SemanticGO: a tool for gene functional similarity analysis in Arabidopsis thaliana and rice

Gene or pathway functional similarities are important information for researchers. However, these similarities are often described sparsely and qualitatively. The latent semantic analysis of Arabidopsis thaliana (Arabidopsis) Gene Ontology (GO) data produced a set of 200-dimension feature vectors for each gene. Pathways were represented by summing the vectors of the pathway member genes. Thus, the similarities between genes and pathways were assessed. Additionally, the gene feature vectors were correlated with external gene data, including gene expression and gene network connectivity, to elucidate the associated functions. The gene feature vectors were decoded, and their applications were demonstrated. A simple online tool, SemanticGO (http://bioinformatics.fafu.edu.cn/semanticGO/), is herein provided to enable researchers to explore the similarities between genes and pathways in both Arabidopsis and rice.