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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.

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An example of search results for the top two modules. (A) The link underlying the thumbnail image will launch the interactive visualization tool and power graph viewer. (B) Description of the module information. (C) The interactive pie chart summarizing a top annotation distribution for the module.
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bau117-F2: An example of search results for the top two modules. (A) The link underlying the thumbnail image will launch the interactive visualization tool and power graph viewer. (B) Description of the module information. (C) The interactive pie chart summarizing a top annotation distribution for the module.

Mentions: There are three ways to utilize the interactome modules in the AIM database. One way is a gene identifier or gene symbol search that users can perform to find modules. The main page of the search results lists all the modules meeting the search criteria and provides brief information, such as module identifier, module thumbnail, node number, edge number, module collection, top annotation and predicted interologs (Figure 2). The second way to find modules is to perform a keyword search across different microarray experiments. The search result delineates ID, description, array number and different experimental conditions that link to the identified modules in the expression experiment. The third way to search for modules is to filter by annotation. In the AIM database, more than 25 000 000 significant annotation terms for modules are recorded, allowing for the filtering of modules according to user-specific interests.Figure 2.


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)

An example of search results for the top two modules. (A) The link underlying the thumbnail image will launch the interactive visualization tool and power graph viewer. (B) Description of the module information. (C) The interactive pie chart summarizing a top annotation distribution for the module.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4256526&req=5

bau117-F2: An example of search results for the top two modules. (A) The link underlying the thumbnail image will launch the interactive visualization tool and power graph viewer. (B) Description of the module information. (C) The interactive pie chart summarizing a top annotation distribution for the module.
Mentions: There are three ways to utilize the interactome modules in the AIM database. One way is a gene identifier or gene symbol search that users can perform to find modules. The main page of the search results lists all the modules meeting the search criteria and provides brief information, such as module identifier, module thumbnail, node number, edge number, module collection, top annotation and predicted interologs (Figure 2). The second way to find modules is to perform a keyword search across different microarray experiments. The search result delineates ID, description, array number and different experimental conditions that link to the identified modules in the expression experiment. The third way to search for modules is to filter by annotation. In the AIM database, more than 25 000 000 significant annotation terms for modules are recorded, allowing for the filtering of modules according to user-specific interests.Figure 2.

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.

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