The KUPKB: A novel Web application to access multiomics data on kidney disease

Julie Klein, Simon Jupp, Panagiotis Moulos, Myriem Fernandez, Bénédicte Buffin-Meyer, Audrey Casemayou, Rana Chaaya, Aristidis Charonis, Jean Loup Bascands, Robert Stevens, Joost P. Schanstra

    Research output: Contribution to journalArticlepeer-review


    The information gathered from the large number of omics experiments in renal biology is underexplored, as it is scattered over many publications or held in supplemental data. To address this, we have developed an open-source Kidney and Urinary Pathway Knowledge Base (KUPKB) that facilitates simple exploration of these omics data. The KUPKB currently comprises 220 data sets (miRNA, mRNA, proteins, and metabolites) extracted from existing publications or databases. Researchers can explore the integrated data using the iKUP browser, and a simple template is provided to submit new omics data sets to the knowledge base. As an example of iKUP's use, we show how we identified, in silico, calreticulin as a protein induced in human interstitial fibrosis and tubular atrophy (IFTA) in chronic kidney transplant rejection; a link that would have been difficult to establish using existing Web-based tools. Using immunohistochemistry, we validated in vivo this in silico result in human and rat biopsies of IFTA, thus identifying calreticulin as a potential new player in chronic kidney transplant rejection. The KUPKB provides a simple tool that enables users to quickly survey a wide range of omics data sets and has been shown to facilitate rapid hypothesis generation in the context of renal pathophysiology. © FASEB.
    Original languageEnglish
    Pages (from-to)2145-2153
    Number of pages8
    JournalFaseb Journal
    Issue number5
    Publication statusPublished - May 2012


    • Bioinformatics
    • Experimental data
    • Genomics
    • Proteomics
    • Renal pathophysiology


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