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	RanchoGSE15245 EtriksGSE15245	load_all_RanchoGSE15245.sh load_all_EtriksGSE15245.sh
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	RanchoGSE15258 EtriksGSE15258	load_all_RanchoGSE15258.sh load_all_EtriksGSE15258.sh
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 EtriksGSE16879	load_all_RanchoGSE16879.sh load_all_EtriksGSE16879.sh
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	EtriksGSE20314	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	EtriksGSE20333	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	RanchoGSE20690 EtriksGSE20690	load_all_RanchoGSE20690.sh 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	EtriksGSE2125	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	EtriksGSE21537	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	EtriksGSE21959	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	RanchoGSE25066 EtriksGSE25066	load_all_RanchoGSE25066.sh 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	EtriksGSE25160	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	EtriksGSE27390	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	EtriksGSE30355	load_all_EtriksGSE30355.sh
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	EtriksGSE30662	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	EtriksGSE30999	load_all_EtriksGSE30999.sh
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) EtriksGSE31773	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	EtriksGSE32407	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	RanchoGSE32583 EtriksGSE32583	load_all_RanchoGSE32583.sh 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	RanchoGSE32591 EtriksGSE32591	load_all_RanchoGSE32591.sh 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	EtriksGSE33377	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 EtriksGSE3365	load_all_RanchoGSE3365.sh 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	EtriksGSE35642	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	EtriksGSE3592	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	EtriksGSE36757	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	load_all_EtriksGSE36941.sh
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	EtriksGSE4302	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 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)	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	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)	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	EtriksGSE6613	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	load_all_EtriksGSE7074.sh
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	load_all_EtriksGSE7138.sh
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 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)	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	EtriksGSE7621	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	load_all_EtriksGSE8512.sh
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	EtriksGSE9329	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 EtriksGSE9872	load_all_RanchoGSE9872.sh 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	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: 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 ID	Author (Published)	Disease	Description	Source	Datatypes
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

Data Type	Subset	Subjects	Platform	Description	Source
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	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	Application	Source
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

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Curated Datasets

Loading the data

Curated GEO (Gene Expression Omnibus) datasets

Curated TCGA (The Cancer Genome Atlas) datasets

Other curated datasets

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

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

Other Test Datasets

Cell Line Use Case

GWAS example data

Dictionary data

Other contributions

Original sources

Rancho Biosciences

Pfizer GWAS

Janssen

CTMM TraIT - Cell Line use case

eTRIKS

Thomson Reuters

ConvergeHEALTH by Deloitte

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Curated Data Repository

Curated Datasets

Loading the data

Curated GEO (Gene Expression Omnibus) datasets

Curated TCGA (The Cancer Genome Atlas) datasets

Other curated datasets

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

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

Other Test Datasets

Cell Line Use Case

GWAS example data

Dictionary data

Other contributions

Original sources

Rancho Biosciences

Pfizer GWAS

Janssen

CTMM TraIT - Cell Line use case

eTRIKS

Thomson Reuters

ConvergeHEALTH by Deloitte