This page contains links to data sets (and supporting documentation) that have been curated for loading into tranSMART by members of the community. In most cases there will be several files for different types of data (clinical, expression, etc.) that must be downloaded. The files can then be loaded into your tranSMART instance by following the instructions given below.
If you have data that you would like to contribute, or one that you would like to see here, please contact a member of the Content Committee.
Curated Datasets
The Content Committee has been working diligently to obtain curated data in tranSMART-ready format. The Foundation has organized these datasets in the tranSMART Foundation libarary server. You can find these data on library.transmartfoundation.org. Descriptions of these datasets are in progress and found below. New data is in progress and will be posted on the wiki shortly. You can load these datasets into your transmart instance using the directions below.
Loading the data
These datasets can be loaded using transmart-data (available on github: https://github.com/tranSMART-Foundation/transmart-data/tree/release-16.3).
From the top level transmart-data directory on your system (on Oracle, replace 'samples/postgres' with 'samples/oracle'):
Select a dataset from the library server and install each datatype in turn, starting with the clinical data (if any) and any platform annotation. Loading the ref_annotation target(s) identifies any platform annotation and installs if it is not already in the database. Finally load the remaining available datatypes(s) by specifying the Load Target shown in the table for each dataset.
For example, to load the complete set of data for study GSE13168 (load target RanchoGSE13168):
cd transmart-data source ./vars make update_datasets make -C samples/postgres load_clinical_RanchoGSE13168 make -C samples/postgres load_ref_annotation_RanchoGSE13168 make -C samples/postgres load_expression_RanchoGSE13168
The files are available to download as tar.xz files from the tranSMART Foundation library server. Each .tar.xz file contains all the required datafiles plus a file with a .params type which defines all the parameters needed by the loading scripts. In general you need several of these files (e.g. clinical, annotation, expression) in order to load the complete study, and must load the clinical data first. This information should be sufficient to load the datasets using any other loader of your choice.
Scripts are also provided to load all targets for a given study from the top level transmart-data directory. The scripts will check they are running from the top-level transmart-data directory and will load all targets for the selected study. See the Script column in the tables below.
Curated GEO (Gene Expression Omnibus) datasets
Study ID | Study Title | Author (Published) | Disease | Subjects | Platform | Description | Source | Datatype | Download Label | Script |
---|---|---|---|---|---|---|---|---|---|---|
GSE10024 | Key Regulatory Molecules of Cartilage Destruction in Rheumatoid Arthritis: An in vitro Study | Andreas (2008) | Rheumatoid Arthritis | 6 | GPL96 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE10024 | load_all_EtriksGSE10024.sh |
GSE10220 | Gene expression profiling of human monocytes and monocyte-derived-macrophages | Cambien (2008) | Macrophage expression | 96 | GPL1946 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE10220 | load_all_EtriksGSE10220.sh |
GSE10500 | Gene expression in rheumatoid arthritis synovial macrophages | Yarilina (2008) | Rheumatoid Arthritis | 8 | GPL8300 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE10500 | load_all_EtriksGSE10500.sh |
GSE10616 | Human colon expression in healthy controls, colon-only CD, ileo-colonic CD, and UC | Denson (2008) | Inflammatory Bowel Disease | 58 | GPL5760 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE10616 | load_all_EtriksGSE10616.sh |
GSE10714 | Expression data from human colonic biopsy sample | Solymosi (2008) | Inflammatory Bowel Disease | 33 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE10714 | load_all_EtriksGSE10714.sh |
GSE11575 | Mutual Antagonistic Relationship Between Prostaglandin E2 and Interferon-(gamma): Implications for Rheumatoid Arthritis | Mathieu (2008) | Rheumatoid Arthritis | 12 | GPL4372 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE11575 | load_all_EtriksGSE11575.sh |
GSE11827 | Identification of markers of responsiveness in rheumatoid arthritis patient | Bansard (2011) | Rheumatoid Arthritis | 49 | GPL5215 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE11827 | load_all_EtriksGSE11827.sh |
GSE11886 | Gene expression analysis of macrophages from ankylosing spondylitis patients reveals interferon-gamma dysregulation | Barnes (2008) | Macrophage expression | 33 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE11886 | load_all_EtriksGSE11886.sh |
GSE11903 | Effective treatment of psoriasis with etanercept is linked to suppression of IL17 signaling, not immediate response TNF | Suarez-Farinas (2009) | Psoriasis | 89 | GPL571 | GEO Public Studies with clinical and gene expression data | Thomson Reuters | clinical ref_annotation expression | RanchoGSE11903 | load_all_RanchoGSE11903.sh |
GSE11909 | A modular analysis framework for the discovery of biomarkers of Systemic Lupus Erythematosus | Chaussabel (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 | EtriksGSE11909 | load_all_EtriksGSE11909.sh |
GSE11947 | Integrated Network and Microarray Analysis to Identify New Biomarkers in Ischemic Heart Disease | Devaux (2008) | Acute Myocardial Infarction (AMI) | 32 | GPL1947 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE11947 | load_all_EtriksGSE11947.sh |
GSE12051 | Microarray predictor of response to infliximab in rheumatoid arthritis (RA) patients | Julia (2009) | Rheumatoid Arthritis | 44 | GPL2507 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE12051 | load_all_EtriksGSE12051.sh |
GSE12196 | Rat exposure to RDX | Dillman (2008) | Epilepsy | 48 | GPL1355 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE12196 | load_all_EtriksGSE12196.sh |
GSE12374 | Interactions of cytokines in peripheral blood cells from Systemic Lupus Erythematosus | Nishimoto (2008) | Systemic Lupus Erythematosus (SLE) | 17 | GPL1291 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE12374 | load_all_EtriksGSE12374.sh |
GSE12653 | Gene Expression Analysis in Peripheral Blood of Patients with Rheumatoid Arthritis | Nishimoto (2008) | Rheumatoid Arthritis | 72 | GPL7220 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE12653 | load_all_EtriksGSE12653.sh |
GSE13026 | Early and long-standing rheumatoid arthritis: molecular signatures identified by gene expression profiling in synovium | Lequerre (2009) | Rheumatoid Arthritis | 45 | GPL5215 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE13026 | load_all_EtriksGSE13026.sh |
GSE13168 | Effects of glucocorticoids and Protein Kinase A on growth factor- and 1beta- regulated gene | Misior (2009) | Asthma | 54 | GPL96 | 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 | RanchoGSE13168 | load_all_RanchoGSE13168.sh |
GSE13355 | Gene expression data of skin from psoriatic patients and normal controls | Abecasis (2008) | Psoriasis | 180 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE13355 | load_all_EtriksGSE13355.sh |
GSE13428 | Gene Expression Profiling of Rat Hippocampus Following Exposure to the Acetylcholinesterase Inhibitor Soman | Dillman (2008) | Epilepsy | 38 | GPL1355 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE13428 | load_all_EtriksGSE13428.sh |
GSE13732 | CIS (multiple sclerosis) (case-control) (time-series) | Baranzini (2008) | Multiple Sclerosis | 113 | GPL570 | GEO Public Studies with clinical and gene expression data | Rancho | clinical ref_annotation expression | RanchoGSE13732 | load_all_RanchoGSE13732.sh |
GSE13887 | Activation of mTOR controls the loss of TCRζ in lupus T cells through HRES-1/Rab4-regulated lysosomal degradation | Middleton (2008) | Systemic Lupus Erythematosus (SLE) | 27 | GPL570 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE13887 | load_all_EtriksGSE13887.sh |
GSE1432 | Transcriptional Response of Human Microglial Cells to Interferon-gamma | Rock (2004) | Macrophage expression | 24 | GPL96 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE1432 | load_all_EtriksGSE1432.sh |
GSE14468 | Gene expression profiling of CEBPA double and single mutant and CEBPA wild type AML | Verhaak (2009) | Acute Myeloid Leukemia | 526 | GPL570 | GEO Public Studies with clinical and gene expression data | Elevada | clinical ref_annotation expression | ElevadaGSE14468 | load_all_ElevadaGSE14668.sh |
