Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping.
Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping.
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DOI：
10.1186/1471-2105-12-289
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发表时间：
2011-07-18
影响因子：
3
通讯作者：
Jarman AP
中科院分区：
文献类型：
--
作者：
Gallone G;Simpson TI;Armstrong JD;Jarman AP
蛋白质相互作用（PPI）数据被广泛用于生成旨在描述生物系统中蛋白质之间关系的网络模型。这种网络的保真度和完整性主要受到蛋白质相互作用信息的缺乏以及这些数据中的大多数仅限于少数广泛研究的实验生物的限制。为了扩展现有PPI的实用性，可以使用计算方法，其利用跨分类群的正向同源蛋白之间的功能保守性来预测推定的PPI或“interrologs”。到目前为止，大多数interlog预测的努力已被限制到特定的生物领域与固定的基础数据源，并有没有软件工具，提供了一个通用的框架，为“在飞”interlog预测。我们引入了Bio：：Homology：：InterlogWalk，这是一个Perl模块，用于通过一个orthology-walk方法来检索、优先排序和可视化假定的蛋白质-蛋白质相互作用。该模块使用正交和实验交互数据来生成假定的PPI，并可选地将元数据整理成交互优先级指数，该指数可用于帮助对interlog进行优先级排序以进行进一步分析。我们展示了我们的interlog预测方法的果蝇，黑腹果蝇的基因组相互作用。我们分析了由此产生的相互作用网络，并表明该方法提出了新的相互作用组成员和相互作用，是未来实验研究的候选人。我们的interlog预测工具采用Ensembl Perl API和PSICQUIC支持的蛋白质相互作用数据源来“即时”生成最新的interlog。这代表了先前用于interlog预测的方法的重大进步，因为它允许使用Ensembl中所有基因组的最新直系和蛋白质相互作用数据。该模块输出简单的文本文件，使其易于通过后处理自定义结果，使假定的PPI数据集可以轻松集成到现有的分析工作流程中。Bio：：Homology：：InterlogWalk模块、示例脚本和完整文档可以在GNU公共许可证下从Comprehensive Perl Archive Network（CPAN）免费获得。
Protein-protein interaction (PPI) data are widely used to generate network models that aim to describe the relationships between proteins in biological systems. The fidelity and completeness of such networks is primarily limited by the paucity of protein interaction information and by the restriction of most of these data to just a few widely studied experimental organisms. In order to extend the utility of existing PPIs, computational methods can be used that exploit functional conservation between orthologous proteins across taxa to predict putative PPIs or 'interologs'. To date most interolog prediction efforts have been restricted to specific biological domains with fixed underlying data sources and there are no software tools available that provide a generalised framework for 'on-the-fly' interolog prediction. We introduce Bio::Homology::InterologWalk, a Perl module to retrieve, prioritise and visualise putative protein-protein interactions through an orthology-walk method. The module uses orthology and experimental interaction data to generate putative PPIs and optionally collates meta-data into an Interaction Prioritisation Index that can be used to help prioritise interologs for further analysis. We show the application of our interolog prediction method to the genomic interactome of the fruit fly, Drosophila melanogaster. We analyse the resulting interaction networks and show that the method proposes new interactome members and interactions that are candidates for future experimental investigation. Our interolog prediction tool employs the Ensembl Perl API and PSICQUIC enabled protein interaction data sources to generate up to date interologs 'on-the-fly'. This represents a significant advance on previous methods for interolog prediction as it allows the use of the latest orthology and protein interaction data for all of the genomes in Ensembl. The module outputs simple text files, making it easy to customise the results by post-processing, allowing the putative PPI datasets to be easily integrated into existing analysis workflows. The Bio::Homology::InterologWalk module, sample scripts and full documentation are freely available from the Comprehensive Perl Archive Network (CPAN) under the GNU Public license.
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影响因子：
14.9
作者：
Jensen LJ;Kuhn M;Stark M;Chaffron S;Creevey C;Muller J;Doerks T;Julien P;Roth A;Simonovic M;Bork P;von Mering C
通讯作者：
von Mering C
影响因子：
12.3
作者：
Kemmer, D;Huang, Y;Ouellette, BFF
通讯作者：
Ouellette, BFF
影响因子：
14.9
作者：
Kersey, P;Bower, L;Apweiler, R
通讯作者：
Apweiler, R
影响因子：
5.8
作者：
Huang, TW;Tien, AC;Huang, CYF
通讯作者：
Huang, CYF
影响因子：
14.9
作者：
Kersey PJ;Lawson D;Birney E;Derwent PS;Haimel M;Herrero J;Keenan S;Kerhornou A;Koscielny G;Kähäri A;Kinsella RJ;Kulesha E;Maheswari U;Megy K;Nuhn M;Proctor G;Staines D;Valentin F;Vilella AJ;Yates A
通讯作者：
Yates A