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QSAR modeling of E. coli promoters with parameters selected by binary matrix shuffling filter

文献类型： 外文期刊

作者： Wang, Kai 2 ; Wang, Li-Feng 1 ; Dai, Zhi-Jun 1 ; Bai, Lian-Yang 3 ; Yuan, Zhe-Ming 1 ;

作者机构： 1.Hunan Prov Key Lab Crop Germplasm Innovat & Utili, Changsha 410128, Hunan, Peoples R China

2.Hunan Prov Key Lab Biol & Control Plant Dis & Ins, Changsha 410128, Hunan, Peoples R China

3.Hunan Acad Agr Sci, Changsha 410125, Hunan, Peoples R China

关键词： Quantitative sequence-activity model;feature selection;support vector regression;promoter

期刊名称：JOURNAL OF THE INDIAN CHEMICAL SOCIETY （ 影响因子：0.284； ）

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收录情况： SCI

摘要： The 1123 topological structure parameters of DNA bases were directly used as descriptors to characterize the sequence of 38 E. coli promoters. For the correspondingly generated high-dimensional feature set, the correlation analysis and binary matrix shuffling filter (BMSF) were successively used to remove the redundancy or useless features, and only 20 features were finally reserved, with definite meanings. Based on reserved features and support vector regression (SVR), a quantitative structure-activity relationship (QSAR) model was established for the analysis of 38 E. coli promoters, and the leave-one-out (LOO) prediction accuracy of this model was of 0.838, superior to that of reference model, i.e. partial least squares (PLS). Referring to the SVR interpretation system, the established QSAR model in this work has extremely significant nonlinear regression, and the relationship between real promoter strength and 11 significant reserved features was directly given out. This work provides an efficient tool for the QSAR analysis of promoters and other similar molecular sequences.

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[2]Quantitative Sequence- Activity Model Analysis of Oligopeptides Coupling an Improved High- Dimension Feature Selection Method with Support Vector Regression. Dai, Zhijun,Zhang, Hongyan,Yuan, Zheming,Wang, Lifeng,Dai, Zhijun,Zhang, Hongyan,Bai, Lianyang,Yuan, Zheming,Bai, Lianyang. 2014

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