887load_all_EtriksGSE27887.sh
GSE27895Global DNA methylation profiling of CD4+ T cells from patients with systemic lupus erythematosusDozmorov (2011)Systemic Lupus Erythematosus (SLE)23GPL8490

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression(methylation)

EtriksGSE27895load_all_EtriksGSE27895.sh
GSE28454Temporal transcriptional changes in human monocytes following acute myocardial infarction: The GerMIFs monocyte expression studySchunkert (2011)Acute Myocardial Infarction (AMI)76GPL6883

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE28454load_all_EtriksGSE28454.sh
GSE29532Exon-array profiling of peripheral blood cells in the first hours of acute coronary syndrome patientsGarcia (2011)Acute Myocardial Infarction (AMI)55GPL5175

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE20532load_all_EtriksGSE29532.sh
GSE30153B cell signature during inactive systemic lupusSchickel (2011)Systemic Lupus Erythematosus (SLE)26GPL570

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE30153load_all_EtriksGSE30153.sh
GSE30355Human keratinocytes have a response to injury that upregulates CCL20 and other genes linking innate and adaptive immunitySuarez-Farinas (2011)Psoriasis30GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE30355


load_all_EtriksGSE30355.sh


GSE30662Comparison of human Rheumatoid arthritis patient peripheral whole blood mRNAs just before and after LeukocytapheresisKusaoi (2011)Rheumatoid Arthritis8GPL5639GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE30662

load_all_EtriksGSE30662.sh
GSE30768Post-therapeutic relapse of psoriasis associated with CD11a blockade is associated with T cells and inflammatory myeloid DCsSuarez-Farinas (2011)Psoriasis14GPL571GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE30768load_all_EtriksGSE30768.sh
GSE30999Expression data from skin biopsy samples from patients with moderate-to-severe psoriasisLi (2011)Psoriasis170GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE30999

load_all_EtriksGSE30999.sh


GSE31652IL-17A is an essential cytokine to sustain pathogenic cell activation and inflammatory gene circuits in psoriasis vulgarisSuarez-Farinas (2011)Psoriasis30GPL571GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE31652load_all_EtriksGSE31652.sh
GSE31773Comparison of mRNA expression in circulating T-cells from patients with severe asthma Tsitsiou (2012)Asthma

(eT) 40

(CH) 20

GPL570

GEO Public Studies with clinical and gene expression data

ConvergeHealth clinical data used to test Across Trial with GSE34466

ConvergeHealth (clinical only)

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

RanchoGSE31773 (clinical only)

EtriksGSE31773

load_all_RanchoGSE31773.sh (clinical only)

load_all_EtriksGSE31773.sh
GSE32407A single intradermal injection of IFN-γ induces a psoriasis-like state in both non-lesional psoriatic and healthy skinSuarez-Farinas (2011)Psoriasis60GPL571GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE32407

load_all_EtriksGSE32407.sh
GSE32583Expression data from lupus NZB/W, NZM2410, NZW/BXSB mouse kidneys prenephritic and nephritic.Berthier (2012)Lupus Nephritis57GPL7546GEO Public Studies with clinical and gene expression data eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

RanchoGSE32583

EtriksGSE32583

load_all_RanchoGSE32583.sh

load_all_EtriksGSE32583.sh
GSE32591Expression data from human with lupus nephritis (LN) 

Berthier (2012)

Lupus Nephritis47GPL14663GEO Public Studies with clinical and gene expression data eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

RanchoGSE32591

EtriksGSE32591

load_all_RanchoGSE32591.sh

load_all_EtriksGSE32591.sh
GSE32620Human keratinocytes stimulated with IL-17CAbbas (2011)Psoriasis16GPL6480GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE32620load_all_EtriksGSE32620.sh
GSE33377Expression profiling of rheumatoid arthritis patients treated with anti-TNFToonen (2012)Rheumatoid Arthritis42GPL5175GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE33377

load_all_EtriksGSE33377.sh
GSE3365 Comparison of PBMCs in Inflammatory Bowel DiseaseBurczynski (2006)Inflammatory Bowel Disease127GPL96GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

