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Latest status (

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4 September 2019 - 16:00 UTC)

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

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

TranSMART version

Release 1619.3 0 (built August 2018September 2019)

Database created

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

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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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