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Classification of genes and putative biomarker identification using distribution metrics on expression profiles
- Source :
- PLoS ONE, Vol 5, Iss 2, p e9056 (2010), PLoS ONE
- Publication Year :
- 2010
- Publisher :
- Public Library of Science (PLoS), 2010.
-
Abstract
- Background Identification of genes with switch-like properties will facilitate discovery of regulatory mechanisms that underlie these properties, and will provide knowledge for the appropriate application of Boolean networks in gene regulatory models. As switch-like behavior is likely associated with tissue-specific expression, these gene products are expected to be plausible candidates as tissue-specific biomarkers. Methodology/Principal Findings In a systematic classification of genes and search for biomarkers, gene expression profiles (GEPs) of more than 16,000 genes from 2,145 mouse array samples were analyzed. Four distribution metrics (mean, standard deviation, kurtosis and skewness) were used to classify GEPs into four categories: predominantly-off, predominantly-on, graded (rheostatic), and switch-like genes. The arrays under study were also grouped and examined by tissue type. For example, arrays were categorized as ‘brain group’ and ‘non-brain group’; the Kolmogorov-Smirnov distance and Pearson correlation coefficient were then used to compare GEPs between brain and non-brain for each gene. We were thus able to identify tissue-specific biomarker candidate genes. Conclusions/Significance The methodology employed here may be used to facilitate disease-specific biomarker discovery.
- Subjects :
- Candidate gene
Public Health and Epidemiology/Screening
Cardiovascular Disorders
Gene regulatory network
Computational Biology/Transcriptional Regulation
lcsh:Medicine
Biology
Computational Biology/Molecular Genetics
symbols.namesake
Mice
Databases, Genetic
Animals
Cluster Analysis
Gene Regulatory Networks
Genetic Predisposition to Disease
Biomarker discovery
lcsh:Science
Developmental Biology/Embryology
Oligonucleotide Array Sequence Analysis
Regulation of gene expression
Genetics
Expressed sequence tag
Multidisciplinary
Computational Biology/Systems Biology
Models, Genetic
Gene Expression Profiling
Myocardium
lcsh:R
Computational Biology
Gene Expression Regulation, Developmental
Proteins
Heart
Genetics and Genomics/Bioinformatics
Pearson product-moment correlation coefficient
Gene expression profiling
symbols
Biomarker (medicine)
lcsh:Q
Pharmacology/Personalized Medicine
Algorithms
Biomarkers
Software
Research Article
Computational Biology/Genomics
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 5
- Issue :
- 2
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....c6183e5446dc4e71f022edc12902019a