北京生物醫(yī)學(xué)工程

基于代謝網(wǎng)絡(luò)拓?fù)浣Y(jié)構(gòu)的基元模塊發(fā)現(xiàn)方法

A method to discover elementary modules of metabolic networks based on topology

作者：操勇鄭浩然

單位：                      中國科學(xué)技術(shù)大學(xué)計(jì)算機(jī)科學(xué)與技術(shù)學(xué)院(合肥 230027)        

關(guān)鍵詞：代謝網(wǎng)絡(luò)；拓?fù)洌荒K；基元模塊

分類號：

出版年·卷·期（頁碼）：2014·33·2（139-143）

摘要：

目的為提取出物種代謝網(wǎng)絡(luò)具有的基本結(jié)構(gòu)模塊即基元模塊，提出一種基于拓?fù)浣Y(jié)構(gòu)的發(fā)現(xiàn)代謝網(wǎng)絡(luò)基元模塊方法。方法首先利用網(wǎng)絡(luò)模塊化方法將不同物種的代謝網(wǎng)絡(luò)劃分為模塊集合，然后通過合并相似的模塊以及分解較大的代表模塊等操作，最終獲得基元模塊集合。同時(shí)，利用超幾何假設(shè)檢驗(yàn)的方法以確定模塊所具有的代謝功能，并在此基礎(chǔ)上驗(yàn)證發(fā)現(xiàn)基元模塊方法的合理性。結(jié)果對KEGG數(shù)據(jù)庫中的1452個(gè)物種代謝網(wǎng)絡(luò)經(jīng)上述方法處理后，最終得到11446個(gè)基元模塊，并且這些基元模塊能夠很好地表示代謝網(wǎng)絡(luò)。結(jié)論提出了一種基于代謝網(wǎng)絡(luò)拓?fù)浣Y(jié)構(gòu)的發(fā)現(xiàn)基元模塊的方法，該方法能夠有效提取出組成物種代謝網(wǎng)絡(luò)的基元模塊。

Objective In order to extract the elementary modules of organisms’ metabolic networks,we propose a method of discovering elementary modules of metabolic networks based on topology.Methods We first decompose organisms’ metabolic networks into a collection of modules using method of network modularity.Then we get the ultimate elementary modules through merging similar modules and breaking down larger representative modules that can be totally represented by other smaller modules.Meanwhile,we identify metabolic functions involved in module by hypergeometric hypothesis testing and validate our method.Results Applying our method to 1452 organisms’ metabolic network from KEGG,we finally acquire 11446 elementary modules.In addition,these elementary modules can excellently represent organisms’ metabolic network.Conclusions We propose a method to discover elementary modules of metabolic networks based on topology,which can efficiently extract the elementary modules that compose organisms’ metabolic network.

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