Annotation-based inference of transporter function.
Annotation-based inference of transporter function.
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DOI：
10.1093/bioinformatics/btn180
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发表时间：
2008-07-01
期刊：
影响因子：
--
通讯作者：
Karp P
中科院分区：
文献类型：
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作者：
Lee TJ;Paulsen I;Karp P
动机：我们提出了一种推断和构建转运蛋白运输反应的方法，主要基于对生物体基因组注释中单个蛋白质的名称的分析。运输反应是对转运蛋白活动的声明性描述，因此可以通过计算来操纵，这与自由文本蛋白质名称不同。一旦将转运体活动编码为转运体反应，就可以进行一些计算分析，包括按转运体活动查询数据库；将转运体纳入自动生成的代谢图，该图可绘制组学数据以协助解释；检测代谢和运输网络中的异常情况，例如转运到细胞内但不是任何代谢反应或途径的输入的底物；以及对不同生物体的运输能力进行比较分析。结果：在随机选择的生物上，该方法在全基因组中按名称识别转运蛋白的准确率和召回率分别为0.93和0.90。该方法对完全输运反应的预测准确率为67.5%，如果考虑到过于笼统但不正确的预测，反应预测的准确率为82.5%。可用性：该方法作为Pathway Tools软件的推理组件病理的一部分实施。路径工具向非商业机构的研究人员免费提供，包括源代码；商业机构需要付费。联系方式：tomlee@ai.sri.com补充信息：生物信息学在线提供补充数据。
Motivation: We present a method for inferring and constructing transport reactions for transporter proteins based primarily on the analysis of the names of individual proteins in the genome annotation of an organism. Transport reactions are declarative descriptions of transporter activities, and thus can be manipulated computationally, unlike free-text protein names. Once transporter activities are encoded as transport reactions, a number of computational analyses are possible including database queries by transporter activity; inclusion of transporters into an automatically generated metabolic-map diagram that can be painted with omics data to aid in their interpretation; detection of anomalies in the metabolic and transport networks, such as substrates that are transported into the cell but are not inputs to any metabolic reaction or pathway; and comparative analyses of the transport capabilities of different organisms. Results: On randomly selected organisms, the method achieves precision and recall rates of 0.93 and 0.90, respectively in identifying transporter proteins by name within the complete genome. The method obtains 67.5% accuracy in predicting complete transport reactions; if allowance is made for predictions that are overly general yet not incorrect, reaction prediction accuracy is 82.5%. Availability: The method is implemented as part of PathoLogic, the inference component of the Pathway Tools software. Pathway Tools is freely available to researchers at non-commercial institutions, including source code; a fee applies to commercial institutions. Contact: tomlee@ai.sri.com Supplementary information: Supplementary data are available at Bioinformatics online.
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