Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy.
Department of Biology, Fondazione Human Technopole, 20157 Milan, Italy.
Bioinformatics. 2022 Mar 4;38(6):1764-1766. doi: 10.1093/bioinformatics/btab865.
SIGNORApp is a Cytoscape 3 (3.8 and later) application that provides access to causal interactions annotated in the SIGNOR resource. The application builds networks that can be represented as weighted, signed, directed graphs, where nodes are interacting biological entities and edges represent causal interactions captured by expert curators from experiments reported in peer reviewed journals. Users can query the SIGNOR dataset with (i) single or multiple entity name(s) or identifier(s) and optionally they may require to include in the output network their interacting partners, (ii) browse pathways that are annotated in the SIGNOR resource and (iii) extract the entire causal interactome. The app offers two visualizations modes: one only displaying entity interactions and a second emphasizing the post-translational modifications occurring as a consequence of the interaction. In addition, users can click on nodes and edges to access entity and interaction annotations. Causal information is available for three model organisms: Homo sapiens, Mus musculus and Rattus norvegicus.
SIGNORApp has been developed for Cytoscape 3 (3.8 and later) in the Java programming language. The latest source code and the plugin can be found at: https://github.com/SIGNORcysAPP/signor-app and https://apps.cytoscape.org/apps/signorapp, respectively.
Supplementary data are available at Bioinformatics online.
SIGNORApp 是 Cytoscape 3（3.8 及更高版本）的一个应用程序，可访问 SIGNOR 资源中注释的因果相互作用。该应用程序构建的网络可以表示为加权、有符号、有向图，其中节点是相互作用的生物实体，边表示从同行评审期刊中报道的实验中由专家策展人捕获的因果相互作用。用户可以使用（i）单个或多个实体名称或标识符，并可选择要求在输出网络中包含其相互作用的伙伴，（ii）浏览 SIGNOR 资源中注释的途径，（iii）提取整个因果相互作用组来查询 SIGNOR 数据集。该应用程序提供两种可视化模式：一种仅显示实体相互作用，另一种强调由于相互作用而发生的翻译后修饰。此外，用户可以单击节点和边来访问实体和相互作用注释。因果信息可用于三种模式生物：智人、小家鼠和褐家鼠。
SIGNORApp 是用 Java 编程语言为 Cytoscape 3（3.8 及更高版本）开发的。最新的源代码和插件可在以下网址找到：https://github.com/SIGNORcysAPP/signor-app 和 https://apps.cytoscape.org/apps/signorapp。
补充数据可在 Bioinformatics 在线获取。
