Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases.
Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases.
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DOI：
10.1186/1471-2105-8-372
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发表时间：
2007-10-04
影响因子：
3
通讯作者：
Ma'ayan A
中科院分区：
文献类型：
--
作者：
Berger SI;Posner JM;Ma'ayan A
近年来，哺乳动物蛋白质 - 蛋白质相互作用网络数据库得到了发展。这些数据库中的相互作用要么是从低通量的实验生物医学研究文献中手动提取的，要么是使用自然语言处理（NLP）等技术从文献中自动提取的，要么是使用酵母双杂交筛选等高通量方法通过实验生成的，或者是使用各种计算方法预测的。在蛋白质组学实验中被确定为显著变化的基因或蛋白质，或者在基因组研究中被确定为疾病易感基因的，可以置于蛋白质相互作用网络的背景下，以便将这些基因和蛋白质归类到通路和蛋白质复合物中。
Genes2Networks是一个整合了十个哺乳动物相互作用网络数据集内容的软件系统。实施了过滤技术以去除低可信度的相互作用。Genes2Networks是作为一个使用AJAX的基于网络的服务提供的。该系统可用于从人类Entrez基因符号的“种子”列表中提取相关子网络。输出包括一个动态的、可链接的基于网络的三色网络图，以及一份统计分析报告，该报告能识别用于连接种子列表的重要中间节点。
Genes2Networks是一款强大的基于网络的软件，它可以帮助实验生物学家解释基因和蛋白质列表，比如那些通常由基因组和蛋白质组学实验产生的列表，以及与疾病过程相关的基因和蛋白质列表。该系统可用于寻找种子列表中基因和蛋白质之间的关系，并预测在常见通路或蛋白质复合物中可能起关键作用的其他基因或蛋白质。
In recent years, mammalian protein-protein interaction network databases have been developed. The interactions in these databases are either extracted manually from low-throughput experimental biomedical research literature, extracted automatically from literature using techniques such as natural language processing (NLP), generated experimentally using high-throughput methods such as yeast-2-hybrid screens, or interactions are predicted using an assortment of computational approaches. Genes or proteins identified as significantly changing in proteomic experiments, or identified as susceptibility disease genes in genomic studies, can be placed in the context of protein interaction networks in order to assign these genes and proteins to pathways and protein complexes. Genes2Networks is a software system that integrates the content of ten mammalian interaction network datasets. Filtering techniques to prune low-confidence interactions were implemented. Genes2Networks is delivered as a web-based service using AJAX. The system can be used to extract relevant subnetworks created from "seed" lists of human Entrez gene symbols. The output includes a dynamic linkable three color web-based network map, with a statistical analysis report that identifies significant intermediate nodes used to connect the seed list. Genes2Networks is powerful web-based software that can help experimental biologists to interpret lists of genes and proteins such as those commonly produced through genomic and proteomic experiments, as well as lists of genes and proteins associated with disease processes. This system can be used to find relationships between genes and proteins from seed lists, and predict additional genes or proteins that may play key roles in common pathways or protein complexes.
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