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United States Department of Agriculture

Agricultural Research Service

Title: Aggoview: Integrated System for Depth Comparison of Multiple Datasets Based Upon Gene Ontology

Authors
item Dowd, Scot
item Zaragoza, Joaquin
item Fitzgerald, Micaiah

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: November 15, 2005
Publication Date: January 15, 2006
Citation: Dowd, S.E., Zaragoza, J., Fitzgerald, M. 2006. AgGOview: Integrated system for depth comparison of multiple datasets based upon gene ontology [abstract]. Plant and Animal Genome Conference, January 13-18, 2006, San Diego, California. Paper No. P883.

Interpretive Summary: There is a need in the field of bioinformatics to develop tools that will allow for categorization and analyses of large genetic and functional datasets such as those derived from microarray experiments. To address this need, a software and database system known as agGOview was developed. AgGOview is a web based system for comparison of sequence datasets mapped to Gene Ontology functional categories and terminologies. A comprehensive solution is available that allows users to derive the mappings, upload genetic data, and perform evaluations. The software developed as part of the agGOview project is freely available at http://liru.ars.usda.gov/mainbioinformatics.html.

Technical Abstract: Analysis of large comparative EST projects and other genomic and proteomic datasets benefit from functional characterizations. Gene Ontology is a language and structure for functional characterization that is growing in popularity. A database user interface and computer code structured to allow comparisons of individual Gene Ontology datasets have been developed. These tools are used to evaluate microarray expression data from different tissues, and to perform characterization of non-subtracted EST libraries from divergent tissues. A software and database system is also provided for mapping of unknown sequence data to Gene Ontology terms, export of database population files, and a web interface for data uploading into the agGOview databases. This interface allows multiple datasets to be compared side by side in a web browser, has basic statistical evaluation of the data, and allows for downloading of comparisons into tabular format for import into advance statistical programs or spreadsheet applications. The software developed as part of the agGOview project is freely available at http://liru.ars.usda.gov/mainbioinformatics.html.

Last Modified: 9/2/2014
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