Data Services
DZD Research Data Platform
The DZD has an extensive amount of clinical data and biosamples for medical research purposes.
The DZD has developed a research data platform for customized storage, processing and provision of clinical data. This platform also offers DZD researchers standardized services for communication, information and secure data exchange. Specific examples are:
- Services for cross-source and trans-study reuse of DZD studies through harmonization and pseudonymization of data
- Services for accessing centrally provided medical data in compliance with data privacy
- Services for secure data exchange among DZD researchers
- Information services (wikis) and collaboration services for researchers and other user groups such as junior scientistsSpecial online tools for the public use of research applications developed at the DZD or for data collection in DZD clinical studies
The DZD research data platform has a modular structure and was largely developed on the basis of open source software. Software developed at the DZD is also made available as open source software wherever possible.
These infrastructures and the data services they provide are described in detail in the DZD Data Privacy Concept (German only).
DZD Online Research Tools
The DZD provides research applications as web services wherever possible to ensure they are easily accessible. The examples described below are available for public use on the Internet.
metaKEGG
metaKEGG is a software for the integration of (multi-)omics data with pathway enrichment analyses. It enables the detailed visualization of differentially expressed genes and transcripts on KEGG pathway maps, including epigenetic data such as DNA methylation and miRNA.
metaKEGG uses various analysis pipelines to provide comprehensive insights into signaling pathways and facilitates direct comparison of different conditions or interventions. A special function is the division of KEGG nodes into subnodes, allowing several genes or transcripts to be displayed per node. In addition, a color-coded display of the log₂FC values facilitates intuitive analysis and direct comparison of biological processes.
miR-QTL-Scan
A system that combines information on QTL, miRNA target genes and corresponding mRNA expression data to identify miRNAs as regulatory elements and factors responsible for QTL. The system provides both theoretical determination of miRNA target genes and experimentally confirmed interactions in three metabolically active tissues – gonadal white adipose tissue (gWAT), brown adipose tissue (BAT) and muscle. In total, data on 170 miRNAs are provided, which are localized in the respective QTL regions. For the functional classification of individual miRNAs, pathway analyses based on KEGG Pathways and Gene Ontology are also available for the corresponding target genes.
Created by Pascal Gottmann at the DIfE.
Original publication:
Gottmann, P. et al. Molecular Metabolism (2018) A computational biology approach of a genome-wide screen connected miRNAs to obesity and type 2 diabetes. PMID:29605715 PMCID:PMC6001404 DOI:10.1016/j.molmet.2018.03.005
Collaborative Diabetes Cross
This tool is based on genome-wide linkage analyses of crossbred populations of obese, diabetes-prone NZO mice and four different lean inbred strains (B6,C3H,DBA,129P2). This allowed to identify more than 290 quantitative trait loci (QTL) for obesity, 190 QTL for diabetes and 100 QTL for plasma metabolites. The results are shown in diagrams, and genes within the QTL regions can be exported for further analysis.
Created by Lisa Zellner and Markus Jähnert at the DIfE.
Original publication:
Vogel, H. et al. Human Molecular Genetics (2018) A collective diabetes cross in combination with a computational framework to dissect the genetics of human obesity and Type 2 diabetes. PMID:29893858 PMCID:PMC6097155 DOI:10.1093/hmg/ddy217
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