New ERGO Feature: Gene Set Enrichment Analysis
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A Gene Set Enrichment ANALYSIS in ERGO
Quickly identify significantly up and down regulated pathway and functional categories using ERGO’s gene set enrichment analysis (GSEA). Gene set enrichment analysis detects concordant movement of gene sets between two phenotypes, usually experimental conditions. In this way the researcher can identify the statistically significant pathways and infer the effect the experimental conditions had upon their organism of study.
ERGO currently supports the following pathway sets:
ERGO Pathway Database
KEGG Pathway Database
Gene Ontology Terms (Biological Process, Molecular Function, Cellular Component)
Creating a new GSEA for RNA-Seq data is easy:
Navigate to your RNA-Seq Experiment of choice
Click the button labeled “+ add analysis”
Select “Gene Set Enrichment Analysis using Gage”
Select a contrast you want to compare - this will decide which samples are to be compared.
Finally, select the gene sets to group genes. There will be up to 5 options depending upon the reference genome: ERGO, KEGG, GO - Biological Process, GO - Molecular Function, GO - Cellular Component. If one of the options you would like to use is unable to be selected, please contact ERGO Support.
Click “Run”. Your analysis will complete in a few minutes!
Setting up A Gene Set Enrichment Analysis in ERGO
When the analysis has completed click on “View” to see the results. Depending on the gene sets you selected, you may see up two top level sections: “Significantly Up Regulated” and “Significantly Down Regulated”. The Tree Map represents the significantly up regulated pathways or pathway categories, filtered by adjusted P value <= 0.1. The size of the area represents the relative size of the gene set that was tested. Areas that are more red are more enriched, while areas that are blue are less so. Clicking on any of the boxes will display a heat map of the genes in that set.
A Pathway Interactive Heatmap Generated By ERGO
For more information about Gene Set Enrichment Analysis or how we can assist you with your projects, please contact us:
