agriGO: a GO analysis toolkit for the agricultural community

By Zhou Du, Xin Zhou, Yi Ling, Zhenhai Zhang, Zhen Su. Nucleic Acids Res., 2010

2,359 citations recorded by the source corpus.

Gene Ontology (GO), the de facto standard in gene functionality description, is used widely in functional annotation and enrichment analysis. Here, we introduce agriGO, an integrated web-based GO analysis toolkit for the agricultural community, using the advantages of our previous GO enrichment tool (EasyGO), to meet analysis demands from new technologies and research objectives. EasyGO is valuable for its proficiency, and has proved useful in uncovering biological knowledge in massive data sets from high-throughput experiments. For agriGO, the system architecture and website interface were redesigned to improve performance and accessibility. The supported organisms and gene identifiers were substantially expanded (including 38 agricultural species composed of 274 data types). The requirement on user input is more flexible, in that user-defined reference and annotation are accepted. Moreover, a new analysis approach using Gene Set Enrichment Analysis strategy and customizable features is provided. Four tools, SEA (Singular enrichment analysis), PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross comparison of SEA), are integrated as a toolkit to meet different demands. We also provide a cross-comparison service so that different data sets can be compared and explored in a visualized way. Lastly, agriGO functions as a GO data repository with search and download functions; agriGO is publicly accessible at http://bioinfo.cau.edu.cn/agriGO/.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ac80db7e5599f9fc2e56fbc68230d8b12b1bc3f9

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Citations in the corpus

The Sequence of 1504 Mutants in the Model Rice Variety Kitaake Facilitates Rapid Functional Genomic Studies (2017, methodology): “7 To test whether the affected genes are biased with respect to a particular biological process, we used gene ontology (GO) analysis to classify all affected genes into major functional categories (Ashburner et al., 2000; Du et al., 2010).”
NOA: a novel Network Ontology Analysis method (2011, background): “Although each tool has distinct strengths (4–8), the common motivation behind these tools is to list the associated GO terms for the interesting gene list and then statistically identify the most enriched or signiﬁcant biological annotations.”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, positive): “AgriGO analysis for Gene Ontology (GO) term enrichment was carried out using Singular Enrichment Analysis with maize Affymetrix Array as a background reference (Du et al., 2010).”
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update (2017, methodology): “Our laboratory developed two GO-based tools for the agricultural community, easyGO (2) and the ensuing agriGO (8), and has continuously maintained them.”
REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms (2011, methodology): “A multitude of Web servers exists to assist in this task, including but not limited to: L2L [3], FatiGO [4], GOrilla [5] or agriGO [6].”
More plant growth but less plant defence? First global gene expression data for plants grown in soil amended with biochar (2015, methodology): “A gene ontology analysis was also performed on AGRIGO (Du et al., 2010) using the tool PAGE (Parametric Analysis of Gene Set Enrichment).”
expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform1[OPEN] (2016, methodology): “GO term enrichment was calculated using Singular Enrichment Analysis provided by agriGO (Du et al., 2010) using default settings.”
Tissue-Specific Functional Networks for Prioritizing Phenotype and Disease Genes (2012, methodology): “We then calculate the gene ontology enrichment of top 100 changed genes for each network against the global network using established techniques [62].”
Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges (2012, neutral): “cn/agriGO/) [80]”