building disease-specific drug-protein connectivity maps from molecular interaction networks and pubmed abstracts建立针对疾病的药物连接的地图从分子间相互作用网络和pubmed抽象.pdf

Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts 1,3 1 2,3,4 Jiao Li , Xiaoyan Zhu , Jake Yue Chen * 1 State Key Laboratory of Intelligent Technology and Systems, Tsinghua National Laboratory for Information Science and Technology, Department of Computer Science and Technology, Tsinghua University, Beijing, China, 2 School of Informatics, Indiana University, Indianapolis, Indiana, United States of America, 3 Department of Computer Information Science, School of Science, Purdue University, Indianapolis, Indiana, United States of America, 4 Indiana Center for Systems Biology and Personalized Medicine, Indiana University–Purdue University, Indianapolis, Indiana, United States of America Abstract The recently proposed concept of molecular connectivity maps enables researchers to integrate experimental measurements of genes, proteins, metabolites, and drug compounds under similar biological conditions. The study of these maps provides opportunities for future toxicogenomics and drug discovery applications. We developed a computational framework to build disease-specific drug-protein connectivity maps. We integrated gene/protein and drug connectivity information based on protein interaction networks and literature mining, without requiring gene expression profile information derived from drug perturbation experiments on disease samples. We described the development and application of this computational framework using Alzheimer’s Disease (AD) as a primary example in three steps. First, molecular interaction networks were incorporated to reduce bias and improve relevance of AD seed prot