Department of Plant Biology, Southern Illinois University Carbondale, 1125 Lincoln Ave,, Life Science II, Carbondale, IL 62901-6509, USA.
Rice (N Y). 2012 Jul 2;5(1):15. doi: 10.1186/1939-8433-5-15.
Protein-protein interactions (PPIs) create the steps in signaling and regulatory networks central to most fundamental biological processes. It is possible to predict these interactions by making use of experimentally determined orthologous interactions in other species.
In this study, prediction of PPIs in rice was carried out by the interolog method of mapping deduced orthologous genes to protein interactions supported by experimental evidence from reference organisms. We predicted 37112 interactions for 4567 rice proteins, including 1671 predicted self interactions (homo-interactions) and 35441 predicted interactions between different proteins (hetero-interactions). These matched 168 of 675 experimentally-determined interactions in rice. Interacting proteins were significantly more co-expressed than expected by chance, which is typical of experimentally-determined interactomes. The rice interacting proteins were divided topologically into 981 free ends (proteins with single interactions), 499 pipes (proteins with two interactions) and 3087 hubs of different sizes ranging from three to more than 100 interactions.
This predicted rice interactome extends known pathways and improves functional annotation of unknown rice proteins and networks in rice, and is easily explored with software tools presented here.
蛋白质-蛋白质相互作用 (PPIs) 构成了信号转导和调控网络的步骤，这些网络是大多数基本生物过程的核心。通过利用其他物种中实验确定的同源相互作用，可以预测这些相互作用。
在这项研究中，通过同源基因映射的互作方法，利用来自参考生物的实验证据，预测了水稻中的蛋白质-蛋白质相互作用。我们预测了 4567 个水稻蛋白中的 37112 个相互作用，包括 1671 个预测的自相互作用（同型相互作用）和 35441 个不同蛋白之间的预测相互作用（异型相互作用）。这些预测与水稻中 675 个实验确定的相互作用中的 168 个相匹配。相互作用的蛋白质比随机预期的更具共表达性，这是实验确定的相互作用组的典型特征。水稻相互作用的蛋白质在拓扑上分为 981 个自由端（具有单个相互作用的蛋白质）、499 个管（具有两个相互作用的蛋白质）和 3087 个大小不同的枢纽，范围从三个到 100 多个相互作用。
这个预测的水稻相互作用组扩展了已知的途径，并改善了未知的水稻蛋白和网络的功能注释，并且可以使用这里提供的软件工具轻松探索。
