ERCB-Nephromine-EuRenOmics Database

The main goal of WP7 is to develop a multiscalar view of rare renal diseases by integrating diverse large-scale data sources. Data generated in WP 2-6 as well as data from cooperating consortia and publically available datasets will be implemented in the EURenOmics platform. The European Renal cDNA Bank (ERCB) hosts over 2600 renal biopsies with anonymized clinical parameters. In this consortium more than 550 genome-wide Affymetrix-based datasets from glomerular and tubulointerstitial specimen from 289 patients have been generated. Out of these, a dataset comprising of 369 samples (183 glomerular, 186 tubulointerstitial) and their basic clinical data has been selected to be integrated in the EURenOmics database. These include data from patients with minimal change disease (n=24), focal segmental glomerulosclerosis (n=47), membranous nephropathy (n=39), but also data from patients with diabetic nephropathy (n=11), hypertensive nephropathy (n=35), IgA nephropathy (n=52) and lupus nephritis (n=64). Pretransplant biopsies from living donors were used as controls (n=84). Another resource for transcriptomic data is Nephromine (http://nephromine.org). It is a web-based kidney specific systems biology search engine that provides data from 20 publically available gene expression datasets from 1757 samples (murine and human), incorporates clinical data and allows various analyses (differential gene expression, coexpression, outlier analysis and concept association). A basic database concept has been defined and a web-based functional data repository allowing a smooth up-and download as well as sharing data amongst partners has been generated. Uploaded data will be used to establish a multilevel analysis domain (EuRenOmics Database), which allows the integration of data from different –omics platforms as well as the implementation of clinical information. The interactive platform provides standardized and harmonized datasets and uses existing architectures from Genomatix’s GePS and ElDorado databases. This search engine will provide a central bioinformatics platform which allows addressing mechanistic, diagnostic and therapeutic challenges at the systems biology level.