RanchoGSE3365

EtriksGSE3365

load_all_RanchoGSE3365.sh

load_all_EtriksGSE3365.sh
GSE34198Determinants of excess genetic risk of acute myocardial infarction – a matched case-control studyKim (2013)Acute Myocardial Infarction (AMI)97GPL6102

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE34198load_all_EtriksGSE34198.sh
GSE34466Airway Epithelial miRNA Expression in Asthma Barczak (2012)Asthma63GPL15016

GEO Public Studies with clinical and gene expression data

ConvergeHealth clinical data used to test Across Trial with GSE31773

ConvergeHealthclinicalRanchoGSE34466 load_all_RanchoGSE34466.sh
GSE34577Routine use of microarray-based gene expression profiling to identify patients with low cytogenetic risk acute myeloid leukemia: accurate results can be obtained even with suboptimal samples (training samples)Guardiola (2012)Acute Myeloid Leukemia89GPL6947

GEO Public Studies with clinical and gene expression data

 

ElevadaclinicalElevadaGSE34577load_all_ElevadaGSE34577.sh
GSE34714Routine use of microarray-based gene expression profiling to identify patients with low cytogenetic risk acute myeloid leukemia: accurate results can be obtained even with suboptimal samples. (test samples)Guardiola (2012)Acute Myeloid Leukemia117GPL6947

GEO Public Studies with clinical and gene expression data

 

ElevadaclinicalElevadaGSE34714load_all_ElevadaGSE34714.sh
GSE35642Transcriptome analysis of a chronic in vitro model of ParkinsonismCabeza-Arvelaiz (2012)Parkinsons Disease18GPL96GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE35642

load_all_EtriksGSE35642.sh
GSE35643Expression data from human bronchial airway smooth muscle (ASM) cellsGounni (2012)Asthma12GPL6244GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE35643load_all_EtriksGSE35643.sh
GSE3592Expression profiling of responsiveness to infliximab in rheumatoid arthritis patientsLequerre (2006)Rheumatoid Arthritis44GPL3064GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE3592

load_all_EtriksGSE3592.sh
GSE36287Expression data from primary human keratinocytes exposed to cytokines in vitro (IL-4, IL-13, IL-17A, IFN-alpha, IFN-gamma, TNF)Swindell (2012)Psoriasis24GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE36287load_all_EtriksGSE36287.sh
GSE36700Gene expression profiles in synovial biopsies from patients with arthritisLauwerys (2012)Rheumatoid Arthritis25GPL570

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE36700load_all_EtriksGSE36700.sh
GSE36757Human Rheumatoid Arthritis Synovial Fibroblasts: Control vs. Tenascin-C StimulatedAsano (2012)Rheumatoid Arthritis1GPL9425GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE36757

load_all_EtriksGSE36757.sh
GSE36807Genome-wide analysis of Crohn's disease and ulcerative colitis biopsy samplesMontero (2012)Inflammatory Bowel Disease35GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE36807load_all_EtriksGSE36807.sh
GSE36941Restoration of regulatory and effector T cell balance and B cell homeostasis in systemic lupus erythematosus patients through vitamin D supplementationDerian (2012)Systemic Lupus Erythematosus (SLE)20

GPL6947

GPL10558

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE36941

load_all_EtriksGSE36941.sh


GSE37356Inflammatory Expression Profiles in Monocyte to Macrophage Differentiation amongst Patients with Systemic Lupus Erythematosus and Healthy Controls with and without an Atherosclerosis PhenotypeHuang (2120)Systemic Lupus Erythematosus (SLE)72GPL10558

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE37356load_all_EtriksGSE37356.sh
GSE37642Prognostic gene signature for AMLHerold (2013)Acute Myeloid Leukemia562GPL97

GEO Public Studies with clinical and gene expression data

 

ElevadaclinicalElevadaGSE37642load_all_ElevadaGSE37642.sh
GSE38039ZNF750 in late keratinocyte differentiationCohen (2012)Psoriasis6GPL6244GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE38039load_all_EtriksGSE38039.sh
GSE38642Expression data from human pancreatic isletsTaneera (2012)Diabetes63GPL6244GEO Public Studies with clinical and gene expression data Sanofi

clinical

ref_annotation

expression

SanofiGSE38642load_all_SanofiGSE38642.sh
GSE38713Expression data from intestinal mucosa of patients with Ulcerative ColitisSalas (2012)Inflammatory Bowel Disease43GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE38713load_all_EtriksGSE38713.sh
GSE39088Down-regulation of Interferon signature in systemic lupus erythematosus patients by active immunization with Interferon alpha-KinoidLauwerys (2012)Systemic Lupus Erythematosus (SLE)142GPL570

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE39088load_all_EtriksGSE39088.sh
GSE3982Human immune cell transcriptome for the major leukocyte types in humansMackay (2006)Macrophage expression32GPL96GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE3982load_all_EtriksGSE3982.sh
GSE40240Expression data from peripheral blood - blood draws at Pre and Post time points of Allergen inhalation challenge (ER and DR)Tebbutt (2012)Asthma28GPL6244GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE40240load_all_EtriksGSE40240.sh
GSE41825Bruton's Tyrosine Kinase Regulates TLR9 but not TLR7 Signaling in Human pDCsLau (2012)Systemic Lupus Erythematosus (SLE)30GPL570

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE41825load_all_EtriksGSE41825.sh
GSE41861Upper airway gene expression is an effective surrogate biomarker for Th2-driven inflammation in the lower airwayCheng (2012)Asthma138GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE41861load_all_EtriksGSE41861.sh
GSE41862Nasal scrape gene expression profiling in asthmaticsCheng (2012)Asthma116GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE41862load_all_EtriksGSE41862.sh
GSE41863Sputum gene expression profiling in asthmaticsCheng (2012)Asthma56GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE41863load_all_EtriksGSE41863.sh
GSE41905A global transcriptome analysis of keratinocytes upon suppression of endogenous microRNA-31Xu (212)Psoriasis6GPL11532GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE41905load_all_EtriksGSE41905.sh
GSE42305TREM-1 is a novel therapeutic target in PsoriasisSuarez-Farinas (2012)Psoriasis15GPL571GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE42305load_all_EtriksGSE42305.sh
GSE4271Molecular subclasses of high-grade glioma: prognosis, disease progression, and neurogenesisPhillips (2006)Brain Cancer77

GPL96

GPL97

GEO Public Studies with clinical and gene expression data Rancho

clinical

ref_annotation

expression

RanchoGSE4271 load_all_RanchoGSE4271.sh
GSE4302Genome-Wide Profiling of Airway Epithelial Cells in Asthmatics, Smokers and Healthy ControlsWoodruff (2007)Asthma118GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE4302

load_all_EtriksGSE4302.sh
GSE43696To identify differentially expressed genes between normal control (NC), mild-moderate asthmatic (MMA) and severe asthmatic (SA) patientsMilosevic (2013)Asthma109GP6480GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE43696load_all_EtriksGSE43696.sh
GSE4382Repeated observation of breast tumor subtypes in independent gene expression data setsSorlie (2003)Breast Cancer167GSE4382PDM

GEO Public Studies with clinical and gene expression data

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

RanchoGSE4382

EtriksGSE4382

load_all_RanchoGSE4382.sh

load_all_EtriksGSE4382.sh
GSE44037

Expression data from airway epithelial cells from patients with asthma, rhinitis, and healthy controls 

Wagener (2013)Asthma34GPL13158GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE44037load_all_EtriksGSE44037.sh
GSE45111

A sputum gene expression signature of six biomarkers identifies asthma inflammatory phenotype and steroid responsiveness 

