agriGO: a GO analysis toolkit for the agricultural community - PubMed (original) (raw)

. 2010 Jul;38(Web Server issue):W64-70.

doi: 10.1093/nar/gkq310. Epub 2010 Apr 30.

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agriGO: a GO analysis toolkit for the agricultural community

Zhou Du et al. Nucleic Acids Res. 2010 Jul.

Abstract

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/.

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Figures

Figure 1.

Figure 1.

Hierarchical tree graph of overrepresented GO terms in biological process category generated by SEA. Boxes in the graph represent GO terms labeled by their GO ID, term definition and statistical information. The significant term (adjusted P ≤ 0.05) are marked with color, while non-significant terms are shown as white boxes. The diagram, the degree of color saturation of a box is positively correlated to the enrichment level of the term. Solid, dashed, and dotted lines represent two, one and zero enriched terms at both ends connected by the line, respectively. The rank direction of the graph is set to from top to bottom.

Figure 2.

Figure 2.

Flash bar chart of overrepresented terms in all three categories. The _Y_-axis is the percentage of genes mapped by the term, and represents the abundance of the GO term. The percentage for the input list is calculated by the number of genes mapped to the GO term divided by the number of all genes in the input list. The same calculation was applied to the reference list to generate its percentage. These two lists are represented using different custom colors. The _X_-axis is the definition of GO terms.

Figure 3.

Figure 3.

Hierarchical clustering of test-sample cluster and cross-comparison of its analysis results by PAGE in HTML table mode. (A) Experiments were performed with different cold treatment time (0.5, 1, 3, 6, 12 and 24 h) by AtGenExpress project (24). Probe set signal intensity was computed using RMA (33), and hierarchical clustering based on log2 Cold/CK ratio of the probe set at each time point was done by Cluster 3.0 (Cluster 3.0, command line version <

http://bonsai.ims.u-tokyo.ac.jp/mdehoon/software/cluster

>). For the test sample, 1921 probe sets showing coordinated upregulation at later time points of cold treatment were selected. (B) The 1921 probe sets in the test sample were analyzed by PAGE, and the comparison is displayed in HTML table mode. The colored blocks represent the level of up/downregulation of each term at a certain time-point. The yellow-to-red, cyan-to-blue and grayscale represent the term is upregulated, downregulated and non-significant, respectively. The adjusted _P-_value of the term determines the degree of color saturation of the corresponding box. Detailed information is provided for each term.

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