Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons
Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons
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DOI：
10.1093/nar/gki545
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发表时间：
2005-01-01
影响因子：
14.9
通讯作者：
Moreno-Hagelsieb, G
中科院分区：
文献类型：
--
作者：
Janga, SC;Collado-Vides, J;Moreno-Hagelsieb, G
由于操纵子在原核生物中是不稳定的，有人认为它们可能以一种保守的方式重新结合。因此，属于一个基因组中给定操纵子的基因可能会在其他基因组中重新关联，揭示基因产物之间的功能关系。我们开发了一个系统，根据基因产物在任何可用基因组中的操纵子组织，建立基因产物的功能关系网络。操纵子的预测是基于基因间的距离。我们的系统可以使用不同类型的阈值来接受功能关系，要么与操纵子的预测有关，要么与支持关联的非冗余基因组的数量有关。我们也通过外壳来工作，这意味着我们决定连接迭代的次数，以允许相关基因集的互补。该方法以功能交互知识库为基准，具有较高的可靠性。我们还举例说明了星云在寻找新的正则基因成员和其他基因功能群方面的应用。操纵子重排在每个原核生物基因组中产生数千个高质量的新相互作用，以及每个基因组对其他预测的数千个确认，使其成为从基因组背景推断功能相互作用的另一个重要工具。
Since operons are unstable across Prokaryotes, it has been suggested that perhaps they re-combine in a conservative manner. Thus, genes belonging to a given operon in one genome might re-associate in other genomes revealing functional relationships among gene products. We developed a system to build networks of functional relationships of gene products based on their organization into operons in any available genome. The operon predictions are based on inter-genic distances. Our system can use different kinds of thresholds to accept a functional relationship, either related to the prediction of operons, or to the number of non-redundant genomes that support the associations. We also work by shells, meaning that we decide on the number of linking iterations to allow for the complementation of related gene sets. The method shows high reliability benchmarked against knowledge-bases of functional interactions. We also illustrate the use of Nebulon in finding new members of regulons, and of other functional groups of genes. Operon rearrangements produce thousands of high-quality new interactions per prokaryotic genome, and thousands of confirmations per genome to other predictions, making it another important tool for the inference of functional interactions from genomic context.