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.

工作包7（WP7）的核心目标是通过整合多类大规模数据源，构建罕见肾病的多尺度研究视角。WP2至WP6产生的数据、合作联盟提供的数据以及公开数据集，均将被纳入EURenOmics平台。欧洲肾脏cDNA库（European Renal cDNA Bank，ERCB）馆藏超过2600份带有匿名化临床参数的肾脏活检样本。该联盟已从289例患者的肾小球及肾小管间质标本中，生成550余套基于Affymetrix平台的全基因组数据集。在此基础上，研究团队筛选出包含369份样本（其中183份为肾小球样本、186份为肾小管间质样本）及其基础临床信息的数据集，将其整合至EURenOmics数据库。该数据集涵盖微小病变肾病（n=24）、局灶节段性肾小球硬化（n=47）、膜性肾病（n=39）患者的数据，同时还纳入糖尿病肾病（n=11）、高血压肾病（n=35）、IgA肾病（n=52）及狼疮性肾炎（n=64）患者的相关数据。研究以活体供肾者的移植前活检样本作为对照（n=84）。另一项转录组学数据资源为Nephromine数据库（http://nephromine.org），该平台是一款基于网页的肾脏特异性系统生物学搜索引擎，整合了20套公开基因表达数据集的1757份样本（包含小鼠及人类样本）的数据，纳入临床信息并支持多种分析功能，包括差异基因表达分析、共表达分析、异常值分析及概念关联分析。团队已确立基础数据库架构，并搭建了基于网页的功能型数据存储库，支持便捷的数据上传与下载，同时可实现合作方间的数据共享。上传的数据将用于构建多级分析域（EuRenOmics数据库），该分析域可整合不同组学平台的数据，并纳入临床信息。该交互式平台提供标准化与规范化的数据集，并采用Genomatix公司的GePS及ElDorado数据库的现有架构。该搜索引擎将打造核心生物信息学平台，可在系统生物学层面应对肾脏疾病的机制研究、诊断及治疗相关挑战。

搜集汇总

背景与挑战

背景概述

ERCB-Nephromine-EuRenOmics Database是一个整合了多种肾脏疾病相关数据的资源，包含369个样本的临床和转录组数据，旨在通过多尺度分析推动罕见肾脏疾病的研究。数据集还整合了Nephromine的公开数据，提供了一个功能强大的生物信息学平台。