title: Separate enrichment analysis of pathways for up- and downregulated genes.
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.
authors.affiliation: Bioinformatics Centre, School of Life Science, University of Electronic Science and Technology of China, , Chengdu 610054, People's Republic of China.
authors.forename: Guini
authors.initials: G
authors.lastname: Hong
authors.forename: Wenjing
authors.initials: W
authors.lastname: Zhang
authors.forename: Hongdong
authors.initials: H
authors.lastname: Li
authors.forename: Xiaopei
authors.initials: X
authors.lastname: Shen
authors.forename: Zheng
authors.initials: Z
authors.lastname: Guo
mesh_terms: D019295:Computational Biology; D030541:Databases, Genetic; D015536:Down-Regulation / Q000502:physiology; D005786:Gene Expression Regulation / Q000502:physiology*; D005796:Genes / Q000235:genetics / Q000502:physiology*; D006801:Humans; D046228:Microarray Analysis; D008957:Models, Genetic; D009369:Neoplasms / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology*; D059467:Transcriptome; D015854:Up-Regulation / Q000502:physiology
keywords: RNA-seq; enrichment analysis; gene expression; microarray