A Web Accessible GO Term Enrichment Analysis Tool for Soybean Expression Data at Soybase

SoyBase, the USDA-ARS soybean genetics and genomics database, provides a comprehensive collection of data and analysis tools for the research community, and is continuously improved with new genetic and genomic data and bioinformatic tools. Recently a GO term enrichment analysis tool was created and deployed on SoyBase. This tool provides a comprehensive GO term analysis without the need to locally install a complete bioinformatic pipeline. The tool accepts as input a list of soybean genes and returns a number of reports including the annotations used in the tool, FASTA sequences of the genes, and GO term enrichment summaries in tabular format. All reports are available for download in formats suitable for further analysis. The tool also produces pie charts depicting the number of genes assigned to the various GO Plant Slim categories, with individual graphs for the three GO aspects (molecular function, biological process, cellular component) suitable for direct inclusion in manuscripts. Tabular presentations showing the PANTHER, PFAM, GO and KOG annotations for the genes are available. Enrichment data for over/underrepresentation based on GO Plant Slim classes are presented as tabular output. Genome-wide gene counts in each GO Plant Slim category along with the number of submitted genes in each category allows users to easily judge the relevance of the enrichment P-value calculated for each gene. The genomic location of the genes can be visualized in a graphical view of the 20 soybean chromosomes, with each gene linked to the comprehensive SoyBase page describing that gene.