Baines (2013)Asthma47GPL6104GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE45111load_all_EtriksGSE45111.sh
GSE45847To identify gene markers which differentiate between Aspirin-exacerbated respiratory disease (AERD) and aspirin-tolerant asthma (ATA) with a high discriminative power.Shin (2013)Asthma42GPL16979GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE45847load_all_EtriksGSE45847.sh
GSE45923The peroxisome proliferator-activated receptor-gamma agonist pioglitazone modulates aberrant T cell responses in systemic lupus erythematosusBerthier (2013)Systemic Lupus Erythematosus (SLE)18GPL11670

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE45923load_all_EtriksGSE45923.sh
GSE46171

Asthmatics with exacerbation during acute respiratory illness exhibit unique transcriptional signatures

McErlean (2013)Asthma91GPL16981GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE46171load_all_EtriksGSE46171.sh
GSE46923Systemic lupus erythematosus monoctye transcripts in 6 combined studiesBaldwin (2013)Systemic Lupus Erythematosus (SLE)142

GPL96

GPL97

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE46923load_all_EtriksGSE46923.sh
GSE4698Molecular characterization of very early relapsed childhood ALL Kirschner, Schwabe (2006)Acute Lymphoblastic Leukemia60GPL96GEO Public Studies with clinical and gene expression data Rancho

clinical

ref_annotation

expression

RanchoGSE4698 load_all_RanchoGSE4698.sh
GSE47516Gene expression alterations in the cerebellum and granule neurons of Cstb-/- mouse are associated with early synaptic changes and inflammationJoensuu (2013)Epilepsy21GPL1261

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE47516load_all_EtriksGSE47516.sh
GSE47598Activated T cell gene expression profile associated with PsoriasisJulia (2013)Psoriasis24GPL10558GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE47598load_all_EtriksGSE47598.sh
GSE47752Transcriptional profiling of dentate granule cells in 4 rat epilepsy modelsLiang (2013)Epilepsy172GPL1355

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE47752load_all_EtriksGSE47752.sh
GSE47908Transcriptional analysis of left-sided colitis, pancolitis and ulcerative colitis-associated dysplasiaBjerrum (2013)Inflammatory Bowel Disease60GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE47908load_all_EtriksGSE47908.sh
GSE48060Transcriptome from circulating cells suggests dysregulated pathways associated with long-term recurrent events following first-time myocardial infarctionLi (2013)Acute Myocardial Infarction (AMI)52GPL570

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE48060load_all_EtriksGSE48060.sh
GSE48957Mucosal miRNA expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC)van der Goten (2013)Inflammatory Bowel Disease27GPL14613GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE48957load_all_EtriksGSE48957.sh
GSE48958Mucosal gene expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC)van der Goten (2013)Inflammatory Bowel Disease21GPL6244GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE48958load_all_EtriksGSE48958.sh
GSE47959Mucosal expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC) from 2 studies GSE48957 GSE48958van der Goten (2013)Inflammatory Bowel Disease48

GPL14613

GPL6244

GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression(x2)

EtriksGSE47959load_all_EtriksGSE47959.sh
GSE4917Time course microarray data following GR activation in MCF10A-Myc breast cellsConzen (2006)Epilepsy24GPL96

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE4917load_all_EtriksGSE4917.sh
GSE4922Genetic Reclassification of Histologic Grade Delineates New Clinical Subtypes of Breast CancerIvshina (2006)Breast Cancer289

GPL96

GPL97

GEO Public Studies with clinical and gene expression dataRancho

clinical

ref_annotation

expression

RanchoGSE4922 load_all_RanchoGSE4922.sh
GSE49925Gene expression profiles associated with acute myocardial infarction and risk of cardiovascular deathKim (2013)Acute Myocardial Infarction (AMI)338GPL10558

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE49925load_all_EtriksGSE49925.sh
GSE50628Gene expression analysis in children with complex seizures by influenza A (H1N1)pdm09 or rotavirus gastroenteritisTsuge (2013)Epilepsy32GPL570

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE50628load_all_EtriksGSE50628.sh
GSE50635Activation of the Interferon Pathway is Dependent upon Autoantibodies in African-American SLE Patients, but not in European-American SLE PatientsNiewold (2013)Systemic Lupus Erythematosus (SLE)49GPL6244

