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PMID: 16404398 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Creation and implications of a phenome-genome network.

Nature biotechnology ·Vol. 24 ·No. 1 ·2006-01-00 ·Pages 55-62

Butte AJ, Kohane IS

Abstract

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 Project.

MeSH Terms
Aging/physiology Animals Artificial Intelligence Cluster Analysis Databases, Protein Environment Gene Expression Regulation/physiology Genomics/methods Mice Mice, Inbred C57BL Models, Biological Muscle Proteins/physiology Muscle, Skeletal/physiology Natural Language Processing Pattern Recognition, Automated/methods Protein Interaction Mapping/methods Signal Transduction/physiology Unified Medical Language System
Chemicals
Muscle Proteins
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Butte Atul J
Stanford Medical Informatics, Department of Medicine, Stanford University School of Medicine, 251 Campus Drive, Room X-215, Stanford, California 94305-5479, USA. [email protected]
Kohane Isaac S
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Article Info
Journal
Nature biotechnology
Abbr.
Nat Biotechnol
ISSN
1087-0156
DOI
10.1038/nbt1150
Email
[email protected]
Published
2006-01-00
Pages
55-62
Language
English
Region
United States
NLM ID
9604648
PMCID
PMC2716377
Subset
IM
Grants
NIDDK NIH HHS · K12 DK063696-03 · United States
NIDDK NIH HHS · R01 DK62948 · United States
NIDDK NIH HHS · R01 DK060837 · United States
NLM NIH HHS · U54 LM008748-01 · United States
NLM NIH HHS · U54 LM008748 · United States
NIDDK NIH HHS · K12 DK063696 · United States
NIDDK NIH HHS · R01 DK062948 · United States
NIDDK NIH HHS · R01 DK060837-03 · United States
NIDDK NIH HHS · K12 DK63696 · United States
NLM NIH HHS · K22 LM008261-01A1 · United States
NLM NIH HHS · K22 LM008261 · United States
NIDDK NIH HHS · R01 DK062948-02 · United States
External Links
PubMed source DOI: 10.1038/nbt1150 PMC Full Text View journal details
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