PlantGSEA: a gene set enrichment analysis toolkit for plant community

Abstract

Gene Set Enrichment Analysis (GSEA) is a powerful method for interpreting biological meaning of a list of genes by computing the overlaps with various previously defined gene sets. As one of the most widely used annotations for defining gene sets, Gene Ontology (GO) system has been used in many enrichment analysis tools. EasyGO and agriGO, two GO enrichment analysis toolkits developed by our laboratory, have gained extensive usage and citations since their releases because of their effective performance and consistent maintenance. Responding to the increasing demands of more comprehensive analysis from the users, we developed a web server as an important component of our bioinformatics analysis toolkit, named PlantGSEA, which is based on GSEA method and mainly focuses on plant organisms. In PlantGSEA, 20 290 defined gene sets deriving from different resources were collected and used for GSEA analysis. The PlantGSEA currently supports gene locus IDs and Affymatrix microarray probe set IDs from four plant model species (Arabidopsis thaliana, Oryza sativa, Zea mays and Gossypium raimondii). The PlantGSEA is an efficient and user-friendly web server, and now it is publicly accessible at http://structuralbiology.cau.edu.cn/PlantGSEA.

Figure 1.

The result page in PlantGSEA. (A) A summary table displayed enriched gene sets with six columns: gene set names, a brief description, the category of the gene set, the number of overlap between queried genes and the gene set, P-value of statistical test and adjusted P-value after the False Discovery Rate (FDR) correction. (B) Detail information about the selected gene set, including gene set name, brief and full description, contributor’s information and overlapped genes. (C) The enriched gene sets displayed in the hierarchical pattern. The color showed the significance of a gene set. (D) An annotation table represented the gene set-based annotation of query genes. Gene sets and queried genes can be further explored for detail information by clicking the links.

Figure 2.

A Bar chart of significantly enriched gene sets in different categories. These terms were selected from significantly enriched gene sets (FDR < 0.05). The y-axis represented the value of log10-converted adjusted P-value. The x-axis displayed the gene sets name. Gene sets belonging to different categories were marked with different colors. GO, gene ontology; PO, plant ontology; TFT, transcription factor target; FDR, False Discovery Rate.