Page History

...

The server is loaded with data and ready for testing.

We have loaded a set of basic studies and the latest 1619.3 0 war file.

Data Loaded. Details below:

Cell-line use case data is loaded as public data (see table for details) including variant data for VCF and RNAseq
Additional data loaded for eTRIKS Asthma and Rheumatoid Arthritis studies to test studies at lower levels in the tree.

Data in preparation. Details below:

Browse tab data is to be loaded for selected studies using new transmart-data targets. Suggestions on values for "Not applicable" fields - either true values, or useful values for testing filter functionallity - are welcome.
Additional data loaded for eTRIKS Asthma and Rheumatoid Arthritis studies..

Data in preparation. Details below:

GWAS data is in preparation loaded for 5 magic analysis files. SNP data is being loaded for all SNPs in the loaded MAGIC datasets. Gene names have been added where available for each analysis.
VCF data

...

Release 1619.3 0 (built August 2018September 2019)

May 2018 July 2019 - using release 1619.3 0 version of transmart-data

...

Top Level	Disease	Study	Datatypes	Notes
Across Trials
eTRIKS Studies	Asthma	GSE23611	Expression
	Rheumatoid arthritis	GSE10024	Expression
		GSE10500	Expression
Public Studies	Acute Lymphoblastic Leukemia	GSE4698	Expression
		Asthma	GSE34466	clinical only
		GSE13168	Expression
			GSE31773	clinical only
		Brain Cancer	GSE4271	Expression
	Breast Cancer	GSE4922	Expression
				GSE5327	Expression
		GSE1456	Expression
			GSE4382	Expression
		COPD	GSE8581	Expression
		Melanoma Uveal	GSE27831	Expression
		Psoriasis	GSE11903	Expression
		Pulmonary Sarcoidosis	GSE19976	Expression
	Rheumatoid Arthritis	GSE20690	Expression
	TraIT Cell-line	Cell-line	ACGH expression MicroRNA proteomics RNAseq VCF	ACGH data under "High-throughput molecular profiling \ Copy number aberrations" Expression data under "High-throughput molecular profiling \ Expression (mRNA)" ("...array") MicroRNA data under "High-throughput molecular profiling \ Expression (miRNA)" Proteomics under "High-throughput molecular profiling \ Expression (protein)" RNAseq under "High-throughput molecular profiling \ Expression (mRNA)" ("Illumina... RNAseq") VCF under "High-throughput molecular profiling \ Small Variants (DNA)" and "... (RNA)"
	Type 2 Diabetes	GSE38642	Expression
TCGA Studies	Breast Cancer	BRCA	Expression
	Lung Adenocarcinoma	LUAD	Expression
	Ovarian Cancer	OV	Expression
Test Studies V1.3			Test diabetes large	clinical only
		Test mannheim with samples	clinical only
				test mass spec proteomics	MsProteomics
				test merged data types	Expression Metabolomics MsProteomics
				test mRNA microarray	Expression
		test_qPCR_miRNA_GSE37425	miRNA-qPCR

Dictionary	Release	Notes
Entrez gene	Nov 2016	Updates to data loaded with transmart-data
Gene ontology	Nov 2016	Where is this used in tranSMART 16.2?
HMDB	Aug 2015	Human metabolite database
KEGG	Jan 2011	Last pre-subscription release
MeSH	2016	Medline subject headings, diseases
MiRBase	Release 21 Aug 2015	MicroRNA database
UniProt/SwissProt	Nov 2016	Human entries only
Observation	-	Diabetes entry for GWAS
VCF	dbSNP 146	SNP data for GWAS MAGIC datasets

...

Space shortcuts