Identification of Protein Complexes by Using a Spatial and Temporal Active Protein Interaction Network

计算机科学 鉴定(生物学) 功能(生物学) 聚类分析 基因本体论 计算生物学 数据挖掘 系统生物学 交互网络 生物网络 人工智能 基因 生物 遗传学 基因表达 植物
作者
Min Li,Xiangmao Meng,Ruiqing Zheng,Fang‐Xiang Wu,Yaohang Li,Yi Pan,Jianxin Wang
出处
期刊:IEEE/ACM Transactions on Computational Biology and Bioinformatics [Institute of Electrical and Electronics Engineers]
卷期号:17 (3): 817-827 被引量:26
标识
DOI:10.1109/tcbb.2017.2749571
摘要

The rapid development of proteomics and high-throughput technologies has produced a large amount of Protein-Protein Interaction (PPI) data, which makes it possible for considering dynamic properties of protein interaction networks (PINs) instead of static properties. Identification of protein complexes from dynamic PINs becomes a vital scientific problem for understanding cellular life in the post genome era. Up to now, plenty of models or methods have been proposed for the construction of dynamic PINs to identify protein complexes. However, most of the constructed dynamic PINs just focus on the temporal dynamic information and thus overlook the spatial dynamic information of the complex biological systems. To address the limitation of the existing dynamic PIN analysis approaches, in this paper, we propose a new model-based scheme for the construction of the Spatial and Temporal Active Protein Interaction Network (ST-APIN) by integrating time-course gene expression data and subcellular location information. To evaluate the efficiency of ST-APIN, the commonly used classical clustering algorithm MCL is adopted to identify protein complexes from ST-APIN and the other three dynamic PINs, NF-APIN, DPIN, and TC-PIN. The experimental results show that, the performance of MCL on ST-APIN outperforms those on the other three dynamic PINs in terms of matching with known complexes, sensitivity, specificity, and f-measure. Furthermore, we evaluate the identified protein complexes by Gene Ontology (GO) function enrichment analysis. The validation shows that the identified protein complexes from ST-APIN are more biologically significant. This study provides a general paradigm for constructing the ST-APINs, which is essential for further understanding of molecular systems and the biomedical mechanism of complex diseases.
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