Chapter

Protein Function Prediction for Omics Era

pp 271-288

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KEGG and GenomeNet Resources for Predicting Protein Function from Omics Data Including KEGG PLANT Resource

  • Toshiaki TokimatsuAffiliated withBioinformatics Center, Institute for Chemical Research, Kyoto University Email author 
  • , Masaaki KoteraAffiliated withBioinformatics Center, Institute for Chemical Research, Kyoto University
  • , Susumu GotoAffiliated withBioinformatics Center, Institute for Chemical Research, Kyoto University
  • , Minoru KanehisaAffiliated withBioinformatics Center, Institute for Chemical Research, Kyoto UniversityHuman Genome Center, Institute of Medical Science, University of Tokyo

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Abstract

With the rise of experimental technologies for omics research in recent years, considerable quantitative data related to transcription, protein and metabolism are available for predicting protein functions. To predict protein functions from large omics data, reference knowledge databases and bioinformatics tools play considerable roles. KEGG (http://​www.​genome.​jp/​kegg/​) database we have been establishing is an integrated database of biological systems including genomic, chemical and systemic functional information. Our group has also been developing the tools for genome or chemical analysis as GenomeNet Bioinformatics Tools (http://​www.​genome.​jp/​en/​gn_​tools.​html). In this chapter, we introduce the KEGG database resources and the GenomeNet Bioinformatics Tools for predicting protein functions from the viewpoint of omics research, as well as some recent topics (KEGG PLANT Resource and PathPred). KEGG PLANT Resource is one of the contents in the KEGG EDRUG database, and contains links for plant secondary metabolite biosynthesis pathways, plant genomes and EST sequences, chemical information of plant natural products and the prediction tool for plant secondary metabolism pathway. PathPred is a recently developed pathway prediction tool based on the chemical structure transformation patterns of enzyme reactions found in metabolic pathways.