GSE1456 | Gene expression of breast cancer tissue in a large population-based cohort of Swedish patients | Pawitan (2005) | Breast Cancer | 159 | GPL96 GPL97 | GEO Public Studies with clinical and gene expression data | Rancho | clinical ref_annotation expression | RanchoGSE1456 | load_all_RanchoGSE1456.sh |
GSE14763 | Whole transcriptome analysis of the hippocampus: toward a molecular portrait of epileptogenesis | Okamoto (2009) | Epilepsy | 18 | GPL2896 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE14763 | load_all_EtriksGSE14763.sh |
GSE14769 | Time course of bone marrow-derived macrophages simulated with LPS | Marzoff (2009) | Macrophage expression | 24 | GPL1261 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE14769 | load_all_EtriksGSE14769.sh |
GSE14905 | Type I Interferon: Potential Therapeutic Target for Psoriasis? | Higgs (2009) | Psoriasis | 82 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE14905 | load_all_EtriksGSE14905.sh |
GSE15245 | Prediction of acute multiple sclerosis relapses by transcription levels of peripheral blood cells | Gurevich (2009) | Multiple Sclerosis | 94 | GPL96 GPL571 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE15245
| |
GSE15258 | Whole blood transcript profiling of rheumatoid arthritis patients | Bienkowska | Rheumatoid Arthritis | 86 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE15258
| |
GSE15316 | Differential expression of rituximab responders vs. non responders on 3 different blood cell types | Julia (2009) | Rheumatoid Arthritis | 23 | GPL2507 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE15316 | load_all_EtriksGSE15316.sh |
GSE15573 | Immunity and Defense Genes in Peripheral Blood Mononuclear Cells of Rheumatoid Arthritis patients | Teixeira (2009) | Rheumatoid Arthritis | 33 | GPL6102 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE15573 | load_all_EtriksGSE15573.sh |
GSE15602 | Differential gene expression in RA synovial biopsies from responders versus non-responders to adalimumab therapy | Badot (2009) | Rheumatoid Arthritis | 11 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE15602 | load_all_EtriksGSE15602.sh |
GSE15615 | Differential effects of TNFalpha and IL1beta on FLS global gene expression profile | Badot (2009) | Rheumatoid Arthritis | 6 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE15615 | load_all_EtriksGSE15615.sh |
GSE15907 | Immunological Genome Project data Phase 1 | Gopalan (2009) | Macrophage expression | 653 | GPL6246 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE15907 | load_all_EtriksGSE15907.sh |
GSE16385 | Expression data from human macrophages | Szanto (2009) | Macrophage expression | 38 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE16385 | load_all_EtriksGSE16385.sh |
GSE1643 | Normal Variance of Gene Expression in the Human Lung | Coldren (2004) | Epilepsy | 40 | GPL570 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE1643 | load_all_EtriksGSE1643.sh |
GSE16879 | Mucosal expression profiling in patients with inflammatory bowel disease before and after first infliximab treatment | Arijs (2009) | Inflammatory Bowel Disease | 73 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | RanchoGSE16879
| |
GSE16969 | Gene expression analysis of TSC-tubers reveals increased expression of adhesion and inflammatory factors | Wittink (2009) | Epilepsy | 10 | GPL570 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE16969 | load_all_EtriksGSE16969.sh |
GSE17755 | Human peripheral blood cells: autoimmune diseases vs. healthy individuals | Nishimoto (2011) | Autoimmune Diseases | 244 | GPL1291 | GEO Public Studies with clinical and gene expression data | Rancho | clinical ref_annotation expression | RanchoGSE17755 | load_all_RanchoGSE17755.sh |
GSE17761 | The type of phagocytic receptor modulates gene expression and phagosome functions in macrophages | Hoffman (2009) | Macrophage expression | 29 | GPL9079 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE17761 | load_all_EtriksGSE17761.sh |
GSE18275 | Macrophages heterogeneity in human atherosclerotic plaques | Maouche (2009) | Macrophage expression | 18 | GPL1946 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE18275 | load_all_EtriksGSE18275.sh |
GSE19821 | Rheumatoid arthritis and anti-TNF treatment | van Baarsen (2010) | Rheumatoid Arthritis | 30 | GPL9869 GPL9870 GPL9871 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE19821 | load_all_EtriksGSE19821.sh |
GSE19236 | Expression analysis of dendritic cells, macrophages and monocytes | Klug (2009) | Macrophage expression | 48 | GPL6480 GPL6848 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE19236 | load_all_EtriksGSE19236.sh |
GSE19976 | Gene expression analysis of lung biopsies from patients with two different forms of pulmonary sarcoidosis | Ho (2010) | Lung Cancer | 15 | GPL6244 | GEO Public Studies with clinical and gene expression data | Sanofi | clinical ref_annotation expression | SanofiGSE19976 | load_all_SanofiGSE19976.sh |
GSE20141 | Expression analysis of laser-dissected SNpc neurons in Parkinson's disease | Zheng (2010) | Parkinsons Disease | 18 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE20141 | load_all_EtriksGSE20141.sh |
GSE20146 | Expression analysis of dissected GPi in Parkinson's disease | Middleton (2010) | Parkinsons Disease | 20 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE20146 | load_all_EtriksGSE20146.sh |
GSE20153 | Expression analysis of lymphoblast cells lines in Parkinson's disease | Zheng (2010) | Parkinsons Disease | 16 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE20153 | load_all_EtriksGSE20153.sh |
GSE20163 | Systematic meta-analysis and replication of genome-wide expression studies of Parkinson's disease: 2 | Zheng (2010) | Parkinsons Disease | 12 | GPL96 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE20163 | load_all_EtriksGSE20163.sh |
GSE20164 | Systematic meta-analysis and replication of genome-wide expression studies of Parkinson's disease: 3 | Zheng (2010) | Parkinsons Disease | 11 | GPL96 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE20164 | load_all_EtriksGSE20164.sh |
GSE20168 | Transcriptional analysis of prefrontal area 9 in Parkinson's disease | Zhang (2005) | Parkinsons Disease | 29 | GPL96 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE20168 | load_all_EtriksGSE20168.sh |
GSE20194 | MAQC-II Project: human breast cancer (BR) data set | Popovici (2010) | Breast Cancer | 278 | GPL96 | GEO Public Studies with clinical and gene expression data | Rancho | clinical ref_annotation expression | RanchoGSE20194 | load_all_EtriksGSE20194.sh |
GSE20291 | Transcriptional analysis of putamen in Parkinson's disease | Zhang (2005) | Parkinsons Disease | 35 | GPL96 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE20291 | load_all_EtriksGSE20291.sh |
GSE20292 | Transcriptional analysis of whole substantia nigra in Parkinson's disease | Zhang (2005) | Parkinsons Disease | 29 | GPL96 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE20292 | load_all_EtriksGSE20292.sh |
GSE20295 | Transcriptional analysis of multiple brain regions in Parkinson's disease | Zhang (2005) | Parkinsons Disease | 93 | GPL96 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE20295 | load_all_EtriksGSE20295.sh |
GSE20314 | Systematic meta-analysis and replication of genome-wide expression studies of Parkinson’s disease: 4 | Zheng (2010) | Parkinsons Disease | 8 | GPL96 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE20314.sh | |
GSE20333 | Gene expression profiling of parkinsonian substantia nigra | Edna | Parkinsons Disease | 12 | GPL201 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE20333.sh | |
GSE20690 | Efficacy of anti-TNF biologic agent, infliximab, for RA patients using transcriptome analysis of white blood cells | Takeuchi (2009) | Rheumatoid Arthritis | 68 | GPL4133 | GEO Public Studies with clinical and gene expression data | Thomson Reuters eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE20690
| load_all_EtriksGSE20690.sh |
GSE20864 | Human peripheral blood cells: systemic lupus erythematosus vs healthy individual. | Nishimoto (2010) | Systemic Lupus Erythematosus (SLE) | 66 | GPL1291 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE20864 | load_all_EtriksGSE20864.sh |
GSE20881 | Colon biopsies from Crohns patients and healthy controls | Abbas (2010) | Inflammatory Bowel Disease | 172 | GPL1708 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE20881 | load_all_EtriksGSE20881.sh |
GSE2125 | isolated alveolar macrophages | Woodruff (2005) | Asthma | 45 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE2125.sh | |
