Genes2FANs: connecting genes through functional association networks.
Genes2FANs: connecting genes through functional association networks.
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DOI：
10.1186/1471-2105-13-156
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发表时间：
2012-07-02
影响因子：
3
通讯作者：
Ma'ayan A
中科院分区：
文献类型：
--
作者：
Dannenfelser R;Clark NR;Ma'ayan A
蛋白质-蛋白质、细胞信号传导、代谢和转录相互作用网络可用于鉴定实验鉴定的基因/蛋白质列表之间的连接。然而，除了物理或共表达相互作用之外，基因对或其蛋白质产物可以以许多方式相关联。通过系统地整合来自不同来源的基因的共享特性的知识来构建功能关联网络（FAN），研究人员可能能够识别出基因组之间不明显的其他功能相互作用。Genes 2FANs是一个基于网络的工具和数据库，它利用14个精心构建的FANs和一个大规模的蛋白质-蛋白质相互作用（PPI）网络来构建连接人类和小鼠基因列表的子网络。FAN是从哺乳动物基因组文库中创建的，其中小鼠基因被转化为其人类直系同源物。该工具将人类或小鼠的基因符号列表作为输入，以生成用于连接查询输入列表的子网络和中间基因的排名列表。此外，用户可以输入任何PubMed检索词，然后系统使用GeneRIF自动将返回的结果转换为基因列表。然后将该基因列表用作输入，以根据用户的PubMed查询生成子网络。作为一个案例研究，我们应用Genes 2FAN连接来自90种研究充分的疾病的疾病基因。我们发现通过PPI连接疾病基因的链接数与通过FAN连接疾病基因的链接数之间存在负相关性，将疾病分为两类。Genes 2FANs是一个有用的工具，用于解释基因/蛋白质列表在其各种功能和网络的背景下之间的关系。将功能关联相互作用与物理PPI相结合，可以用于揭示新的生物学，并有助于形成进一步实验的假设。我们发现，许多癌症中的疾病基因主要通过PPI连接，而其他复杂疾病，如自闭症和2型糖尿病，主要通过FAN连接，而没有PPI，可以指导疾病基因发现的更好策略。Genes 2FANs可在http://actin.pharm.mssm.edu/genes2FANs上获得。
Protein-protein, cell signaling, metabolic, and transcriptional interaction networks are useful for identifying connections between lists of experimentally identified genes/proteins. However, besides physical or co-expression interactions there are many ways in which pairs of genes, or their protein products, can be associated. By systematically incorporating knowledge on shared properties of genes from diverse sources to build functional association networks (FANs), researchers may be able to identify additional functional interactions between groups of genes that are not readily apparent. Genes2FANs is a web based tool and a database that utilizes 14 carefully constructed FANs and a large-scale protein-protein interaction (PPI) network to build subnetworks that connect lists of human and mouse genes. The FANs are created from mammalian gene set libraries where mouse genes are converted to their human orthologs. The tool takes as input a list of human or mouse Entrez gene symbols to produce a subnetwork and a ranked list of intermediate genes that are used to connect the query input list. In addition, users can enter any PubMed search term and then the system automatically converts the returned results to gene lists using GeneRIF. This gene list is then used as input to generate a subnetwork from the user’s PubMed query. As a case study, we applied Genes2FANs to connect disease genes from 90 well-studied disorders. We find an inverse correlation between the counts of links connecting disease genes through PPI and links connecting diseases genes through FANs, separating diseases into two categories. Genes2FANs is a useful tool for interpreting the relationships between gene/protein lists in the context of their various functions and networks. Combining functional association interactions with physical PPIs can be useful for revealing new biology and help form hypotheses for further experimentation. Our finding that disease genes in many cancers are mostly connected through PPIs whereas other complex diseases, such as autism and type-2 diabetes, are mostly connected through FANs without PPIs, can guide better strategies for disease gene discovery. Genes2FANs is available at: http://actin.pharm.mssm.edu/genes2FANs.
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影响因子：
30.8
作者：
Cordeddu, Viviana;Di Schiavi, Elia;Pennacchio, Len A.;Ma'ayan, Avi;Sarkozy, Anna;Fodale, Valentina;Cecchetti, Serena;Cardinale, Alessio;Martin, Joel;Schackwitz, Wendy;Lipzen, Anna;Zampino, Giuseppe;Mazzanti, Laura;Digilio, Maria C.;Martinelli, Simone;Flex, Elisabetta;Lepri, Francesca;Bartholdi, Deborah;Kutsche, Kerstin;Ferrero, Giovanni B.;Anichini, Cecilia;Selicorni, Angelo;Rossi, Cesare;Tenconi, Romano;Zenker, Martin;Merlo, Daniela;Dallapiccola, Bruno;Iyengar, Ravi;Bazzicalupo, Paolo;Gelb, Bruce D.;Tartaglia, Marco
通讯作者：
Tartaglia, Marco
影响因子：
14.9
作者：
Blake JA;Bult CJ;Eppig JT;Kadin JA;Richardson JE;Mouse Genome Database Group
通讯作者：
Mouse Genome Database Group
影响因子：
3
作者：
Berger SI;Posner JM;Ma'ayan A
通讯作者：
Ma'ayan A
影响因子：
5.8
作者：
Lachmann, Alexander;Xu, Huilei;Ma'ayan, Avi
通讯作者：
Ma'ayan, Avi
影响因子：
3
作者：
Jiang, TJ;Keating, AE
通讯作者：
Keating, AE