Malick Rauf Ahmed Shams, Munir Siraj, Jami Syed Imran, Rauf Shoaib, Ferretti Stefano, Cherifi Hocine
Department of Computer Science, National University of Computer and Emerging Sciences, Karachi, Pakistan.
Department of Applied and Pure Sciences, University of Urbino Carlo Bo, Urbino, Italy.
Data Brief. 2024 Jan 3;52:110003. doi: 10.1016/j.dib.2023.110003. eCollection 2024 Feb.
Diabetes has emerged as a prevalent disease, affecting millions of individuals annually according to statistics. Numerous studies have delved into identifying key genes implicated in the causal mechanisms of diabetes. This paper specifically concentrates on 20 functional genes identified in various studies contributing to the complexities associated with Type 2 diabetes (T2D), encompassing complications such as nephropathy, retinopathy, cardiovascular disorders, and foot ulcers. These functional genes serve as a foundation for identifying regulatory genes, their regulators, and protein-protein interactions. The current study introduces a multi-layer Knowledge Graph (DbKB based on MSNMD: Multi-Scale Network Model for Diabetes), encompassing biological networks such as gene regulatory networks and protein-protein interaction networks. This Knowledge Graph facilitates the visualization and querying of inherent relationships between biological networks associated with diabetes, enabling the retrieval of regulatory genes, functional genes, interacting proteins, and their relationships. Through the integration of biologically relevant genetic, molecular, and regulatory information, we can scrutinize interactions among T2D candidate genes [1] and ascertain diseased genes [2]. The first layer of regulators comprises direct regulators to the functional genes, sourced from the TRRUST database in the human transcription factors dataset, thereby forming a multi-layered directed graph. A comprehensive exploration of these direct regulators reveals a total of 875 regulatory transcription factors, constituting the initial layer of regulating transcription factors. Moving to the second layer, we identify 550 regulatory genes. These functional genes engage with other proteins to form complexes, exhibiting specific functions. Leveraging these layers, we construct a Knowledge Graph aimed at identifying interaction-driven sub-networks involving (i) regulating functional genes, (ii) functional genes, and (iii) protein-protein interactions.
糖尿病已成为一种普遍存在的疾病,据统计每年影响数百万人。众多研究致力于确定与糖尿病致病机制相关的关键基因。本文特别关注在各种研究中确定的20个功能基因,这些基因导致了与2型糖尿病(T2D)相关的复杂性,包括肾病、视网膜病变、心血管疾病和足部溃疡等并发症。这些功能基因为识别调控基因、其调节因子以及蛋白质 - 蛋白质相互作用奠定了基础。当前的研究引入了一个多层知识图谱(基于MSNMD的糖尿病知识库:糖尿病多尺度网络模型),其中包含基因调控网络和蛋白质 - 蛋白质相互作用网络等生物网络。这个知识图谱有助于可视化和查询与糖尿病相关的生物网络之间的内在关系,从而能够检索调控基因、功能基因、相互作用的蛋白质及其关系。通过整合生物学相关的遗传、分子和调控信息,我们可以仔细研究T2D候选基因之间的相互作用[1]并确定患病基因[2]。第一层调节因子包括功能基因的直接调节因子,其来源于人类转录因子数据集中的TRRUST数据库,从而形成一个多层有向图。对这些直接调节因子的全面探索揭示了总共875个调控转录因子,构成了调控转录因子的初始层。进入第二层,我们确定了550个调控基因。这些功能基因与其他蛋白质相互作用形成复合物,表现出特定功能。利用这些层次,我们构建了一个知识图谱,旨在识别涉及(i)调节功能基因、(ii)功能基因和(iii)蛋白质 - 蛋白质相互作用的相互作用驱动的子网。