GSE21537 | The relationship between the gene expression profile in the synovium of RA patients at baseline and the clinical response to infliximab treatment | Lindberg (2010) | Rheumatoid Arthritis | 62 | GPL7768 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE21537.sh | |
GSE21548 | Gene Expression Profiles of RAW264.7 Macrophages Stimulated with Two Commonly Used Preparations of LPS | Yang (2010) | Macrophage expression | 46 | GPL891 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE21548 | load_all_EtriksGSE21548.sh |
GSE21959 | Transcriptional response to hypoxia of normal and rheumatoid arthritis synovial fibroblasts | Del Rey (2010) | Rheumatoid Arthritis | 36 | GPL4133 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE21959.sh | |
GSE22138 | Expression Data from Uveal Melanoma primary tumors | Laurent (2010) | Melanoma Uveal | 63 | GPL570 | GEO Public Studies with clinical and gene expression data | Pfizer | clinical ref_annotation expression | PfizerGSE22138 | load_all_PfizerGSE22138.sh |
GSE22324 | Mapping of disease-associated expression polymorphisms in primary peripheral blood CD4+ lymphocytes | Raby (2010) | Asthma | 200 | GPL6104 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE22324 | load_all_EtriksGSE22324.sh |
GSE23076 | Gene Expression Profiles in a Rabbit Model of Systemic Lupus Erythematosus | Lempicki (2010) | Systemic Lupus Erythematosus (SLE) | 66 | GPL8300 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE23076 | load_all_EtriksGS23076E.sh |
GSE23611 | Lung biopsies from asthmatics pre- and post- steroid treatment and from healthy control | Choy (2011) | Asthma | 62 | GPL6480 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE23611 | load_all_EtriksGSE23611.sh |
GSE23622 | Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes | Benner (2010) | Macrophage expression | 55 | GPL6100 GPL7202 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE23622 | load_all_EtriksGSE23622.sh |
GSE23676 | Expression 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) subjects | Soreq (2012) | Parkinsons Disease | 27 | GPL5188 | 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 | EtriksGSE23676 | load_all_EtriksGSE23676.sh |
GSE24060 | Peripheral Blood Cells Gene Expression Profiles from Discordant Monozygotic Twins with Systemic Autoimmune disease (SAIDs) | O'Hanlon (2011) | Autoimmune Diseases | 80 | GPL7264 | GEO Public Studies with clinical and gene expression data | Rancho | clinical ref_annotation expression | RanchoGSE24060 | load_all_RanchoGSE24060.sh |
GSE24780 | Peritoneal and testicular macrophage mrna expression after exposure to UPEC CFT073 | Geisler (2010) | Macrophage expression | 24 | GPL11067 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE24780 | load_all_EtriksGSE24780.sh |
GSE25066 | Genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer | Hatzis (2011) | Breast Cancer | 508 | GPL96 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE25066.sh | |
GSE25160 | Combination of peripheral blood gene expression profiles and clinical parameters predicts response for tocilizumab (anti-IL6) treatment in rheumatoid arthritis | Mesko (2012) | Rheumatoid Arthritis | 26 | GPL6244 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE25160.sh | |
GSE26246 | Polyglutamine Atrophin provokes neurodegeneration in Drosophila | Blanc (2010) | Epilepsy | 36 | GPL1322 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE26246 | load_all_EtriksGSE26246.sh |
GSE26952 | Expression data for human epithelium from subjects with atopic dermatitis, psoriasis and nonatopic controls | Berger (2011) | Psoriasis | 16 | GPL2700 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE26952 | load_all_EtriksGSE26952.sh |
GSE27015 | Rat model of MTLE: Animals with epilepsy vs animals without epilepsy | Winden (2011) | Epilepsy | 20 | GPL2882 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE27015 | load_all_EtriksGSE27015.sh |
GSE27045 | Expression data from macrophages isolated from lupus NZB/W mouse kidneys prenephritic, nephritic or after complete remission. | Berthier (2011) | Systemic Lupus Erythematosus (SLE) | 17 | GPL7546 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE27045 | load_all_EtriksGSE27045.sh |
GSE27268 | Rat model of MTLE: Animals with epilepsy vs animals without epilepsy | Winden (2011) | Epilepsy | 44 | GPL2882 GPL2896 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE27268 | load_all_EtriksGSE27268.sh |
GSE27390 | Human bone marrow-derived mononuclear cells (BMMC): rheumatoid arthritis vs. osteoarthritis | Lee (2011) | Rheumatoid Arthritis | 19 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE27390.sh | |
GSE27628 | Expression data from affected skin from psoriasis mouse models and normal skin from control mice | Swindell (2011) | Psoriasis | 34 | GPL1261 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE27628 | load_all_EtriksGSE27628.sh |
GSE27831 | Syntenin-1 is expressed in uveal melanoma and correlates with metastatic progression | Gangemi (2012) | Melanoma Uveal | 29 | GPL570 | 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 |
GSE27887 | Reversal of Atopic Dermatitis with Narrow-Band UVB Phototherapy and Biomarkers for Therapeutic Response | Suarez-Farinas (2011) | Psoriasis | 35 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE27887 | load_all_EtriksGSE27887.sh |
GSE27895 | Global DNA methylation profiling of CD4+ T cells from patients with systemic lupus erythematosus | Dozmorov (2011) | Systemic Lupus Erythematosus (SLE) | 23 | GPL8490 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression(methylation) | EtriksGSE27895 | load_all_EtriksGSE27895.sh |
GSE28454 | Temporal transcriptional changes in human monocytes following acute myocardial infarction: The GerMIFs monocyte expression study | Schunkert (2011) | Acute Myocardial Infarction (AMI) | 76 | GPL6883 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE28454 | load_all_EtriksGSE28454.sh |
GSE29532 | Exon-array profiling of peripheral blood cells in the first hours of acute coronary syndrome patients | Garcia (2011) | Acute Myocardial Infarction (AMI) | 55 | GPL5175 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE20532 | load_all_EtriksGSE29532.sh |
GSE30153 | B cell signature during inactive systemic lupus | Schickel (2011) | Systemic Lupus Erythematosus (SLE) | 26 | GPL570 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE30153 | load_all_EtriksGSE30153.sh |
GSE30355 | Human keratinocytes have a response to injury that upregulates CCL20 and other genes linking innate and adaptive immunity | Suarez-Farinas (2011) | Psoriasis | 30 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | ||
GSE30662 | Comparison of human Rheumatoid arthritis patient peripheral whole blood mRNAs just before and after Leukocytapheresis | Kusaoi (2011) | Rheumatoid Arthritis | 8 | GPL5639 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE30662.sh | |
GSE30768 | Post-therapeutic relapse of psoriasis associated with CD11a blockade is associated with T cells and inflammatory myeloid DCs | Suarez-Farinas (2011) | Psoriasis | 14 | GPL571 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE30768 | load_all_EtriksGSE30768.sh |
GSE30999 | Expression data from skin biopsy samples from patients with moderate-to-severe psoriasis | Li (2011) | Psoriasis | 170 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | ||
GSE31652 | IL-17A is an essential cytokine to sustain pathogenic cell activation and inflammatory gene circuits in psoriasis vulgaris | Suarez-Farinas (2011) | Psoriasis | 30 | GPL571 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE31652 | load_all_EtriksGSE31652.sh |
GSE31773 | Comparison 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) | load_all_RanchoGSE31773.sh (clinical only) load_all_EtriksGSE31773.sh |
GSE32407 | A single intradermal injection of IFN-γ induces a psoriasis-like state in both non-lesional psoriatic and healthy skin | Suarez-Farinas (2011) | Psoriasis | 60 | GPL571 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE32407.sh | |
GSE32583 | Expression data from lupus NZB/W, NZM2410, NZW/BXSB mouse kidneys prenephritic and nephritic. | Berthier (2012) | Lupus Nephritis | 57 | GPL7546 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE32583.sh | |
GSE32591 | Expression data from human with lupus nephritis (LN) | Berthier (2012) | Lupus Nephritis | 47 | GPL14663 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE32591.sh | |
GSE32620 | Human keratinocytes stimulated with IL-17C | Abbas (2011) | Psoriasis | 16 | GPL6480 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE32620 | load_all_EtriksGSE32620.sh |
