脂滴表面蛋白质的预测和分类.docVIP

 脂滴表面蛋白质的预测和分类# 董琼叶1，汪小我1，刘平生2，张奇伟1** （1. 生物信息学教育部重点实验室，清华信息国家实验室生物信息学研究部，合成与系统 5 10 15 20 25 30 35 40 生物学研究中心，清华大学自动化系； 2. 中国科学院生物物理研究所） 摘要：脂滴是细胞内用于存储中性脂的场所，由磷脂单层膜包被，其膜表面有多种脂滴表面 的相关蛋白。有研究表明，脂滴表面的相关蛋白与中性脂的代谢密切相关，而脂质代谢的紊 乱会导致多种代谢类疾病。因此，预测脂滴表面蛋白，发现它们共有的关键特征具有重要意 义。在本研究中，我们采用机器学习的方法对脂滴表面的相关蛋白进行了分析：我们从 NCBI 数据库收集了目前已知的 perilipin, ADRP, Oleosin 等六类脂滴表面蛋白的氨基酸序列，提取 了这些蛋白质序列的氨基酸组成和与其物理化学性质相关的伪氨基酸序列等特征；利用支持 向量机的方法，训练出两类分类器来区分脂滴表面的蛋白和定位于其他细胞器的蛋白质，并 对高维的特征向量采用 F-score 的方法进行特征筛选和降维；通过交叉验证表明预测结果的 F-value 均值达到 0.842。 关键词：生物信息学；脂滴表面蛋白质；支持向量机；特征选择 中图分类号：Q734 The prediction and classification of the lipid droplet-surface proteins Dong Qiongye1, Wang Xiaowo1, Liu Pingsheng2, Zhang Q.Michael1 (1. MOE Key Laboratory Bioinformatics, Bioinformatics Division for SyntheticSystems Biology, TNLIST, Department of Automation,Tsinghua University 2. Institute of Biophysics, Chinese Academy of Sciences) Abstract: Lipid droplets are the organelles for storing neutrol lipid in the cell. It is located by the phospholipid monolayer, whose surfaces are associated with different kinds of lipid droplet-surface proteins. Recently, studies have shown that the proteins located on the surface of the lipid body involves in the lipid metabolism, whose disturbance results in many different kinds of metabolic diseases. Up to now, only a small number of lipid droplet surface proteins have been reported, and their common sequence or structure features have not well characterized. In this work, we analyzed the proteins associated with the surface of the lipid droplet using a machine learning method. First, we collected the amino acid sequences of the known lipid body proteins, such as the perilipin, ADRP and Oleosin from NCBI database. secondly, we constructed the feature vectors by using the amino acid composition and the pseudo-amino acid composition based on the physico-chemical features. Then, a binary classifier based on Surpport vector machine was built to predict whether a protein is a lipid droplet s