Pathway Enrichment Analysis: KEGG & WikiPathways for RNA-Seq
📖 RNA-Seq Data Analysis Workflow — check it out for an overview.
Pathway analysis (also called pathway enrichment analysis) is a method for identifying biological pathways that are significantly overrepresented in a given gene list compared to the full set of genes.
In RNA-Seq analysis, it is commonly used to determine which pathways are most strongly associated with differentially expressed genes.
What is a Pathway?
A pathway describes how genes, proteins, and other molecules interact with one another. Pathways encompass metabolic routes, signaling cascades, protein-protein interactions, and gene regulatory networks.
Two widely used pathway databases are Kyoto Encyclopedia of Genes and Genomes (KEGG) and WikiPathways. KEGG is free for academic researchers, but commercial use requires a license. WikiPathways is a community-curated resource that is freely available to everyone.
Example of a Pathway (WikiPathways)
What is Pathway Enrichment Analysis?
Pathway enrichment analysis detects pathways that appear significantly more often in a given gene list than would be expected by chance.
For example, suppose an RNA-Seq experiment identifies 600 differentially expressed genes. Among those 600 genes, 30 belong to the "Cytoplasmic ribosomal proteins" pathway. In the background set of 5,598 genes, only 87 are associated with this pathway. Compared to what you would expect from randomly drawing 600 genes from the background, the "Cytoplasmic ribosomal proteins" pathway is significantly overrepresented -- and is therefore reported as enriched.
RNA-Seq Data Analysis Software
This is an RNA-Seq Data Analysis Software recommended for those who:
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Users can perform gene expression quantification, identification of differentially expressed genes, gene ontology(GO) analysis, pathway analysis, as well as drawing volcano plots, MA plots, and heatmaps.
About the Author
BxINFO LLC
A research support company specializing in bioinformatics.
We provide tools and information to support life science research, with a focus on RNA-Seq analysis.