GSE33377 | Expression profiling of rheumatoid arthritis patients treated with anti-TNF | Toonen (2012) | Rheumatoid Arthritis | 42 | GPL5175 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE33377.sh | |
GSE3365 | Comparison of PBMCs in Inflammatory Bowel Disease | Burczynski (2006) | Inflammatory Bowel Disease | 127 | GPL96 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | RanchoGSE3365 | load_all_EtriksGSE3365.sh |
GSE34198 | Determinants of excess genetic risk of acute myocardial infarction – a matched case-control study | Kim (2013) | Acute Myocardial Infarction (AMI) | 97 | GPL6102 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE34198 | load_all_EtriksGSE34198.sh |
GSE34466 | Airway Epithelial miRNA Expression in Asthma | Barczak (2012) | Asthma | 63 | GPL15016 | GEO Public Studies with clinical and gene expression data ConvergeHealth clinical data used to test Across Trial with GSE31773 | ConvergeHealth | clinical | RanchoGSE34466 | load_all_RanchoGSE34466.sh |
GSE34577 | Routine 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 Leukemia | 89 | GPL6947 | GEO Public Studies with clinical and gene expression data
| Elevada | clinical | ElevadaGSE34577 | load_all_ElevadaGSE34577.sh |
GSE34714 | Routine 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 Leukemia | 117 | GPL6947 | GEO Public Studies with clinical and gene expression data
| Elevada | clinical | ElevadaGSE34714 | load_all_ElevadaGSE34714.sh |
GSE35642 | Transcriptome analysis of a chronic in vitro model of Parkinsonism | Cabeza-Arvelaiz (2012) | Parkinsons Disease | 18 | GPL96 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE35642.sh | |
GSE35643 | Expression data from human bronchial airway smooth muscle (ASM) cells | Gounni (2012) | Asthma | 12 | GPL6244 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE35643 | load_all_EtriksGSE35643.sh |
GSE3592 | Expression profiling of responsiveness to infliximab in rheumatoid arthritis patients | Lequerre (2006) | Rheumatoid Arthritis | 44 | GPL3064 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE3592.sh | |
GSE36287 | Expression data from primary human keratinocytes exposed to cytokines in vitro (IL-4, IL-13, IL-17A, IFN-alpha, IFN-gamma, TNF) | Swindell (2012) | Psoriasis | 24 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE36287 | load_all_EtriksGSE36287.sh |
GSE36700 | Gene expression profiles in synovial biopsies from patients with arthritis | Lauwerys (2012) | Rheumatoid Arthritis | 25 | GPL570 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE36700 | load_all_EtriksGSE36700.sh |
GSE36757 | Human Rheumatoid Arthritis Synovial Fibroblasts: Control vs. Tenascin-C Stimulated | Asano (2012) | Rheumatoid Arthritis | 1 | GPL9425 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE36757.sh | |
GSE36807 | Genome-wide analysis of Crohn's disease and ulcerative colitis biopsy samples | Montero (2012) | Inflammatory Bowel Disease | 35 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE36807 | load_all_EtriksGSE36807.sh |
GSE36941 | Restoration of regulatory and effector T cell balance and B cell homeostasis in systemic lupus erythematosus patients through vitamin D supplementation | Derian (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 | |
GSE37356 | Inflammatory Expression Profiles in Monocyte to Macrophage Differentiation amongst Patients with Systemic Lupus Erythematosus and Healthy Controls with and without an Atherosclerosis Phenotype | Huang (2120) | Systemic Lupus Erythematosus (SLE) | 72 | GPL10558 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE37356 | load_all_EtriksGSE37356.sh |
GSE37642 | Prognostic gene signature for AML | Herold (2013) | Acute Myeloid Leukemia | 562 | GPL97 | GEO Public Studies with clinical and gene expression data
| Elevada | clinical | ElevadaGSE37642 | load_all_ElevadaGSE37642.sh |
GSE38039 | ZNF750 in late keratinocyte differentiation | Cohen (2012) | Psoriasis | 6 | GPL6244 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE38039 | load_all_EtriksGSE38039.sh |
GSE38642 | Expression data from human pancreatic islets | Taneera (2012) | Diabetes | 63 | GPL6244 | GEO Public Studies with clinical and gene expression data | Sanofi | clinical ref_annotation expression | SanofiGSE38642 | load_all_SanofiGSE38642.sh |
GSE38713 | Expression data from intestinal mucosa of patients with Ulcerative Colitis | Salas (2012) | Inflammatory Bowel Disease | 43 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE38713 | load_all_EtriksGSE38713.sh |
GSE39088 | Down-regulation of Interferon signature in systemic lupus erythematosus patients by active immunization with Interferon alpha-Kinoid | Lauwerys (2012) | Systemic Lupus Erythematosus (SLE) | 142 | GPL570 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE39088 | load_all_EtriksGSE39088.sh |
GSE3982 | Human immune cell transcriptome for the major leukocyte types in humans | Mackay (2006) | Macrophage expression | 32 | GPL96 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE3982 | load_all_EtriksGSE3982.sh |
GSE40240 | Expression data from peripheral blood - blood draws at Pre and Post time points of Allergen inhalation challenge (ER and DR) | Tebbutt (2012) | Asthma | 28 | GPL6244 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE40240 | load_all_EtriksGSE40240.sh |
GSE41825 | Bruton's Tyrosine Kinase Regulates TLR9 but not TLR7 Signaling in Human pDCs | Lau (2012) | Systemic Lupus Erythematosus (SLE) | 30 | GPL570 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE41825 | load_all_EtriksGSE41825.sh |
GSE41861 | Upper airway gene expression is an effective surrogate biomarker for Th2-driven inflammation in the lower airway | Cheng (2012) | Asthma | 138 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE41861 | load_all_EtriksGSE41861.sh |
GSE41862 | Nasal scrape gene expression profiling in asthmatics | Cheng (2012) | Asthma | 116 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE41862 | load_all_EtriksGSE41862.sh |
GSE41863 | Sputum gene expression profiling in asthmatics | Cheng (2012) | Asthma | 56 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE41863 | load_all_EtriksGSE41863.sh |
GSE41905 | A global transcriptome analysis of keratinocytes upon suppression of endogenous microRNA-31 | Xu (212) | Psoriasis | 6 | GPL11532 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE41905 | load_all_EtriksGSE41905.sh |
GSE42305 | TREM-1 is a novel therapeutic target in Psoriasis | Suarez-Farinas (2012) | Psoriasis | 15 | GPL571 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE42305 | load_all_EtriksGSE42305.sh |
GSE4271 | Molecular subclasses of high-grade glioma: prognosis, disease progression, and neurogenesis | Phillips (2006) | Brain Cancer | 77 | GPL96 GPL97 | GEO Public Studies with clinical and gene expression data | Rancho | clinical ref_annotation expression | RanchoGSE4271 | load_all_RanchoGSE4271.sh |
GSE4302 | Genome-Wide Profiling of Airway Epithelial Cells in Asthmatics, Smokers and Healthy Controls | Woodruff (2007) | Asthma | 118 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE4302.sh | |
GSE43696 | To identify differentially expressed genes between normal control (NC), mild-moderate asthmatic (MMA) and severe asthmatic (SA) patients | Milosevic (2013) | Asthma | 109 | GP6480 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE43696 | load_all_EtriksGSE43696.sh |
GSE4382 | Repeated observation of breast tumor subtypes in independent gene expression data sets | Sorlie (2003) | Breast Cancer | 167 | GSE4382PDM | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | RanchoGSE4382 | load_all_EtriksGSE4382.sh |
GSE44037 | Expression data from airway epithelial cells from patients with asthma, rhinitis, and healthy controls | Wagener (2013) | Asthma | 34 | GPL13158 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE44037 | load_all_EtriksGSE44037.sh |
GSE45111 | A sputum gene expression signature of six biomarkers identifies asthma inflammatory phenotype and steroid responsiveness | Baines (2013) | Asthma | 47 | GPL6104 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE45111 | load_all_EtriksGSE45111.sh |
GSE45847 | To identify gene markers which differentiate between Aspirin-exacerbated respiratory disease (AERD) and aspirin-tolerant asthma (ATA) with a high discriminative power. | Shin (2013) | Asthma | 42 | GPL16979 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE45847 | load_all_EtriksGSE45847.sh |
GSE45923 | The peroxisome proliferator-activated receptor-gamma agonist pioglitazone modulates aberrant T cell responses in systemic lupus erythematosus | Berthier (2013) | Systemic Lupus Erythematosus (SLE) | 18 | GPL11670 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE45923 | load_all_EtriksGSE45923.sh |
