Data_Sheet_1_FLIM-MAP: Gene Context Based Identification of Functional Modules in Bacterial Metabolic Pathways.XLS

Prediction of functional potential of bacteria can only be ascertained by the accurate annotation of its metabolic pathways. Homology based methods decipher metabolic gene content but ignore the fact that homologs of same protein can function in different pathways. Therefore, mere presence of all constituent genes in an organism is not sufficient to indicate a pathway. Contextual occurrence of genes belonging to a pathway on the bacterial genome can hence be exploited for an accurate estimation of functional potential of a bacterium. In this communication, we present a novel annotation resource to accurately identify pathway presence by using gene context. Our tool FLIM-MAP (Functionally Important Modules in bacterial Metabolic Pathways) predicts biologically relevant functional units called ‘GCMs’ (Gene Context based Modules) from a given metabolic reaction network. We benchmark the accuracy of our tool on amino acids and carbohydrate metabolism pathways.

细菌功能潜能的预测，唯有通过其代谢通路的精准注释方能得以确定。基于同源性的方法虽可解析代谢基因组成，但却忽略了同一蛋白质的同源物可在不同代谢通路中发挥功能这一事实。因此，仅依靠生物体中所有组成基因的存在，并不足以证明某条代谢通路的实际存在。故而可利用细菌基因组上属于某通路的基因的上下文共现特征，来精准估算细菌的功能潜能。本研究中，我们提出了一种全新的注释资源，可通过基因上下文特征精准识别代谢通路的存在情况。我们开发的工具FLIM-MAP（细菌代谢通路功能重要模块，Functionally Important Modules in bacterial Metabolic Pathways）可从给定的代谢反应网络中，预测具有生物学相关性的功能单元——即‘GCMs（基于基因上下文的模块，Gene Context based Modules）’。我们在氨基酸代谢与碳水化合物代谢通路上对本工具的准确性开展了基准测试。