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE50635load_all_EtriksGSE50635.sh
GSE50790Gene expression in psoriasis lesions and uninvolved skinSwindell (2130)Psoriasis8GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE50790load_all_EtriksGSE50790.sh
GSE5099Expression Data from Macrophage Maturation and Polarization ExperimentMartinez-Estrada (2006)Macrophage expression30

GPL96

GPL97

GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE5099load_all_EtriksGSE5099.sh
GSE51785Molecular patterns in human ulcerative colitis and correlation with response to infliximabChang (2013)Inflammatory Bowel Disease56GPL15207GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE51785load_all_EtriksGSE51785.sh
GSE51997T helper lymphocyte- and monocyte-specific type I interferon (IFN) signatures in autoimmunity and viral infection.Durek (2013)Systemic Lupus Erythematosus (SLE)36GPL570

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE51997load_all_EtriksGSE51997.sh
GSE52074Human rhinovirus infection causes different DNA methylation changes in nasal epithelial cells from healthy and asthmatic subjectsMcErlean (2013)Asthma18GPL13534GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE52074load_all_EtriksGSE52074.sh
GSE52471Dominant Th1 and Minimal Th17 Skewing in Discoid Lupus Revealed by Transcriptomic Comparison with PsoriasisSuarez-Farinas (2013)Psoriasis38GPL571GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE52471load_all_EtriksGSE52471.sh
GSE5320Whole brains from nicotinic acetylcholine receptor subunit mutant mice and littermate controlsOrr-Urtreger (2006)Epilepsy11GPL81

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE5320load_all_EtriksGSE5320.sh
GSE5327Breast cancer relapse free survival and lung metastasis free survivalMinn (2007)
Breast Cancer58GPL96

GEO Public Studies with clinical and gene expression data

General oncology set to test main functionality

Rancho

clinical

ref_annotation

expression

RanchoGSE5327load_all_RanchoGSE5327.sh
GSE53552Gene expression profiling in psoriatic lesional and non-lesional skin [brodalumab treatment]Bigler (2013)Psoriasis99GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE53552load_all_EtriksGSE53552.sh
GSE54282Systems-based analyses of brain regions functionally impacted in Parkinson's disease reveals underlying causal mechanismsRiley (2014)Parkinsons Disease33GPL17047GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE54282

load_all_EtriksGSE54282.sh
GSE54605

Human rhinovirus infection causes different DNA methylation changes in nasal epithelial cells from healthy and asthmatic subjects

Xiang (2014)Asthma10GPL1162GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE54605load_all_EtriksGSE54605.sh
GSE55447Divergent genome wide transcriptional profiles from immune cell subsets isolated from SLE patients with different ancestral backgroundsNiewold (2014)Systemic Lupus Erythematosus (SLE)208GPL10558

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE55447load_all_EtriksGSE55447.sh
GSE56553Short-term exposure to diesel exhaust is associated with dynamic changes in DNA methylation of circulating mononuclear cells in asthmaticsKober (2014)Asthma96GPL13534

GEO Public Studies with clinical and gene expression data.

Very large platform with 30 million probes. ETL can stall on smaller systems.

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE56553load_all_EtriksGSE56553.sh
GSE57585Gene coexpression network and community detection analyses of CA3 trascriptome reveal distinct pathogenic and compensatory pathways in early and late onset febrile forms of temporal lobe epilepsyMoreira-Filho (2014)Epilepsy14GPL6480

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE57585load_all_EtriksGSE57585.sh
GSE57869DNA methylation in systemic lupus erythematosus patientsSong (2014)Systemic Lupus Erythematosus (SLE)12GPL8490

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression(methylation)

EtriksGSE57869load_all_EtriksGSE57869.sh
GSE59217Intrinsic self-DNA triggers inflammatory disease dependent on STING (I)Isaac (2014)Systemic Lupus Erythematosus (SLE)12GPL6887