GSE46171 | Asthmatics with exacerbation during acute respiratory illness exhibit unique transcriptional signatures | McErlean (2013) | Asthma | 91 | GPL16981 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE46171 | load_all_EtriksGSE46171.sh |
GSE46923 | Systemic lupus erythematosus monoctye transcripts in 6 combined studies | Baldwin (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 | EtriksGSE46923 | load_all_EtriksGSE46923.sh |
GSE4698 | Molecular characterization of very early relapsed childhood ALL | Kirschner, Schwabe (2006) | Acute Lymphoblastic Leukemia | 60 | GPL96 | GEO Public Studies with clinical and gene expression data | Rancho | clinical ref_annotation expression | RanchoGSE4698 | load_all_RanchoGSE4698.sh |
GSE47516 | Gene expression alterations in the cerebellum and granule neurons of Cstb-/- mouse are associated with early synaptic changes and inflammation | Joensuu (2013) | Epilepsy | 21 | GPL1261 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE47516 | load_all_EtriksGSE47516.sh |
GSE47598 | Activated T cell gene expression profile associated with Psoriasis | Julia (2013) | Psoriasis | 24 | GPL10558 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE47598 | load_all_EtriksGSE47598.sh |
GSE47752 | Transcriptional profiling of dentate granule cells in 4 rat epilepsy models | Liang (2013) | Epilepsy | 172 | GPL1355 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE47752 | load_all_EtriksGSE47752.sh |
GSE47908 | Transcriptional analysis of left-sided colitis, pancolitis and ulcerative colitis-associated dysplasia | Bjerrum (2013) | Inflammatory Bowel Disease | 60 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE47908 | load_all_EtriksGSE47908.sh |
GSE48060 | Transcriptome from circulating cells suggests dysregulated pathways associated with long-term recurrent events following first-time myocardial infarction | Li (2013) | Acute Myocardial Infarction (AMI) | 52 | GPL570 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE48060 | load_all_EtriksGSE48060.sh |
GSE48957 | Mucosal miRNA expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC) | van der Goten (2013) | Inflammatory Bowel Disease | 27 | GPL14613 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE48957 | load_all_EtriksGSE48957.sh |
GSE48958 | Mucosal gene expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC) | van der Goten (2013) | Inflammatory Bowel Disease | 21 | GPL6244 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE48958 | load_all_EtriksGSE48958.sh |
GSE47959 | Mucosal expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC) from 2 studies GSE48957 GSE48958 | van der Goten (2013) | Inflammatory Bowel Disease | 48 | GPL14613 GPL6244 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression(x2) | EtriksGSE47959 | load_all_EtriksGSE47959.sh |
GSE4917 | Time course microarray data following GR activation in MCF10A-Myc breast cells | Conzen (2006) | Epilepsy | 24 | GPL96 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE4917 | load_all_EtriksGSE4917.sh |
GSE4922 | Genetic Reclassification of Histologic Grade Delineates New Clinical Subtypes of Breast Cancer | Ivshina (2006) | Breast Cancer | 289 | GPL96 GPL97 | GEO Public Studies with clinical and gene expression data | Rancho | clinical ref_annotation expression | RanchoGSE4922 | load_all_RanchoGSE4922.sh |
GSE49925 | Gene expression profiles associated with acute myocardial infarction and risk of cardiovascular death | Kim (2013) | Acute Myocardial Infarction (AMI) | 338 | GPL10558 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE49925 | load_all_EtriksGSE49925.sh |
GSE50628 | Gene expression analysis in children with complex seizures by influenza A (H1N1)pdm09 or rotavirus gastroenteritis | Tsuge (2013) | Epilepsy | 32 | GPL570 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE50628 | load_all_EtriksGSE50628.sh |
GSE50635 | Activation of the Interferon Pathway is Dependent upon Autoantibodies in African-American SLE Patients, but not in European-American SLE Patients | Niewold (2013) | Systemic Lupus Erythematosus (SLE) | 49 | GPL6244 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE50635 | load_all_EtriksGSE50635.sh |
GSE50790 | Gene expression in psoriasis lesions and uninvolved skin | Swindell (2130) | Psoriasis | 8 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE50790 | load_all_EtriksGSE50790.sh |
GSE5099 | Expression Data from Macrophage Maturation and Polarization Experiment | Martinez-Estrada (2006) | Macrophage expression | 30 | GPL96 GPL97 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE5099 | load_all_EtriksGSE5099.sh |
GSE51785 | Molecular patterns in human ulcerative colitis and correlation with response to infliximab | Chang (2013) | Inflammatory Bowel Disease | 56 | GPL15207 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE51785 | load_all_EtriksGSE51785.sh |
GSE51997 | T helper lymphocyte- and monocyte-specific type I interferon (IFN) signatures in autoimmunity and viral infection. | Durek (2013) | Systemic Lupus Erythematosus (SLE) | 36 | GPL570 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE51997 | load_all_EtriksGSE51997.sh |
GSE52074 | Human rhinovirus infection causes different DNA methylation changes in nasal epithelial cells from healthy and asthmatic subjects | McErlean (2013) | Asthma | 18 | GPL13534 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE52074 | load_all_EtriksGSE52074.sh |
GSE52471 | Dominant Th1 and Minimal Th17 Skewing in Discoid Lupus Revealed by Transcriptomic Comparison with Psoriasis | Suarez-Farinas (2013) | Psoriasis | 38 | GPL571 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE52471 | load_all_EtriksGSE52471.sh |
GSE5320 | Whole brains from nicotinic acetylcholine receptor subunit mutant mice and littermate controls | Orr-Urtreger (2006) | Epilepsy | 11 | GPL81 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE5320 | load_all_EtriksGSE5320.sh |
GSE5327 | Breast cancer relapse free survival and lung metastasis free survival | Minn (2007) | Breast Cancer | 58 | GPL96 | GEO Public Studies with clinical and gene expression data General oncology set to test main functionality | Rancho | clinical ref_annotation expression | RanchoGSE5327 | load_all_RanchoGSE5327.sh |
GSE53552 | Gene expression profiling in psoriatic lesional and non-lesional skin [brodalumab treatment] | Bigler (2013) | Psoriasis | 99 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE53552 | load_all_EtriksGSE53552.sh |
GSE54282 | Systems-based analyses of brain regions functionally impacted in Parkinson's disease reveals underlying causal mechanisms | Riley (2014) | Parkinsons Disease | 33 | GPL17047 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE54282.sh | |
GSE54605 | Human rhinovirus infection causes different DNA methylation changes in nasal epithelial cells from healthy and asthmatic subjects | Xiang (2014) | Asthma | 10 | GPL1162 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE54605 | load_all_EtriksGSE54605.sh |
GSE55447 | Divergent genome wide transcriptional profiles from immune cell subsets isolated from SLE patients with different ancestral backgrounds | Niewold (2014) | Systemic Lupus Erythematosus (SLE) | 208 | GPL10558 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE55447 | load_all_EtriksGSE55447.sh |
GSE56553 | Short-term exposure to diesel exhaust is associated with dynamic changes in DNA methylation of circulating mononuclear cells in asthmatics | Kober (2014) | Asthma | 96 | GPL13534 | 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 | EtriksGSE56553 | load_all_EtriksGSE56553.sh |
GSE57585 | Gene 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 epilepsy | Moreira-Filho (2014) | Epilepsy | 14 | GPL6480 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE57585 | load_all_EtriksGSE57585.sh |
GSE57869 | DNA methylation in systemic lupus erythematosus patients | Song (2014) | Systemic Lupus Erythematosus (SLE) | 12 | GPL8490 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression(methylation) | EtriksGSE57869 | load_all_EtriksGSE57869.sh |
GSE59217 | Intrinsic self-DNA triggers inflammatory disease dependent on STING (I) | Isaac (2014) | Systemic Lupus Erythematosus (SLE) | 12 | GPL6887 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE59217 | load_all_EtriksGSE59217.sh |
GSE59339 | Characteristic DNA methylation profiles in peripheral blood monocytes are associated with inflammatory phenotypes of asthma | Baines (2014) | Asthma | 62 | GPL8490 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE59339 | load_all_EtriksGSE59339.sh |
