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George M. O’Brien Kidney Resource Alliance (OKRA)
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University Michigan The George M. O'Brien Michigan Kidney Translational Core Center (MKTC)


Summary

The George M. O’Brien Michigan Kidney Translational Core Center (MKTC) was established to assist investigators and clinicians worldwide in kidney disease research. Their core objective is to enable muti-omic multi-scalar data integration. MKTC consists of two Biomedical Cores: The Applied Systems Biology Core (ASBC) and Data Analytics Services Core (DASC). They provide specialized core services as well as user-friendly tools to enable kidney researchers and trainees to apply to their work.

Applied Systems Biology Core (ASBC)

  • Description

    The Applied Systems Biology Core (ASBC) primary role is to empower national kidney researchers to analyze, integrate and extract pertinent knowledge from multi-omic datasets (genetic, transcriptomic, epigenomic, metabolomic, proteomic data) from model systems and human studies in support of their individual research needs.

  • Services
    • Interactive, shared data mining services
      • ASBC will provide initial study design consultation and assist with developing customized workflow for integrative analysis for projects of individual investigators
      • Clinical and molecular interactions in investigators’ data sets
      • Quantitative morphometric analyses of kidney biopsy samples
      • Model systems studies to identify pathways shared cross-species
      • Structured RNA-DNA sequence data integration
    • Standardized workflows of recurrent service elements
      • Transcript driven data-mining workflow
        • Single cell RNA Sequencing analysis pipeline
        • Streamlined self-organizing map (SOM) to identify functional subgroups
        • Weighted Correlation Network Analysis (WGCNA) to identify co-expressed molecular elements within datasets
      • Metabolomics driven analysis workflow
        • Platform specific data processing, data normalization, identification of differentially expressed metabolites
      • Multi-scalar data analysis and integration
        • Integration of different combinations of available clinical phenotype, morphology, genetic, epigenomic, transcriptomic, proteomic, metabolomic datasets.
        • Building models for classification or statistical association purposes
        • pathway mapping and enrichment analysis
        • clinical and molecular interactions in investigators’ data sets
        • Multi-omic data integration to identify biomarkers and regulatory networks
        • Metscape applications

Data Analytic Services Core (DASC)

  • Description

    The Data Analytic Services Core (DASC) provides access to unique sets of data through distinct data analysis platforms. The database is updated quarterly to provide investigators with quick and easy access to all the data being generated as part of the Center and their web portals include sophisticated and user-friendly analytic tools that allow for mining of these datasets.

  • Services
    • Access, training, and support for data exploration with user-friendly web-based analysis tools
      • Nephroseq
        • A fully automated web-based systems biology search engine for context specific renal disease gene expression and data mining
      • TranSMART
        • An open-source platform that allows user-specified exploration of cohort study datasets to researchers
        • A new tranSMART custom configuration for the CPROBE and multiple other cohort studies, including NEPTUNE, H3Africa, M2C2, CPROBE, CRIC and CureGN networks
      • CELLxGENE and Vitessce
        • Single cell and spatial data mining instances for murine and human kidney disease data sets adapted by the DASC for the kidney investigative community

    • Investigating biomarker association (gene, protein, metabolite level) in clinical existing cohorts such as C-PROBE through TranSMART instance (in collaboration with the primary study investigators)

    • Developing generalized workflow for integrative web-based analysis

Contact Information

If you would like more information regarding services provided by MKTC, please contact:

Wenjun Ju
This email address is being protected from spambots. You need JavaScript enabled to view it.
Website

 

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