Functional Annotation of Protein Interactome Graphs

我们的项目旨在通过不同生物之间的系统比较来了解代谢紊乱，如糖尿病和胰岛素抵抗，因为代谢途径在物种之间高度保守。 创建二分图需要不同生物分子及其反应的数据库。在将生物分子数据整合到数据库中之后，需要进行酶-底物、蛋白质-蛋白质和辅因子-酶反应。目前，我们的信息来源是基因和基因组的京都百科全书（KEGG）。由于生物数据源发展迅速，新的数据源经常出现，可扩展性对程序的数据结构至关重要。 因此，我们决定创建自己的XML模式来存储数据。 客户端-服务器软件设计实现了浏览器嵌入式软件设计难以实现的功能。此外，模块化的设计是可扩展的，以便其他科学家能够轻松地将功能/数据添加到现有的数据结构中。 该软件主要设计用于数据库和显示人的相互作用在一个二分的方式。然而，目前正在将其他功能设计到程序结构中。这些能力包括： (1)显示从一个分子（化合物或蛋白质）到另一个分子的一系列反应（最短路径或其他）的能力， (2)在常数（分子浓度或反应动力学）扰动时证明信号沿着路径传播的能力， (3)选择性地创建推定反应作为正常相互作用组数据集的一部分的能力，以及 (4)能够对不同生物体之间的途径进行系统比较，以便在数学模型构建中利用不同生物体的实验数据。

Our project aims at understanding metabolic disorders such as diabetes and insulin resistence by means of a phyletic comparison between different organisms since metabolic pathways are highly conserved between species. Creating the bipartite graph requires a database of the different biomolecules and their reactions. After integrating biomolecule data into the database, enzyme-substrate, protein-protein, and cofactor-enzyme reactions are required. Currently, our source for this information is the Kyoto Encyclopedia of Genes and Genomes (KEGG). Since biological data sources develop rapidly and new data sources appear very often, extensibility is extremely important to the data structure of the program. We therefore decided to create our own XML schema to store the data. A client-server software design enables features that would be hard to do otherwise with a browser-embedded software design. Additionally, the modular design was adapted to be extensible so that other scientists are able to add features/data to the existing data structure with ease. The software is designed primarily to database and display the human interactome in a bipartite manner. Additional capabilities however, are also currently being designed into the program structure. Some of these abilities are: (1) The ability to display a series of reaction (shortest path or otherwise) from one molecule (either a compound or protein), to another molecule, (2) The ability to demonstrate a signals propagation along a pathway upon perturbation of a constant (either a molecular concentration or reaction kinetic), (3) The ability to selectively create putative reactions as part of the normal interactome dataset, and (4) The ability to do a phyletic comparison of pathways between different organisms to enable the utilization of experimental data from different organisms in mathematical model building.