Genome comparison using Gene Ontology (GO) with statistical testing

Background: Automated comparison of complete sets of genes encoded in two genomes can provide insight on the genetic basis of differences in biological traits between species. Gene ontology (GO) is used as a common vocabulary to annotate genes for comparison. Current approaches calculate the fold of unweighted or weighted differences between two species at the high-level GO functional categories. However, to ensure the reliability of the differences detected, it is important to evaluate their statistical significance. It is also useful to search for differences at all levels of GO. Results: We propose a statistical approach to find reliable differences between the complete sets of genes encoded in two genomes at all levels of GO. The genes are first assigned GO terms from BLAST searches against genes with known GO assignments, and for each GO term the abundance of genes in the two genomes is compared using a chi-squared test followed by false discovery rate (FDR) correction. We applie...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Zhaotao Cai, Xizeng Mao, Songgang Li, Liping Wei
• Keywords: BMCBI 2006, Complete Sets, Genetic Basis, Genomes