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE59217load_all_EtriksGSE59217.sh
GSE59339Characteristic DNA methylation profiles in peripheral blood monocytes are associated with inflammatory phenotypes of asthma

Baines (2014)

Asthma62GPL8490GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE59339load_all_EtriksGSE59339.sh
GSE6054Monocytes of patients with familial hypercholesterolemia show alterations in cholesterol metabolismMozig (2006)Macrophage expression23GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE6054load_all_EtriksGSE6054.sh
GSE61225Gene expression changes in blood RNA after swimming in a poolSumoy (2014)Asthma74GPL19169GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE61225load_all_EtriksGSE61225.sh
GSE61635Gene expression in RNP autoantibody+ systemic lupus erythematosus (SLE) patient bloodHoffman (2014)Systemic Lupus Erythematosus (SLE)129GPL570

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE61635load_all_EtriksGSE61635.sh
GSE62646Altered gene expression pattern in peripheral blood mononuclear cells in patients with acute myocardial infarctionBurzynska (2014)Acute Myocardial Infarction (AMI)98GPL6244

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE62646load_all_EtriksGSE62646.sh
GSE63270Expression profiles of normal hematopoietic stem and progenitor cells and acute myeloid leukemia sub-populationsGentles (2015)Acute Myeloid Leukemia104GPL17810

GEO Public Studies with clinical and gene expression data

 

Elevada

clinical

ref_annotation

expression

ElevadaGSE63270load_all_ElevadaGSE63270.sh
GSE63383Expression data from asthmatic and healthy airway smooth muscle cellsFaiz (2014)Asthma24GPL6244GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE63383load_all_EtriksGSE63383.sh
GSE63808Chronic temporal lobe epilepsy: biopsy hippocampusBecker (2014)Epilepsy129GPL6947

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE63808load_all_EtriksGSE63808.sh
GSE63829Genome-wide analysis of atypical NK cell subset in mouse model of Systemic Lupus Erythematosus (SLE)Bolland (2014)Systemic Lupus Erythematosus (SLE)6GPL6887

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE63829load_all_EtriksGSE63829.sh
GSE65163The Nasal Methylome and Childhood Atopic AsthmaSchwartz (2015)Asthma72GPL13534GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE65163load_all_EtriksGSE65163.sh
GSE65204

The Nasal Gene Expression and Childhood Atopic Asthma

Schwartz (2015)Asthma69GPL14550GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE65204load_all_EtriksGSE65204.sh
GSE65205Childhood Atopic AsthmaSchwartz (2015)Asthma141GPL13534GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE65205load_all_EtriksGSE65205.sh
GSE6613Parkinson's disease vs. controls, whole bloodScherzer (2007)Parkinsons Disease105GPL96GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE6613

load_all_EtriksGSE6613.sh
GSE6614Expression changes in mouse brains following nicotine-induced seizures; the modulation of transcription factor networksOrr-Urtreger (2006)Epilepsy28GPL81

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE6614load_all_EtriksGSE6614.sh
GSE66360A Whole Blood Molecular Signature for the Identification of Acute Myocardial Infarction Without Relying Upon Myonecrosis (microarray)Kramer (2015)Acute Myocardial Infarction (AMI)99GPL570

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE66360load_all_EtriksGSE66360.sh
GSE66762HT-project: Expression profiling after prolonged experimental febrile seizures suggests structural remodeling in the hippocampusGroet Koerkamp (2015)Epilepsy49GPL14726

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE66762load_all_EtriksGSE66762.sh
GSE6710Expression data from human skin biposies (lesional and uninvolved) from psoriatic patientsTernes (2007)Psoriasis26GPL96GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE6710load_all_EtriksGSE6710.sh
GSE6731Genome-wide gene expression differences between Crohn’s and ulcerative colitis from endoscopic pinch biopsiesChakravarti (2007)Inflammatory Bowel Disease36GPL8300GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE6731load_all_EtriksGSE6731.sh
GSE67472

