Construction of Protein Phosphorylation Network Based on Boolean Network Methods Using Proteomics Data
Post-translational Modification (PTM) of Proteins is a key biological process in the regulation of protein function. This paper discusses the problem of construction of PTM network based on the reverse engineering principles, which is constructed by using
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School of Information Science and Engineering, University of Jinan, Jinan 250022, China [email protected], [email protected] Shandong Provincial Key Laboratory of Network Based Intelligent Computing, Jinan 250022, China 3 School of Biological Science and Technology, University of Jinan, Jinan 250022, China [email protected]
Abstract. Post-translational Modification (PTM) of Proteins is a key biological process in the regulation of protein function. This paper discusses the problem of construction of PTM network based on the reverse engineering principles, which is constructed by using PBIL and TDE algorithms. Experiments which are based on two well-known pathways by the time series data of protein phosphorylation data show that the new method can be successfully validated and further reveal the regulation of protein phosphorylation. Keywords: PTM PBIL TDE
Computational intelligence
Phosphorylation network
1 Introduction Post-translational Modification (PTM) of Proteins plays a key role in many biological processes. PTM could alter protein structure, activity, stability and interaction with other molecule. With the development of modern biological mass spectrometry technology, the high-throughput screening and quantitative analysis of PTM have been greatly facilitated, and the detection sensitivity has been greatly improved [1]. Currently, nearly 400 kinds of PTM such as ubiquitination, methylation, nitration, and other similar things have been found. Of those, there are more than 300 kinds of PTM of proteins is widely involved in many life activities [2]. However, it is very likely to cause disease, once the abnormal PTM of proteins. Phosphorylation of a protein may lead to activation or repression of its activity, alternative subcellular localization and interaction with different binding partners [3]. Through damaging the functions of kinases and phosphatases, some signaling pathways of normal biological processes may be changed and cause many diseases. Recently, with deep learning, ‘networks’ has emerged as a hotspot that takes into consideration both key genes/proteins and their relationship with specific modules, © Springer International Publishing Switzerland 2016 D.-S. Huang et al. (Eds.): ICIC 2016, Part I, LNCS 9771, pp. 268–277, 2016. DOI: 10.1007/978-3-319-42291-6_26
Construction of Protein Phosphorylation Network
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pathway and processes [4]. There is a wealth of experimental data through proteomics methods. However, the data analysis methods are not perfect and this has brought about great challenges. In addition, how to construct PTM networks, analyze its spatialtemporal variance and the influence to the outside environment, is still a problem. In this research, we construct a phosphorylation network based on Boolean network method with PBIL and TDE algorithm, to discover and explore the regulation of protein phosphorylation.
2 Methods 2.1
Boolean Network Model
Boolean network consists of N Boolean variables, and each variable is defined as a binary number to describe their states
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