CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components.
CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components.
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DOI：
10.1186/s12859-017-1787-5
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发表时间：
2017-09-13
影响因子：
3
通讯作者：
Minghim R
中科院分区：
文献类型：
--
作者：
Heberle H;Carazzolle MF;Telles GP;Meirelles GV;Minghim R
“组学”科学的出现通过对分子相互作用的高通量分析为当代生物学带来了新的视角，为蛋白质/基因功能和生物途径的组织提供了新的线索。生物分子相互作用网络或图形是简单的抽象表示，其中细胞的组成部分（例如蛋白质，代谢物等）由节点表示，它们的相互作用由边缘表示。适当的数据可视化对于理解这种网络至关重要，因为通路与细胞特定区域发生的功能有关。力定向布局是一种重要的、广泛应用的根据网络拓扑结构绘制网络的技术。将网络放置在蜂窝隔间中有助于快速确定网络元素的位置，更具体地说，是集中的位置。目前，只有少数工具提供了可视地按细胞隔间组织网络的能力。它们中的大多数无法处理大型和密集的网络。即使对于具有数百个节点的小型网络，可用的工具也无法在用户交互时重新定位网络，从而限制了视觉探索能力。在这里，我们提出CellNetVis，这是一个网络工具，可以使用约束力定向布局算法在细胞图中轻松显示生物网络。该工具是免费提供的，并且是开源的。它最初是为集成交互系统（Integrated Interactome System）生成的网络设计的，可以与来自其他数据库的网络一起使用，比如InnateDB。CellNetVis已被证明适用于复杂网络的动态调查，该网络通过Web上的一致单元表示，具有其他地方无法比拟的功能。本文的在线版本（doi:10.1186/s12859-017-1787-5）包含补充材料，可供授权用户使用。
The advent of “omics” science has brought new perspectives in contemporary biology through the high-throughput analyses of molecular interactions, providing new clues in protein/gene function and in the organization of biological pathways. Biomolecular interaction networks, or graphs, are simple abstract representations where the components of a cell (e.g. proteins, metabolites etc.) are represented by nodes and their interactions are represented by edges. An appropriate visualization of data is crucial for understanding such networks, since pathways are related to functions that occur in specific regions of the cell. The force-directed layout is an important and widely used technique to draw networks according to their topologies. Placing the networks into cellular compartments helps to quickly identify where network elements are located and, more specifically, concentrated. Currently, only a few tools provide the capability of visually organizing networks by cellular compartments. Most of them cannot handle large and dense networks. Even for small networks with hundreds of nodes the available tools are not able to reposition the network while the user is interacting, limiting the visual exploration capability. Here we propose CellNetVis, a web tool to easily display biological networks in a cell diagram employing a constrained force-directed layout algorithm. The tool is freely available and open-source. It was originally designed for networks generated by the Integrated Interactome System and can be used with networks from others databases, like InnateDB. CellNetVis has demonstrated to be applicable for dynamic investigation of complex networks over a consistent representation of a cell on the Web, with capabilities not matched elsewhere. The online version of this article (doi:10.1186/s12859-017-1787-5) contains supplementary material, which is available to authorized users.
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影响因子：
5.8
作者：
Garcia, Olivier;Saveanu, Cosmin;Aittokallio, Tero
通讯作者：
Aittokallio, Tero
影响因子：
5.8
作者：
Barsky, Aaron;Gardy, Jennifer L.;Munzner, Tamara
通讯作者：
Munzner, Tamara
DOI：
10.1109/tvcg.2011.185
发表时间：
2011-12-01
影响因子：
5.2
作者：
Bostock, Michael;Ogievetsky, Vadim;Heer, Jeffrey
通讯作者：
Heer, Jeffrey
DOI：
10.1093/database/bar009
发表时间：
2011
期刊：
Database : the journal of biological databases and curation
影响因子：
--
作者：
Magrane M;UniProt Consortium
通讯作者：
UniProt Consortium
DOI：
10.1093/bioinformatics/btt159
发表时间：
2013-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Krause F;Schulz M;Ripkens B;Flöttmann M;Krantz M;Klipp E;Handorf T
通讯作者：
Handorf T