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Latest status (16 August 2018 - 12:00 UTC)

The server is loaded with data and ready for testing.

We have loaded a set of basic studies and the latest 16.3 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
  • Browse tab data is loaded for selected studies. 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

Known Issues

See JIRA

Server address

http://postgres-test.transmartfoundation.org/transmart 

TranSMART version

Release 16.3 (built August 2018)

Database created

May 2018 - using release 16.3 version of transmart-data

Studies loaded

GWAS data loading is in preparation

Top LevelDiseaseStudyDatatypesNotes
 Across Trials    
eTRIKS Studies AsthmaGSE23611Expression 
  Rheumatoid arthritisGSE10024Expression 
  GSE10500Expression 
Public StudiesAcute Lymphoblastic LeukemiaGSE4698Expression  
 AsthmaGSE34466 clinical only  
  GSE13168Expression  
  GSE31773 clinical only  
 Brain CancerGSE4271Expression 
 Breast Cancer GSE4922 Expression  
  GSE5327 Expression  
  GSE1456 Expression  
  GSE4382Expression 
 COPD GSE8581Expression 
 Melanoma UvealGSE27831Expression  
 PsoriasisGSE11903Expression  
 Pulmonary SarcoidosisGSE19976Expression 
 Rheumatoid ArthritisGSE20690 Expression 

TraIT Cell-lineCell-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 DiabetesGSE38642 Expression  
TCGA StudiesBreast CancerBRCAExpression

Lung AdenocarcinomaLUADExpression

Ovarian CancerOVExpression
Test Studies V1.3 Test diabetes largeclinical only
  Test mannheim with samples clinical only 
  test mass spec proteomics MsProteomics  
  test merged data typesExpression Metabolomics MsProteomics 
  test mRNA microarrayExpression 
  test_qPCR_miRNA_GSE37425miRNA-qPCR 

 Dictionaries loaded

DictionaryReleaseNotes
Entrez geneNov 2016Updates to data loaded with transmart-data
Gene ontologyNov 2016Where is this used in tranSMART 16.2?

HMDB

Aug 2015Human metabolite database
KEGGJan 2011Last pre-subscription release
MeSH2016Medline subject headings, diseases
MiRBase

Release 21

Aug 2015

MicroRNA database
UniProt/SwissProt Nov 2016Human entries only 
Observation-Diabetes entry for GWAS
VCFdbSNP 146SNP data for GWAS MAGIC datasets
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