From Function Prediction to Pathway Prediction: A New Pipeline Based on KAAS and GENIES

The number of complete and draft genomes has increased in recent years. The prediction of precise biological roles of the genes of such sequenced organisms is becoming an important issue in computational biology. We have recently developed two novel systems: KAAS (KEGG Automatic Annotation Server) [2, 4] and GENIES (Gene Network Inference Engine based on Supervised Analysis) [3] as computational tools in the KEGG database [1]. The KAAS enables us to automatically conduct function annotations to genes of newly sequenced organisms, based on sequence similarity to genes belonging the KEGG Orthology (KO) system. The GENIES enables us to predict potential functional associations between genes, based on other genomic data or high-throughput experimental data such as phylogenetic profiles and gene expression profiles. In this study we present a novel procedure for assigning molecular functions to genes and predicting their precise biological roles in metabolic or regulatory pathways, by the combined use of the KAAS and GENIES. We show a possibility for obtaining new biological insights through a case study of pathway prediction.