Airway epithelial gene expression in asthma versus healthy controls

Christenson (2015)Asthma105GPL16311GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE67472load_all_EtriksGSE67472.sh
GSE6932Identification and characterization of small molecule inducers of epidermal keratinocyte differentiationWalker (2007)Psoriasis18GPL96GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE6932load_all_EtriksGSE6932.sh
GSE7074Similarities and differences in the transcriptome of human atherosclerotic and non-atherosclerotic macrophagesVolger (207)Macrophage expression30GPL4868GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE7074

load_all_EtriksGSE7074.sh


GSE7138Induction of Dendritic Cell-like Phenotype in Macrophages during Foam Cell FormationGleissner (2007)Macrophage expression22GPL96GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE7138

load_all_EtriksGSE7138.sh


GSE7216Cytokine treated normal human epidermal keratinocytesJung (2007)Psoriasis25GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE7216load_all_EtriksGSE7216.sh
GSE72747Global gene expression profiles in whole blood total RNA from patients with lupus nephritis, before and after initiation of therapyLauwerys (2015)Systemic Lupus Erythematosus (SLE)30GPL570

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE72747load_all_EtriksGSE72747.sh
GSE72754Down-regulation of Interferon signature in systemic lupus erythematosus patients by active immunization with Interferon alpha-Kinoid extended follow-upLauwerys (2015)Systemic Lupus Erythematosus (SLE)52GPL570

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE72754load_all_EtriksGSE72754.sh
GSE72798IFNalpha kinoid induces neutralizing anti-IFNalpha antibodies that decrease the expression of IFN-induced and B cell activation associated transcripts: analysis of extended follow-up data from the IFN-K phase I/II studyLauwerys (2015)Systemic Lupus Erythematosus (SLE)82GPL570

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE72798load_all_EtriksGSE72798.sh
GSE73878Time-dependent transcriptomic profiles of mouse hippocampus in kainic acid-induced mesial temporal lobe epilepsy (MTLE)Hamby (2015)Epilepsy80GPL6885

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE73878load_all_EtriksGSE73878.sh
GSE7390Strong Time Dependence of the 76-Gene Prognostic Signature Desmedt (2007)Breast Cancer198GPL96GEO Public Studies with clinical and gene expression data eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

RanchoGSE7390

EtriksGSE7390

load_all_RanchoGSE7390.sh

load_all_EtriksGSE7390.sh
GSE74075

Changes in Expression of Genes Regulating Airway Inflammation Following a High-Fat Mixed Meal in Asthmatics

Li (2016)Asthma16GPL6883GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE74075load_all_EtriksGSE74075.sh
GSE7486Gene expression analysis in absence epilepsy using a monozygotic twin designMatigian (2007)Epilepsy30GPL570

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE7486load_all_EtriksGSE7486.sh
GSE7621Expression data of substantia nigra from postmortem human brain of Parkinson's disease patients (PD)Lesnick (2007)Parkinsons Disease25GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE7621

load_all_EtriksGSE7621.sh
GSE77578Molecular consequences of Csf1R (M-CSF receptor) inhibition by PLX3397 in the pilocarpine-induced chronic epileptic mouse hippocampusvan Eyli (2016)Epilepsy56GPL6885

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE77578load_all_EtriksGSE77578.sh
GSE78193Blockade of interferon-γ normalizes IFN regulated gene expression in subjects with systemic lupus erythematosus (SLE)Campbell (2016)Systemic Lupus Erythematosus (SLE)125

GPL6480

GPL6848

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE78193load_all_EtriksGSE78193.sh
GSE81024Hippocampal gene expression signature following inflammation in epileptic miceBozzi (2016)Epilepsy12GPL7202

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE81024load_all_EtriksGSE81024.sh
GSE82218Whole genome transcription and DNA methylation analysis of peripheral blood mononuclear cells identified aberrant gene regulation pathways in systemic lupus erythematosus [metylation]Lian (2016)Systemic Lupus Erythematosus (SLE)55GPL13534

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression(methylation)

