title: SecretP: a new method for predicting mammalian secreted proteins.
abstract: In contrast to a large number of classically secreted proteins (CSPs) and non-secreted proteins (NSPs), only a few proteins have been experimentally proved to enter non-classical secretory pathways. So it is difficult to identify non-classically secreted proteins (NCSPs), and no methods are available for distinguishing the three types of proteins simultaneously. In order to solve this problem, a data mining has been taken firstly, and mammalian proteins exported via ER-Golgi-independent pathways are collected through extensive literature searches. In this paper, a support vector machine (SVM)-based ternary classifier named SecretP is proposed to predict mammalian secreted proteins by using pseudo-amino acid composition (PseAA) and five additional features. When distinguishing the three types of proteins, SecretP yielded an accuracy of 88.79%. Evaluating the performance of our method by an independent test set of 92 human proteins, 76 of them are correctly predicted as NCSPs. When performed on another public independent data set, the prediction result of SecretP is comparable to those of other existing computational methods. Therefore, SecretP can be a useful supplementary tool for future secretome studies. The web server SecretP and all supplementary tables listed in this paper are freely available at http://cic.scu.edu.cn/bioinformatics/secretp/index.htm.
authors.affiliation: College of Chemistry, Sichuan University, Chengdu 610064, PR China.
authors.forename: Lezheng
authors.initials: L
authors.lastname: Yu
authors.forename: Yanzhi
authors.initials: Y
authors.lastname: Guo
authors.forename: Zheng
authors.initials: Z
authors.lastname: Zhang
authors.forename: Yizhou
authors.initials: Y
authors.lastname: Li
authors.forename: Menglong
authors.initials: M
authors.lastname: Li
authors.forename: Gongbing
authors.initials: G
authors.lastname: Li
authors.forename: Wenjia
authors.initials: W
authors.lastname: Xiong
authors.forename: Yuhong
authors.initials: Y
authors.lastname: Zeng
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods; D057225:Data Mining / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D008969:Molecular Sequence Data; D021382:Protein Sorting Signals / Q000235:genetics; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
chemical_list: D000596:Amino Acids; D021382:Protein Sorting Signals; D011506:Proteins