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Separate enrichment analysis of pathways for up- and downregulated genes.
- Source :
-
Journal of the Royal Society, Interface [J R Soc Interface] 2013 Dec 18; Vol. 11 (92), pp. 20130950. Date of Electronic Publication: 2013 Dec 18 (Print Publication: 2014). - Publication Year :
- 2013
-
Abstract
- Two strategies are often adopted for enrichment analysis of pathways: the analysis of all differentially expressed (DE) genes together or the analysis of up- and downregulated genes separately. However, few studies have examined the rationales of these enrichment analysis strategies. Using both microarray and RNA-seq data, we show that gene pairs with functional links in pathways tended to have positively correlated expression levels, which could result in an imbalance between the up- and downregulated genes in particular pathways. We then show that the imbalance could greatly reduce the statistical power for finding disease-associated pathways through the analysis of all-DE genes. Further, using gene expression profiles from five types of tumours, we illustrate that the separate analysis of up- and downregulated genes could identify more pathways that are really pertinent to phenotypic difference. In conclusion, analysing up- and downregulated genes separately is more powerful than analysing all of the DE genes together.
- Subjects :
- Computational Biology
Databases, Genetic
Down-Regulation physiology
Genes genetics
Humans
Microarray Analysis
Models, Genetic
Neoplasms genetics
Neoplasms metabolism
Sequence Analysis, RNA
Signal Transduction genetics
Transcriptome
Up-Regulation physiology
Gene Expression Regulation physiology
Genes physiology
Signal Transduction physiology
Subjects
Details
- Language :
- English
- ISSN :
- 1742-5662
- Volume :
- 11
- Issue :
- 92
- Database :
- MEDLINE
- Journal :
- Journal of the Royal Society, Interface
- Publication Type :
- Academic Journal
- Accession number :
- 24352673
- Full Text :
- https://doi.org/10.1098/rsif.2013.0950