蛋白质相互作用网络功能模块检测的研究综述

冀俊忠; 刘志军; 刘红欣; 刘椿年

doi:10.3724/SP.J.1004.2014.00577

蛋白质相互作用网络功能模块检测的研究综述

doi: 10.3724/SP.J.1004.2014.00577

1.
北京工业大学计算机学院多媒体与智能软件技术北京市重点实验室北京 100124

基金项目:

国家重点基础研究发展计划（973计划）（2014CB744601），国家自然科学基金（61375059，61332016），教育部博士点学科专项科研博导类基金（20121103110031），北京市教委科研计划重点项目（北京市自然科学基金重点B类项目）（KZ201410005004）资助

详细信息

作者简介:
刘志军北京工业大学硕士研究生.主要研究方向为机器学习，生物数据挖掘.E-mail：lzhj@emails.bjut.edu.cn

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出版历程
- 收稿日期: 2013-01-05
- 修回日期: 2013-05-07
- 刊出日期: 2014-04-20

An Overview of Research on Functional Module Detection for Protein-protein Interaction Networks

1.
Beijing Municipal Key Laboratory of Multimedia and Intelligent Software Technology, College of Computer Science and Technology, Beijing University of Technology, Beijing 100124

Funds:

Supported by National Basic Research Program of China (973 Program）（2014CB744601), National Natural Science Foundation of China (61375059, 61332016), Specialized Research Fund for the Doctoral Program of Higher Education (201211031100 31), and the Beijing Municipal Education Research Plan Key Project (Beijing Municipal Fund Class B）（KZ201410005004)

摘要

摘要: 蛋白质相互作用（Protein-protein interaction，PPI）网络是生命活动中一种极其重要的生物分子关系网络，利用计算方法从PPI网络中检测功能模块是目前生物信息学中一项重要的研究课题. 本文首先总结了功能模块检测过程的基本流程，说明了预处理和后处理的作用；其次，提出了一种模块检测方法的分类体系，并对其中一些代表性的检测算法进行了阐述；再次，给出了模块检测常用的数据库、评价指标和相关软件工具，并通过实验对代表性算法进行了性能对比. 最后，通过对该领域挑战性问题的分析预测了模块检测未来的研究方向，以期对相关研究提供一定的参考.
- 蛋白质相互作用网络 /
- 功能模块检测 /
- 检测流程 /
- 分类体系 /
- 性能对比
Abstract: As a bimolecular relationship network, the protein-protein interaction (PPI) network plays an important role in biological activities. Using computational approaches, mining functional modules from a PPI network is currently a challenge in bioinformatics. This paper firstly gives a workflow of detecting functional modules from PPI data, and illustrates the effects of preprocessing and post processing. Next, a systematic category of functional module detection is proposed, and many typical detecting algorithms in each category are described. And then, the paper lists some public databases, evaluating metrics, related software tools, and experimentally compares and analyzes the performances of some representative algorithms on the same data. Finally, the existing problems and prospects in this field are presented, which offers some references for researchers engaged in PPI network analyzing.
- Protein-protein interaction (PPI) network /
- functional module detection /
- detection process /
- classification system /
- performance comparisons

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