EtriksGSE82218load_all_EtriksGSE82218.sh
GSE8512Expression data from mouse bone marrow macrophages from a strain intercrossSmith (2070)Macrophage expression207GPL1261GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE8512

load_all_EtriksGSE8512.sh


GSE8581Human Chronic Obstructive Pulmonary Disorder (COPD) Biomarker Bhattacharya  (2009)COPD58GPL570GEO Public Studies with clinical and gene expression data Rancho

clinical

ref_annotation

expression

RanchoGSE8581 load_all_RanchoGSE8581.sh
GSE8650Blood Leukocyte Microarrays to Diagnose Systemic Onset Juvenile Idiopathic Arthritis and Follow IL-1 blockade Allantaz (2007)Juvenile Idiopathic Arthritis115

GPL96

GPL97

GEO Public Studies with clinical and gene expression data Rancho

clinical

ref_annotation

expression

RanchoGSE8650 load_all_RanchoGSE8650.sh
GSE9120IL-1 treatment of human epidermal keratinocytesBlumenberg (2007)Psoriasis8GPL571GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE9120load_all_EtriksGSE9120.sh
GSE9329Expression data of synovial cells isolated from patients with rheumatoid arthritisKabuyama (2008)Rheumatoid Arthritis2GPL201GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE9329

load_all_EtriksGSE9329.sh
GSE9452Definition of an ulcerative colitis preinflammatory stateOlsen (2007)Inflammatory Bowel Disease26GPL570GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE9452load_all_EtriksGSE9452.sh
GSE9686Human colon expression in healthy, Crohn's Disease, treated Crohn's Disease, and Ulcerative ColitisDenson (2007)Inflammatory Bowel Disease34GPL5760GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE9686load_all_EtriksGSE9686.sh
GSE97320Differential gene expression profiles in peripheral blood in Northeast Chinese Han people with acute myocardial infarctionMeng (2017)Acute Myocardial Infarction (AMI)6GPL570

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE97320load_all_EtriksGSE97320.sh
GSE974Left ventricular apex samplesGrindle (2004)Acute Myocardial Infarction (AMI)38GPL96

GEO Public Studies with clinical and gene expression data

 

eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE974load_all_EtriksGSE974.sh
GSE9782Gene expression profiling and correlation with outcome in clinical trials of the proteasome inhibitor bortezomibMulligan (2007)Multiple Myeloma264

GPL96

GPL97

GEO Public Studies with clinical and gene expression data eTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

RanchoGSE9872

EtriksGSE9872

load_all_RanchoGSE9872.sh

load_all_EtriksGSE9872.sh
GSE9820Circulating Mononuclear Cell Transcriptomes in Patients with Atherosclerotic Coronary Artery DiseaseSchirmer (2007)Macrophage expression153GPL6255GEO Public Studies with clinical and gene expression dataeTRIKS (University of Luxembourg)

clinical

ref_annotation

expression

EtriksGSE9820load_all_EtriksGSE9820.sh

...

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 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.

Study IDStudy Title Author  (Published)DiseaseSubjectsPlatformDescriptionSourceDatatypesDownloadScript
ETLCLIN
Test dataTesting

Clinical data with large number of tree nodestranSMART Foundation

clinical



ETLCLINSH
Test dataTesting

Clinical data with large number of tree nodestranSMART Foundation

clinical



ETLGSE15222
 Test data Testing 

tranSMART Foundation

clinical

ref_annotation

expression



MultiGSE10024
Test dataTesting  
tranSMART Foundation

clinical

ref_annotation

mirnaqpcr



MultiGSE10500
Test dataTesting  
tranSMART Foundation

clinical

ref_annotation

mirnaqpcr



TESTIC50
Test dataTesting  
tranSMART Foundation

clinical

ref_annotation

mirnaqpcr



Cell Line Use Case 

The Cell Line Use Case data is provided by CTMM TraIT for testing multiple datatypes on public data.

...

  • Asthma_Tsitsiou_GSE31773
  • Asthma_Woodruff_GSE34466

 

 

Test data