GSE6054 | Monocytes of patients with familial hypercholesterolemia show alterations in cholesterol metabolism | Mozig (2006) | Macrophage expression | 23 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE6054 | load_all_EtriksGSE6054.sh |
GSE61225 | Gene expression changes in blood RNA after swimming in a pool | Sumoy (2014) | Asthma | 74 | GPL19169 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE61225 | load_all_EtriksGSE61225.sh |
GSE61635 | Gene expression in RNP autoantibody+ systemic lupus erythematosus (SLE) patient blood | Hoffman (2014) | Systemic Lupus Erythematosus (SLE) | 129 | GPL570 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE61635 | load_all_EtriksGSE61635.sh |
GSE62646 | Altered gene expression pattern in peripheral blood mononuclear cells in patients with acute myocardial infarction | Burzynska (2014) | Acute Myocardial Infarction (AMI) | 98 | GPL6244 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE62646 | load_all_EtriksGSE62646.sh |
GSE63270 | Expression profiles of normal hematopoietic stem and progenitor cells and acute myeloid leukemia sub-populations | Gentles (2015) | Acute Myeloid Leukemia | 104 | GPL17810 | GEO Public Studies with clinical and gene expression data
| Elevada | clinical ref_annotation expression | ElevadaGSE63270 | load_all_ElevadaGSE63270.sh |
GSE63383 | Expression data from asthmatic and healthy airway smooth muscle cells | Faiz (2014) | Asthma | 24 | GPL6244 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE63383 | load_all_EtriksGSE63383.sh |
GSE63808 | Chronic temporal lobe epilepsy: biopsy hippocampus | Becker (2014) | Epilepsy | 129 | GPL6947 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE63808 | load_all_EtriksGSE63808.sh |
GSE63829 | Genome-wide analysis of atypical NK cell subset in mouse model of Systemic Lupus Erythematosus (SLE) | Bolland (2014) | Systemic Lupus Erythematosus (SLE) | 6 | GPL6887 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE63829 | load_all_EtriksGSE63829.sh |
GSE65163 | The Nasal Methylome and Childhood Atopic Asthma | Schwartz (2015) | Asthma | 72 | GPL13534 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE65163 | load_all_EtriksGSE65163.sh |
GSE65204 | The Nasal Gene Expression and Childhood Atopic Asthma | Schwartz (2015) | Asthma | 69 | GPL14550 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE65204 | load_all_EtriksGSE65204.sh |
GSE65205 | Childhood Atopic Asthma | Schwartz (2015) | Asthma | 141 | GPL13534 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE65205 | load_all_EtriksGSE65205.sh |
GSE6613 | Parkinson's disease vs. controls, whole blood | Scherzer (2007) | Parkinsons Disease | 105 | GPL96 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE6613.sh | |
GSE6614 | Expression changes in mouse brains following nicotine-induced seizures; the modulation of transcription factor networks | Orr-Urtreger (2006) | Epilepsy | 28 | GPL81 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE6614 | load_all_EtriksGSE6614.sh |
GSE66360 | A Whole Blood Molecular Signature for the Identification of Acute Myocardial Infarction Without Relying Upon Myonecrosis (microarray) | Kramer (2015) | Acute Myocardial Infarction (AMI) | 99 | GPL570 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE66360 | load_all_EtriksGSE66360.sh |
GSE66762 | HT-project: Expression profiling after prolonged experimental febrile seizures suggests structural remodeling in the hippocampus | Groet Koerkamp (2015) | Epilepsy | 49 | GPL14726 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE66762 | load_all_EtriksGSE66762.sh |
GSE6710 | Expression data from human skin biposies (lesional and uninvolved) from psoriatic patients | Ternes (2007) | Psoriasis | 26 | GPL96 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE6710 | load_all_EtriksGSE6710.sh |
GSE6731 | Genome-wide gene expression differences between Crohn’s and ulcerative colitis from endoscopic pinch biopsies | Chakravarti (2007) | Inflammatory Bowel Disease | 36 | GPL8300 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE6731 | load_all_EtriksGSE6731.sh |
GSE67472 | Airway epithelial gene expression in asthma versus healthy controls | Christenson (2015) | Asthma | 105 | GPL16311 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE67472 | load_all_EtriksGSE67472.sh |
GSE6932 | Identification and characterization of small molecule inducers of epidermal keratinocyte differentiation | Walker (2007) | Psoriasis | 18 | GPL96 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE6932 | load_all_EtriksGSE6932.sh |
GSE7074 | Similarities and differences in the transcriptome of human atherosclerotic and non-atherosclerotic macrophages | Volger (207) | Macrophage expression | 30 | GPL4868 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE7074 | |
GSE7138 | Induction of Dendritic Cell-like Phenotype in Macrophages during Foam Cell Formation | Gleissner (2007) | Macrophage expression | 22 | GPL96 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE7138 | |
GSE7216 | Cytokine treated normal human epidermal keratinocytes | Jung (2007) | Psoriasis | 25 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE7216 | load_all_EtriksGSE7216.sh |
GSE72747 | Global gene expression profiles in whole blood total RNA from patients with lupus nephritis, before and after initiation of therapy | Lauwerys (2015) | Systemic Lupus Erythematosus (SLE) | 30 | GPL570 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE72747 | load_all_EtriksGSE72747.sh |
GSE72754 | Down-regulation of Interferon signature in systemic lupus erythematosus patients by active immunization with Interferon alpha-Kinoid extended follow-up | Lauwerys (2015) | Systemic Lupus Erythematosus (SLE) | 52 | GPL570 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE72754 | load_all_EtriksGSE72754.sh |
GSE72798 | IFNalpha 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 study | Lauwerys (2015) | Systemic Lupus Erythematosus (SLE) | 82 | GPL570 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE72798 | load_all_EtriksGSE72798.sh |
GSE73878 | Time-dependent transcriptomic profiles of mouse hippocampus in kainic acid-induced mesial temporal lobe epilepsy (MTLE) | Hamby (2015) | Epilepsy | 80 | GPL6885 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE73878 | load_all_EtriksGSE73878.sh |
GSE7390 | Strong Time Dependence of the 76-Gene Prognostic Signature | Desmedt (2007) | Breast Cancer | 198 | GPL96 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | RanchoGSE7390 | load_all_EtriksGSE7390.sh |
GSE74075 | Changes in Expression of Genes Regulating Airway Inflammation Following a High-Fat Mixed Meal in Asthmatics | Li (2016) | Asthma | 16 | GPL6883 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE74075 | load_all_EtriksGSE74075.sh |
GSE7486 | Gene expression analysis in absence epilepsy using a monozygotic twin design | Matigian (2007) | Epilepsy | 30 | GPL570 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE7486 | load_all_EtriksGSE7486.sh |
GSE7621 | Expression data of substantia nigra from postmortem human brain of Parkinson's disease patients (PD) | Lesnick (2007) | Parkinsons Disease | 25 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE7621.sh | |
GSE77578 | Molecular consequences of Csf1R (M-CSF receptor) inhibition by PLX3397 in the pilocarpine-induced chronic epileptic mouse hippocampus | van Eyli (2016) | Epilepsy | 56 | GPL6885 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE77578 | load_all_EtriksGSE77578.sh |
GSE78193 | Blockade 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 | EtriksGSE78193 | load_all_EtriksGSE78193.sh |
GSE81024 | Hippocampal gene expression signature following inflammation in epileptic mice | Bozzi (2016) | Epilepsy | 12 | GPL7202 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE81024 | load_all_EtriksGSE81024.sh |
GSE82218 | Whole 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) | 55 | GPL13534 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression(methylation) | EtriksGSE82218 | load_all_EtriksGSE82218.sh |
GSE8512 | Expression data from mouse bone marrow macrophages from a strain intercross | Smith (2070) | Macrophage expression | 207 | GPL1261 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE8512 | |
GSE8581 | Human Chronic Obstructive Pulmonary Disorder (COPD) Biomarker | Bhattacharya (2009) | COPD | 58 | GPL570 | GEO Public Studies with clinical and gene expression data | Rancho | clinical ref_annotation expression | RanchoGSE8581 | load_all_RanchoGSE8581.sh |
