Tetsuro Toyoda1, Akiyoshi Wada. 1. Genomic Knowledge Base Research Team, Bioinformatics Group, RIKEN Yokohama Institute, Kanagawa 230-0045, Japan. toyop@gsc.riken.go.jp
Abstract
MOTIVATION: With the recent progress in genomics, various data sets of omic interactions describing networks of omic elements have become available. In order to obtain reliable hypotheses from the data, it is effective to integrate interactions from different sorts of data sets. In order to facilitate a coordinate-based integration and analysis of omic interactions, we introduce the concept of an omic space comprising a comprehensive set of omic planes. Genomic, transcriptomic, proteomic, metabolomic, phenomic and other omic planes are defined by two orthogonal genomic-coordinate axes. RESULTS: We show that the omic space concept helps us to assimilate biological findings comprehensively into hypotheses or models combining higher-order phenomena and lower-order mechanisms by demonstrating that a comprehensive ranking of correspondences among interactions in the space can be used effectively for estimating candidates of responsible gene pairs for epistatic interacting loci of tumors in mice. We also show that the omic space offers a convenient framework for database integration, by presenting a system named the 'Genome <==> Phenome Superhighway' (GPS) that serves as a framework for integration and visualization of omic interactions based on omic spaces of some model species including Homo sapiens, Mus musculus, Caenorhabditis elegans and Arabidopsis thaliana. AVAILABILITY: For the GPS web site, see http://omicspace.riken.jp/gps/.
MOTIVATION: With the recent progress in genomics, various data sets of omic interactions describing networks of omic elements have become available. In order to obtain reliable hypotheses from the data, it is effective to integrate interactions from different sorts of data sets. In order to facilitate a coordinate-based integration and analysis of omic interactions, we introduce the concept of an omic space comprising a comprehensive set of omic planes. Genomic, transcriptomic, proteomic, metabolomic, phenomic and other omic planes are defined by two orthogonal genomic-coordinate axes. RESULTS: We show that the omic space concept helps us to assimilate biological findings comprehensively into hypotheses or models combining higher-order phenomena and lower-order mechanisms by demonstrating that a comprehensive ranking of correspondences among interactions in the space can be used effectively for estimating candidates of responsible gene pairs for epistatic interacting loci of tumors in mice. We also show that the omic space offers a convenient framework for database integration, by presenting a system named the 'Genome <==> Phenome Superhighway' (GPS) that serves as a framework for integration and visualization of omic interactions based on omic spaces of some model species including Homo sapiens, Mus musculus, Caenorhabditis elegans and Arabidopsis thaliana. AVAILABILITY: For the GPS web site, see http://omicspace.riken.jp/gps/.
Authors: Csaba Vadasz; Mariko Saito; Beatrix M Gyetvai; Melinda Oros; Istvan Szakall; Krisztina M Kovacs; Vidudala V T S Prasad; Grant Morahan; Reka Toth Journal: Neurochem Res Date: 2007-02-02 Impact factor: 3.996
Authors: Subha Madhavan; Yuriy Gusev; Thanemozhi G Natarajan; Lei Song; Krithika Bhuvaneshwar; Robinder Gauba; Abhishek Pandey; Bassem R Haddad; David Goerlitz; Amrita K Cheema; Hartmut Juhl; Bhaskar Kallakury; John L Marshall; Stephen W Byers; Louis M Weiner Journal: Front Genet Date: 2013-11-20 Impact factor: 4.599