Analysis of Metabolic Pathway Using Hybrid Properties
Analysis of Metabolic Pathway Using Hybrid Properties
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DOI：
10.2174/092986612798472857
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发表时间：
2012-01-01
影响因子：
1.6
通讯作者：
Huang, Tao
中科院分区：
文献类型：
--
作者：
Chen, Lei;Cai, Yu-Dong;Huang, Tao
给定化合物形成系统，即由某些化合物及其关系组成的系统，它可以形成一种具有生物学意义的途径吗？这是系统生物学中的一个基本问题。如今，在某些特定数据库中收集并存储了有关遗传和代谢水平的许多不同生物的许多信息。基于这些数据，解决此类基本问题是可行的。代谢途径是一种形成化合物的系统，我们通过从13,736个化合物形成系统中的每一个中提取不同的（生物学和图形）特征在酵母中分析它们，其中136个是正途径，即已知的代谢途径，从KEGG中;而13,600则负面。这些化合物形成的系统中的每一个都由144个特征表示，其中88个是图形特征和56个生物学特征。利用“最小冗余最大相关性”和“增量特征选择”来分析这些功能，并选择了16个最佳特征，因为能够最成功地预测质量化合物形成系统。通过折刀交叉验证发现，识别正途径的总体成功率为74.26％。预计这种新颖的方法和令人鼓舞的结果可能会带来有意义的照明来研究这个重要的话题。
Given a compounds-forming system, i.e., a system consisting of some compounds and their relationship, can it form a biologically meaningful pathway? It is a fundamental problem in systems biology. Nowadays, a lot of information on different organisms, at both genetic and metabolic levels, has been collected and stored in some specific databases. Based on these data, it is feasible to address such an essential problem. Metabolic pathway is one kind of compounds-forming systems and we analyzed them in yeast by extracting different (biological and graphic) features from each of the 13,736 compounds-forming systems, of which 136 are positive pathways, i.e., known metabolic pathway from KEGG; while 13,600 were negative. Each of these compounds-forming systems was represented by 144 features, of which 88 are graph features and 56 biological features. "Minimum Redundancy Maximum Relevance" and "Incremental Feature Selection" were utilized to analyze these features and 16 optimal features were selected as being able to predict a query compounds-forming system most successfully. It was found through Jackknife cross-validation that the overall success rate of identifying the positive pathways was 74.26%. It is anticipated that this novel approach and encouraging result may give meaningful illumination to investigate this important topic.