GSE8650 | Blood Leukocyte Microarrays to Diagnose Systemic Onset Juvenile Idiopathic Arthritis and Follow IL-1 blockade | Allantaz (2007) | Juvenile Idiopathic Arthritis | 115 | GPL96 GPL97 | GEO Public Studies with clinical and gene expression data | Rancho | clinical ref_annotation expression | RanchoGSE8650 | load_all_RanchoGSE8650.sh |
GSE9120 | IL-1 treatment of human epidermal keratinocytes | Blumenberg (2007) | Psoriasis | 8 | GPL571 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE9120 | load_all_EtriksGSE9120.sh |
GSE9329 | Expression data of synovial cells isolated from patients with rheumatoid arthritis | Kabuyama (2008) | Rheumatoid Arthritis | 2 | GPL201 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | load_all_EtriksGSE9329.sh | |
GSE9452 | Definition of an ulcerative colitis preinflammatory state | Olsen (2007) | Inflammatory Bowel Disease | 26 | GPL570 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE9452 | load_all_EtriksGSE9452.sh |
GSE9686 | Human colon expression in healthy, Crohn's Disease, treated Crohn's Disease, and Ulcerative Colitis | Denson (2007) | Inflammatory Bowel Disease | 34 | GPL5760 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE9686 | load_all_EtriksGSE9686.sh |
GSE97320 | Differential gene expression profiles in peripheral blood in Northeast Chinese Han people with acute myocardial infarction | Meng (2017) | Acute Myocardial Infarction (AMI) | 6 | GPL570 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE97320 | load_all_EtriksGSE97320.sh |
GSE974 | Left ventricular apex samples | Grindle (2004) | Acute Myocardial Infarction (AMI) | 38 | GPL96 | GEO Public Studies with clinical and gene expression data
| eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE974 | load_all_EtriksGSE974.sh |
GSE9782 | Gene expression profiling and correlation with outcome in clinical trials of the proteasome inhibitor bortezomib | Mulligan (2007) | Multiple Myeloma | 264 | GPL96 GPL97 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | RanchoGSE9872 | load_all_EtriksGSE9872.sh |
GSE9820 | Circulating Mononuclear Cell Transcriptomes in Patients with Atherosclerotic Coronary Artery Disease | Schirmer (2007) | Macrophage expression | 153 | GPL6255 | GEO Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSE9820 | load_all_EtriksGSE9820.sh |
Curated TCGA (The Cancer Genome Atlas) datasets
Study ID | Study Title | Author (Published) | Disease | Subjects | Platform | Description | Source | Datatype | Download | Script |
---|---|---|---|---|---|---|---|---|---|---|
Breast | Breast | Breast invasive carcinoma | 849 | Agi_G4502A | TCGA Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksTCGAbreast | load_all_EtriksTCGAbreast.sh | |
Colorectal | CRC | Colon adenocarcinoma | 276 | Agi_UNC_244 | TCGA Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksTCGAcolorectal | load_all_EtriksTCGAcolorectal.sh | |
Endomet | Endo | Uterine corpus endometrial carcinoma | 373 | Affy_microarray | TCGA Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksTCGAendomet | load_all_EtriksTCGAendomet.sh | |
Ovarian | OV | Ovarian serous cystadenocarcinoma | 488 | Agi_Affy_HuEX_U133A | TCGA Public Studies with clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksTCGAovarian | load_all_EtriksTCGAovarian.sh |
Other curated datasets
Study ID | Study Title | Author (Published) | Disease | Subjects | Platform | Description | Source | Datatype | Download | Script |
---|---|---|---|---|---|---|---|---|---|---|
CCLE | Cancer Cell-Line Encyclopedia | Cancers | 1070 | GPL570 modified | Cancer cell-line encyclopedia clinical and gene expression data | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksCCLE | load_all_EtriksCCLE.sh | |
GSK Cell Lines | Glaxo SmithKline Cell Lines | (many) | 950 | GPL570 | Clinical data and gene expression data for cell line catalog | eTRIKS (University of Luxembourg) | clinical ref_annotation expression | EtriksGSKCellLines | load_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 ID | Study Title | Author (Published) | Disease | Subjects | Platform | Description | Source | Datatypes | Download | Script |
---|---|---|---|---|---|---|---|---|---|---|
TEST_MANNHEIM_V13 | Test Mannheim with samples | Test data | DIabetes | 45 | - | Serial Loading of data and analysis on longitudinal studies | Sanofi | clinical | SanofiV13Clinical | load_all_SanofiV13Clinical.sh |
TESTLARGEV13 | Test diabetes large | Test data | Diabetes | 25422 | - | Large number of patients, loaded as multiple input files. | Sanofi | clinical | SanofiV13ClinicalLarge | load_all_SanofiV13ClinicalLarge.sh |
V13_MRNAMICROARRAY | Test data for mRNA expression | Test data | Muscle tissue | 17 | GPL96 | Muscle tissue for expression data, survival similar for both sexes | Sanofi | clinical ref_annotation expression | SanofiV13Expression | load_all_SanofiV13Expression.sh |
V1.3_PROTEOMICS | Test mass spec proteomics | Test data | Unknown | 17 | PROTEOMICS | Test mass spec proteomics data | Sanofi | clinical ref_annotation msproteomics | SanofiV13Proteomics | load_all_SanofiV13Proteomics.sh |
V1.3_QPCRMIRNA | Test data for miRNA qPCR | GSE37425 | Rheumatoid arthritis | 8 | GPL15467 | Test miRNA qPCR data | Sanofi | clinical ref_annotation mirnaqpcr | SanofiV13Mirna | load_all_SanofiV13Mirna.sh |
V1.3_MERGED_DATA_TYPES | Multiple datatypes for the same subjects, from GSE4382 | Test data | Breast cancer | 17 | 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 study | Sanofi | clinical ref_annotation expression metabolomics msproteomics | SanofiiV13Merged | load_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 ID | Study Title | Author (Published) | Disease | Subjects | Platform | Description | Source | Datatypes | Download | Script |
---|---|---|---|---|---|---|---|---|---|---|
TEST_MANNHEIM | Test Mannheim with samples Test data for serial clinical (low-dimensional) data | Test data | Diabetes | 30 | - | Serial Loading of data and analysis on longitudinal studies | Sanofi | clinical | SanofiMannheim | load_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 Cancer | 2 | GPL6244 | Serial Loading of expression data and analysis on longitudinal studies | Sanofi | clinical ref_annotation expression | SanofiSerialHighdim | load_all_SanofiSerialHighdim.sh |
TEST_SERIAL_RICERCA | Test data for serial expression | GPL570 | Serial Loading of expression data | Sanofi | clinical ref_annotation expression | SanofiSerialRicerca | load_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 miRBase | Sanofi | clinical ref_annotation mirnaqpcr | SanofiMirnaGSE37424 | load_all_SanofiMirnaGSE37424.sh | ||
TEST_GSE37425 | miRNA qPCR data derived from GSE37425 miRNAs expression in synovial tissues of rheumatoid arthritis (RA) individuals | Shen | Rheumatoid 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 miRBase | Sanofi | clinical ref_annotation mirnaqpcr | SanofiMirnaGSE37425 | load_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 miRBase | Sanofi | clinical ref_annotation mirnaqpcr | SanofiMirnaGSE42468 | load_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 miRBase | Sanofi | ref_annotation mirnaqpcr (no clinical) | SanofiMirnaGSE49520 | load_all_SanofiMirnaGSE49520.sh | ||
TEST_WITTEN_2010 | miRNAseq test data | Witten (2010) | Test Data | 31 | 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 miRBase | Sanofi | clinical ref_annotation mirnaseq | SanofiMirnaseqWitten | load_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 Cancer | 56 | GPL10999 | Test 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 Refseq | Sanofi | clinical ref_annotation rnaseq | SanofiRnaseqGSE48213 | load_all_SanofiRnaseqGSE48213.sh |
TEST_METABOLOMICS | Metabolomics test data | Test data | Test Data | 24 | 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 names | Sanofi | clinical ref_annotation metabolomics | SanofiMetabolomics | load_all_SanofiMetabolomics.sh |
TEST_MASS_ SPEC_PROTEOMICS | Mass-spec proteomics test data | Test data | Test Data | 17 | 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 Symbol | Sanofi | clinical ref_annotation msproteomics | SanofiProteomics | load_all_SanofiProteomics.sh |
TEST_RBM_ADNI | RBM proteomics test data | Alzheimers Disease | Test Data | 158 | 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 name | Sanofi | clinical ref_annotation rbm | SanofiRbmAdni | load_all_SanofiRbmAdni.sh |
TEST_GSE4382_INC | Test data derived from GSE4382 Repeated observation of breast tumor subtypes in independent gene expression data sets | Breast Cancer | Test Data | 143 + 22 | - | Clinical test data loaded in 4 incremental steps:
| Sanofi | clinical clinical clinical clinical | load_all_SanofiGSE4382Inc.sh |
Other Test Datasets
These datasets are used for testing tranSMART releases. Data may be changed for testing purposes.
