INSERM U1048, Institut of Cardiovascular and Metabolic Disease, 1 Avenue Jean Poulhes, Toulouse Cedex 4, 31432, France.
FASEB J. 2012 May;26(5):2145-53. doi: 10.1096/fj.11-194381. Epub 2012 Feb 17.
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.
从大量肾脏生物学组学实验中收集到的信息尚未得到充分利用，因为这些信息分散在许多出版物或补充数据中。为了解决这个问题，我们开发了一个开源的肾脏和尿路知识库（KUPKB），它可以方便地探索这些组学数据。KUPKB 目前包含 220 个数据集（miRNA、mRNA、蛋白质和代谢物），这些数据集是从现有出版物或数据库中提取的。研究人员可以使用 iKUP 浏览器探索整合数据，并且提供了一个简单的模板，用于将新的组学数据集提交到知识库中。作为 iKUP 使用的一个示例，我们展示了如何使用计算方法识别钙网蛋白是慢性肾移植排斥反应中人类间质纤维化和肾小管萎缩（IFTA）中的一种诱导蛋白；如果使用现有的基于网络的工具，这个联系将很难建立。通过免疫组织化学，我们在人类和大鼠 IFTA 活检中验证了这个计算结果，从而鉴定钙网蛋白是慢性肾移植排斥反应中的一个潜在新角色。KUPKB 提供了一个简单的工具，使用户能够快速调查广泛的组学数据集，并已被证明在肾脏病理生理学背景下有助于快速产生假说。
