T2D@ZJU: a knowledgebase integrating heterogeneous connections associated with type 2 diabetes mellitus

Abstract

Type 2 diabetes mellitus (T2D), affecting >90% of the diabetic patients, is one of the major threats to human health. A comprehensive understanding of the mechanisms of T2D at molecular level is essential to facilitate the related translational research. Here, we introduce a comprehensive and up-to-date knowledgebase for T2D, i.e. T2D@ZJU. T2D@ZJU contains three levels of heterogeneous connections associated with T2D, which is retrieved from pathway databases, protein-protein interaction databases and literature, respectively. In current release, T2D@ZJU contains 1078 T2D related entities such as proteins, protein complexes, drugs and others together with their corresponding relationships, which include 3069 manually curated connections, 14,893 protein-protein interactions and 26,716 relationships identified by text-mining technology. Moreover, T2D@ZJU provides a user-friendly web interface for users to browse and search data. A Cytoscape Web-based interactive network browser is available to visualize the corresponding network relationships between T2D-related entities. The functionality of T2D@ZJU is shown by means of several case studies. Database URL: http://tcm.zju.edu.cn/t2d.

Figure 1.

Overview of the T2D@ZJU, which is composed of three data sets, i.e. CDC data set, PPI data set and TMR data set.

Figure 2.

The T2D network constructed on the basis of CDC data set. In the network, blue circle, round rectangle, purple diamond and red triangle represented protein, protein complex, small molecule and drug, respectively.

Figure 3.

Graphical summary of the main functions of theT2D@ZJU web interface.

Figure 4.

The outcome of the search with ‘SOCS3’ as the query keyword.

Figure 5.

The extending of HMGA1 with PPI and TMR data sets. The yellow edges represented relationships derived from PPI data set, whereas the pink represented relationships from TMR data set.

Figure 6.

Visualization of transcriptomics data on the T2D network. (A) The gene expression status of the T2D network. (B) The expression of genes involved in citrate cycle. The fold changes of the gene expression were depicted by colors, as indicated by the bar. The networks were constructed in Cytoscape.