Study ID | Study Title | Author (Published) | Disease | Subjects | Platform | Description | Source | Datatypes | Download | Script |
---|---|---|---|---|---|---|---|---|---|---|
ETLCLIN | Test data | Testing | Clinical data with large number of tree nodes | tranSMART Foundation | clinical | |||||
ETLCLINSH | Test data | Testing | Clinical data with large number of tree nodes | tranSMART Foundation | clinical | |||||
ETLGSE15222 | Test data | Testing | tranSMART Foundation | clinical ref_annotation expression | ||||||
MultiGSE10024 | Test data | Testing | tranSMART Foundation | clinical ref_annotation mirnaqpcr | ||||||
MultiGSE10500 | Test data | Testing | tranSMART Foundation | clinical ref_annotation mirnaqpcr | ||||||
TESTIC50 | Test data | Testing | 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.
A copy of the data is available from the TranSMART Foundation library server
See also the Tutorial: How to load the Cell Line Use Case dataset with transmart-data.
Data Type | Subset | Subjects | Platform | Description | Source | Load target |
---|---|---|---|---|---|---|
clinical | Single set | 19 | - | Clinical data | CTMM TraIT | |
aCGH | regions 180k | 5 | 180k region | Copy number variation data | CTMM TraIT | |
aCGH | regions 224k | 10 | 224k region | aCGH data | CTMM TraIT | |
aCGH | genes 180k | 5 | GPL8687 | aCGH data | CTMM TraIT | |
aCGH | genes 224k | 10 | GPL8687 | aCGH data | CTMM TraIT | |
expression | Affymetrix exon array | 2 | Affymetrix exon array | expression data | CTMM TraIT | |
expression | Agilent 4k mRNA microarray | 16 | Agilent 4k mRNA microarray | expression data | CTMM TraIT | |
mirna_qpcr | MicroRNA qPCR data | 2 | Cell-line mirna | miRNA qPCR data | CTMM TraIT | |
proteomics | Proteomics data | 8 | Cell-line proteomics | Mass-spec proteomics data | CTMM TraIT | |
rnaseq | Illumina GA II | 6 | Illumina | RNAseq data | CTMM TraIT | |
rnaseq | Illumina HiSeq2000 Untreated 1 | 1 | Illumina | RNAseq data | CTMM TraIT | |
rnaseq | Illumina HiSeq2000 Untreated 2 | 1 | Illumina | RNAseq data | CTMM TraIT | |
rnaseq | Illumina HiSeq2000 DMSO control 1 | 1 | Illumina | RNAseq data | CTMM TraIT | |
rnaseq | Illumina HiSeq2000 DMSO control 2 | 1 | Illumina | RNAseq data | CTMM TraIT | |
rnaseq | Illumina HiSeq2000 siNon-Targeting 1 | 1 | Illumina | RNAseq data | CTMM TraIT | |
rnaseq | Illumina HiSeq2000 siNon-Targeting 2 | 1 | Illumina | RNAseq data | CTMM TraIT | |
vcf | Complete genomics DNAseq | 2 | - | Genomic variation data | CTMM TraIT | |
vcf | Illumina GA II RNAseq | 6 | - | Variation data from RNAseq | CTMM TraIT | |
vcf | Illumina HiSeq2000 RNAseq Untreated 1 | 1 | - | Variation data from RNAseq | CTMM TraIT | |
vcf | Illumina HiSeq2000 RNAseq Untreated 2 | 1 | - | Variation data from RNAseq | CTMM TraIT | |
vcf | Illumina HiSeq2000 RNAseq DMSO control 1 | 1 | - | Variation data from RNAseq | CTMM TraIT | |
vcf | Illumina HiSeq2000 RNAseq DMSO control 2 | 1 | - | Variation data from RNAseq | CTMM TraIT | |
vcf | Illumina HiSeq2000 RNAseq siNon-Targeting 1 | 1 | - | Variation data from RNAseq | CTMM TraIT | |
vcf | Illumina HiSeq2000 RNAseq siNon-Targeting 2 | 1 | - | Variation data from RNAseq | CTMM TraIT |
GWAS example data
Contributed by Pfizer
Dataset | Disease | Application | Source | Download |
---|---|---|---|---|
MAGIC_2hrGlucose_AdjustedForBMI | GWAS | Pfizer | SNP Annotations and GWAS Data | |
MAGIC_FastingGlucose | GWAS | Pfizer | ||
MAGIC_ln_FastingInsulin | GWAS | Pfizer | ||
MAGIC_ln_HOMA-B | GWAS | Pfizer | ||
MAGIC_ln_HOMA-IR | GWAS | Pfizer |
Dictionary data
Loaders are available for the most useful dictionaries for searching and linking data in tranSMART.
Some datasets (e.g. KEGG) can only be used with an appropriate license.
The scripts on the test servers use the loader in tranSMART-ETL which has been tested on both Postgres and Oracle.
Dictionary | Description | Source | Load script on test servers | Download |
---|---|---|---|---|
Entrez Gene Info | Entrez gene names and IDs | Imperial | load-entrez.sh | Human and mouse genes |
MeSH | Medline search terms | Imperial | load-mesh.sh | MeSH terms |
KEGG | KEGG Pathways | Imperial | load-kegg.sh | Last public release |
UniProt | UniProt / SwissProt human | Imperial | load-uniprot.sh load-uniprot-sprot.sh | Human swissprot |
MiRBase | MiRBase | Imperial | load-mirbase.sh | MiRBase |
Gene Ontology | Gene Ontology | Imperial | load-go.sh | Gene Ontology |
HMDB | Human metabolite database | Imperial | load-hmdb.sh | HMDB |
Other contributions
Dataset | Disease | Application | Source | Download |
---|---|---|---|---|
Cancer Cell Line Encyclopedia (CCLE) with SNP | Subset of original Study loaded for testing purposes - 30 Subjects out of 947 Subjects. Uploaded Clinical, Gene Expression, RNASEQ-RPKM, and SNP data for 30 Subjects. | Thomson Reuters | ||
VCF Test (VCF Browser needed for functionality testing) | Truncated VCF file for testing, located in the 'Test' Folder in Dataset Explorer | Thomson Reuters | ||
aCGH Data | CTMM TraIT (The Hyve) | |||
RNAseq (Other than Sanofi) | CTMM TraIT (The Hyve) | |||
VCF (Genome Browser needed for functionality testing) | CTMM TraIT (The Hyve) |
Original sources
Rancho Biosciences
Rancho Biosciences provides a selection of studies for testing early tranSMART releases, and have collected and curated all available public studies from the 2015 testathons.
The original Rancho curated studies are at: http://ranchobiosciences.com/free-downloads/
Pfizer GWAS
The tranSMART GWAS code repository has an "External Dep" folder that includes all of the dependencies (DB as well as ETL). README.md has configuration changes.
https://github.com/transmart/transmart-gwas-plugin/tree/pfizer/External%20Dep
Janssen
GSE8581 was one of the three GEO datasets provided by Janssen for early testing. The data is now loaded from transmart-data.
CTMM TraIT - Cell Line use case
CTMM TraIT has brought together a diverse set of data from 6 different cell lines under the Cell Line use case, to test tranSMART on public data without complicated privacy regulations. A detailed tutorial can be found here: Loading data with transmart-data (Cell Line Use Case dataset).
eTRIKS
The eTRIKS project has over 150 curated studies loaded in the public eTRIKS server: https://public.etriks.org/. This includes both clinical and mRNA gene expression data fro GEO studies plus studies from The Cancer Genome Atlas (TCGA) and other sources.
The datasets are curated by the University of Luxembourg eTRIKS partners, and have been made available to the tranSMART community.
Thomson Reuters
For the first public release of tranSMART, Thomson Reuters released 10 curated GEO studies. These studies are now included in the curated set from Rancho Biosciences.
The original curated files in tranSMART-ready format can be downloaded from https://github.com/eugene-rakhmatulin/tMDataSamples
ConvergeHEALTH by Deloitte
For the across trials functionality, ConvergeHEALTH contributed alternative data loading for the following studies for early tranSMART testing.
The original set are available on Github (https://github.com/transmart/tranSMART-ETL/tree/master/V1.2_Hackathon/Data)
- Asthma_Tsitsiou_GSE31773
- Asthma_Woodruff_GSE34466
Test data