Bioinformatics Advance Access originally published online on March 22, 2004
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Bioinformatics 20(11) © Oxford University Press 2004; all rights reserved.
Omic space: coordinate-based integration and analysis of genomic phenomic interactions
1 Genomic Knowledge Base Research Team, Bioinformatics Group and 2 Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Received on September 16, 2003; revised on February 11, 2004; accepted on February 27, 2004
Advance Access Publication March 22, 2004
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/.
Contact: toyop{at}gsc.riken.go.jp
* To whom correspondence should be addressed.
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