Limits...
AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants.

Wang Y, Thilmony R, Zhao Y, Chen G, Gu YQ - Database (Oxford) (2014)

Bottom Line: Both interactive Venn diagram and power graph viewer are integrated into the database for easy comparison of modules.In addition, predicted interologs from other plant species (homologous proteins from different species that share a conserved interaction module) are available for each Arabidopsis module.AIM is a powerful systems biology platform for obtaining valuable insights into the function of proteins in Arabidopsis and other plants using the modules of the Arabidopsis interactome.

View Article: PubMed Central - PubMed

Affiliation: USDA-ARS, Western Regional Research Center, Genomics and Gene Discovery Research Unit, Albany, CA 94710, USA, Department of Plant Sciences, University of California, Davis, CA 95616, USA, Bioengineering College, Campus A, Chongqing University, Chongqing 400030, China, USDA-ARS, Western Regional Research Center, Crop Improvement and Utilization Research Unit, Albany, CA 94710, USA and Energy Biosciences Institute, University of California, Berkeley, CA 94720, USA USDA-ARS, Western Regional Research Center, Genomics and Gene Discovery Research Unit, Albany, CA 94710, USA, Department of Plant Sciences, University of California, Davis, CA 95616, USA, Bioengineering College, Campus A, Chongqing University, Chongqing 400030, China, USDA-ARS, Western Regional Research Center, Crop Improvement and Utilization Research Unit, Albany, CA 94710, USA and Energy Biosciences Institute, University of California, Berkeley, CA 94720, USA USDA-ARS, Western Regional Research Center, Genomics and Gene Discovery Research Unit, Albany, CA 94710, USA, Department of Plant Sciences, University of California, Davis, CA 95616, USA, Bioengineering College, Campus A, Chongqing University, Chongqing 400030, China, USDA-ARS, Western Regional Research Center, Crop Improvement and Utilization Research Unit, Albany, CA 94710, USA and Energy Biosciences Institute, University of California, Berkeley, CA 94720, USA Yong.Gu@ars.usda.gov.

Show MeSH
Viewer and network analysis tools. (A) Module (MT779) viewer with various interactive options including highlighting the proteins in the network with a significant term, filtering nodes or edges and modifying display parameters. (B) MT779 with power graph representation. (C) Predicted interologs for MT779 in rice.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4256526&req=5

bau117-F3: Viewer and network analysis tools. (A) Module (MT779) viewer with various interactive options including highlighting the proteins in the network with a significant term, filtering nodes or edges and modifying display parameters. (B) MT779 with power graph representation. (C) Predicted interologs for MT779 in rice.

Mentions: AIM uses the Cytoscape Web application (27) for visualizing and manipulating the graphs of the interactions in the module network. The network can be panned and zoomed in different layouts, and the ID of query proteins is marked in red in the center of the figure, and each associated protein is linked by a uniquely colored line based on the interaction detection method. For modules in the expression experiment, red nodes represent up-regulated expression and green indicates down-regulated expression, different node size means the level of the DE (Figure 3A). The information of all the nodes and edges is shown in the properties panel and users can customize their size and color. Various interactive options are available, such as to highlight the proteins in the network with a significant term from different database in the annotation panel, or filter nodes or edges based on their characteristics in the filter panel (Figure 3A). Combining these options with the other filtering options provides a quick and powerful way to explore the module. In addition, the users can export the module network as XGMML, GraphML and SIF file for other network tools for subsequent additional analysis. The module network also can be saved as different image format such as SVG, PDF and PNG.Figure 3.


AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants.

Wang Y, Thilmony R, Zhao Y, Chen G, Gu YQ - Database (Oxford) (2014)

Viewer and network analysis tools. (A) Module (MT779) viewer with various interactive options including highlighting the proteins in the network with a significant term, filtering nodes or edges and modifying display parameters. (B) MT779 with power graph representation. (C) Predicted interologs for MT779 in rice.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4256526&req=5

bau117-F3: Viewer and network analysis tools. (A) Module (MT779) viewer with various interactive options including highlighting the proteins in the network with a significant term, filtering nodes or edges and modifying display parameters. (B) MT779 with power graph representation. (C) Predicted interologs for MT779 in rice.
Mentions: AIM uses the Cytoscape Web application (27) for visualizing and manipulating the graphs of the interactions in the module network. The network can be panned and zoomed in different layouts, and the ID of query proteins is marked in red in the center of the figure, and each associated protein is linked by a uniquely colored line based on the interaction detection method. For modules in the expression experiment, red nodes represent up-regulated expression and green indicates down-regulated expression, different node size means the level of the DE (Figure 3A). The information of all the nodes and edges is shown in the properties panel and users can customize their size and color. Various interactive options are available, such as to highlight the proteins in the network with a significant term from different database in the annotation panel, or filter nodes or edges based on their characteristics in the filter panel (Figure 3A). Combining these options with the other filtering options provides a quick and powerful way to explore the module. In addition, the users can export the module network as XGMML, GraphML and SIF file for other network tools for subsequent additional analysis. The module network also can be saved as different image format such as SVG, PDF and PNG.Figure 3.

Bottom Line: Both interactive Venn diagram and power graph viewer are integrated into the database for easy comparison of modules.In addition, predicted interologs from other plant species (homologous proteins from different species that share a conserved interaction module) are available for each Arabidopsis module.AIM is a powerful systems biology platform for obtaining valuable insights into the function of proteins in Arabidopsis and other plants using the modules of the Arabidopsis interactome.

View Article: PubMed Central - PubMed

Affiliation: USDA-ARS, Western Regional Research Center, Genomics and Gene Discovery Research Unit, Albany, CA 94710, USA, Department of Plant Sciences, University of California, Davis, CA 95616, USA, Bioengineering College, Campus A, Chongqing University, Chongqing 400030, China, USDA-ARS, Western Regional Research Center, Crop Improvement and Utilization Research Unit, Albany, CA 94710, USA and Energy Biosciences Institute, University of California, Berkeley, CA 94720, USA USDA-ARS, Western Regional Research Center, Genomics and Gene Discovery Research Unit, Albany, CA 94710, USA, Department of Plant Sciences, University of California, Davis, CA 95616, USA, Bioengineering College, Campus A, Chongqing University, Chongqing 400030, China, USDA-ARS, Western Regional Research Center, Crop Improvement and Utilization Research Unit, Albany, CA 94710, USA and Energy Biosciences Institute, University of California, Berkeley, CA 94720, USA USDA-ARS, Western Regional Research Center, Genomics and Gene Discovery Research Unit, Albany, CA 94710, USA, Department of Plant Sciences, University of California, Davis, CA 95616, USA, Bioengineering College, Campus A, Chongqing University, Chongqing 400030, China, USDA-ARS, Western Regional Research Center, Crop Improvement and Utilization Research Unit, Albany, CA 94710, USA and Energy Biosciences Institute, University of California, Berkeley, CA 94720, USA Yong.Gu@ars.usda.gov.

Show MeSH