Nature Biotechnology 24, 55 - 62 (2006)
Published online: 10 January 2006; | doi:10.1038/nbt1150
Creation and implications of a phenome-genome networkAtul J Butte1
& Isaac S Kohane21
Stanford Medical Informatics, Departments of Medicine and Pediatrics, Stanford University School of Medicine, 251 Campus Drive, Room X-215, Stanford, California 94305-5479 USA. 2
Informatics Program and Division of Endocrinology, Children's Hospital Boston and Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts 02115 USA.
Correspondence should be addressed to Atul J Butte abutte@stanford.edu Although gene and protein measurements are increasing in quantity and comprehensiveness, they do not characterize a sample's entire phenotype in an environmental or experimental context. Here we comprehensively consider associations between components of phenotype, genotype and environment to identify genes that may govern phenotype and responses to the environment. Context from the annotations of gene expression data sets in the Gene Expression Omnibus is represented using the Unified Medical Language System, a compendium of biomedical vocabularies with nearly 1-million concepts. After showing how data sets can be clustered by annotative concepts, we find a network of relations between phenotypic, disease, environmental and experimental contexts as well as genes with differential expression associated with these concepts. We identify novel genes related to concepts such as aging. Comprehensively identifying genes related to phenotype and environment is a step toward the Human Phenome Project5.
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