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
(A) The active module (AM606236) with up-regulated AFP2 in the ABA treatment condition. The interaction prediction methods used are annotated as identified in the properties tab. (B) The active module (AM604130) with up-regulated AFP2 in the drought condition. (C) AM606236 and AM604130 comparison with Venn. Protein nodes highlighted with yellow border are related with abscisic acid mediated signaling pathway (GO:0009738). The shared proteins in the three modules are highlighted with red labels.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4256526&req=5

bau117-F4: (A) The active module (AM606236) with up-regulated AFP2 in the ABA treatment condition. The interaction prediction methods used are annotated as identified in the properties tab. (B) The active module (AM604130) with up-regulated AFP2 in the drought condition. (C) AM606236 and AM604130 comparison with Venn. Protein nodes highlighted with yellow border are related with abscisic acid mediated signaling pathway (GO:0009738). The shared proteins in the three modules are highlighted with red labels.

Mentions: In the AIM database, each module can be compared with other modules, which can show the conserved nodes in the modules and changes of functional components in different conditions. We developed an efficient module comparison tool, which provides a Venn diagram view for comparing two to four modules at a time. Two Arabidopsis AFP2 (ABI FIVE BINDING PROTEIN 2) modules (AM606236 and AM604130) are shown in Figure 4A and B. The interaction prediction methods linking each node in these modules are annotated on the edges shown in the diagrams illustrating that there is significant evidence linking each of these proteins to the other proteins in the module (Figure 4A and B). Although this information is not typically displayed on the module edges, it is available under the properties tab by selecting an edge in the interactive module viewer. The diagram view of the comparison of these two related modules is an interactive Venn diagram showing the number of nodes in each grouping (Figure 4C). Clicking on any area in the diagram selects the corresponding nodes in the current comparison modules network view. The Venn diagram view uses a symmetrical layout that supports two to four modules. The Venn diagram views for two and three modules use two and three circles, respectively. For four modules, a symmetrical construction of four ellipses is used.Figure 4.


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)

(A) The active module (AM606236) with up-regulated AFP2 in the ABA treatment condition. The interaction prediction methods used are annotated as identified in the properties tab. (B) The active module (AM604130) with up-regulated AFP2 in the drought condition. (C) AM606236 and AM604130 comparison with Venn. Protein nodes highlighted with yellow border are related with abscisic acid mediated signaling pathway (GO:0009738). The shared proteins in the three modules are highlighted with red labels.
© Copyright Policy
Related In: Results  -  Collection

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

bau117-F4: (A) The active module (AM606236) with up-regulated AFP2 in the ABA treatment condition. The interaction prediction methods used are annotated as identified in the properties tab. (B) The active module (AM604130) with up-regulated AFP2 in the drought condition. (C) AM606236 and AM604130 comparison with Venn. Protein nodes highlighted with yellow border are related with abscisic acid mediated signaling pathway (GO:0009738). The shared proteins in the three modules are highlighted with red labels.
Mentions: In the AIM database, each module can be compared with other modules, which can show the conserved nodes in the modules and changes of functional components in different conditions. We developed an efficient module comparison tool, which provides a Venn diagram view for comparing two to four modules at a time. Two Arabidopsis AFP2 (ABI FIVE BINDING PROTEIN 2) modules (AM606236 and AM604130) are shown in Figure 4A and B. The interaction prediction methods linking each node in these modules are annotated on the edges shown in the diagrams illustrating that there is significant evidence linking each of these proteins to the other proteins in the module (Figure 4A and B). Although this information is not typically displayed on the module edges, it is available under the properties tab by selecting an edge in the interactive module viewer. The diagram view of the comparison of these two related modules is an interactive Venn diagram showing the number of nodes in each grouping (Figure 4C). Clicking on any area in the diagram selects the corresponding nodes in the current comparison modules network view. The Venn diagram view uses a symmetrical layout that supports two to four modules. The Venn diagram views for two and three modules use two and three circles, respectively. For four modules, a symmetrical construction of four ellipses is used.Figure 4.

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