agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update

Abstract

The agriGO platform, which has been serving the scientific community for >10 years, specifically focuses on gene ontology (GO) enrichment analyses of plant and agricultural species. We continuously maintain and update the databases and accommodate the various requests of our global users. Here, we present our updated agriGO that has a largely expanded number of supporting species (394) and datatypes (865). In addition, a larger number of species have been classified into groups covering crops, vegetables, fish, birds and insects closely related to the agricultural community. We further improved the computational efficiency, including the batch analysis and P-value distribution (PVD), and the user-friendliness of the web pages. More visualization features were added to the platform, including SEACOMPARE (cross comparison of singular enrichment analysis), direct acyclic graph (DAG) and Scatter Plots, which can be merged by choosing any significant GO term. The updated platform agriGO v2.0 is now publicly accessible at http://systemsbiology.cau.edu.cn/agriGOv2/.

Plant-Specific Histone Deacetylases HDT1/2 Regulate GIBBERELLIN 2-OXIDASE2 Expression to Control Arabidopsis Root Meristem Cell Number

“…DEGs are defined based on relatively stringent statistics and filtering (fold change > 2, false discovery rate, P value < 0.05) within the CLC. GO enrichment analyses were performed using agriGO v2.0 (Tian et al, 2017).…”

The effects of putrescine are partly overlapping with osmotic stress processes in wheat

“…Singular enrichment analysis (SEA) was performed on the Arabidopsis protein accessions using the web-based agriGO toolkit [24] with the Arabidopsis gene model (TAIR10) as a reference, Fisher statistical test and the Yekutieli multiple comparison correction method (FDR under dependency) [25] at P-value < 0.05 level.…”

Assessment of Genetic Diversity, Population Structure, and Evolutionary Relationship of Uncharacterized Genes in a Novel Germplasm Collection of Diploid and Allotetraploid Gossypium Accessions Using EST and Genomic SSR Markers

“…We analyzed the features of these genes and the results showed several categories related to stress and fiber development in upland cotton. We further analyzed the genes through annotations and Gene Ontology (GO) terms that were associated with the mined genes, which describe the genes in relation to cellular components (CCs), molecular function (MF), and biological process (BP) [56]. In cellular components, functions such as microtubule organizing center (11%), microtubule-associated complex (10%), membrane coat (13%), coated membrane (13%), cytoskeleton part (10%), microtubule cytoskeleton (%), cytoskeleton (10%), and protein complex (23%) were observed.…”