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fix spelling error in pathway analysis
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obigriffith committed Apr 29, 2024
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In this secion we will use the GAGE tool in R to test for significantly enriched sets of genes within those genes found to be significantly "up" and "down" in our UHR vs HBR differential gene expression analysis. Do we see enrichment for genes associated with brain related cell types and processes in the list of DE genes that have significant differential expression beween the UHR samples compared to the HBR samples?
In this section we will use the GAGE tool in R to test for significantly enriched sets of genes within those genes found to be significantly "up" and "down" in our UHR vs HBR differential gene expression analysis. Do we see enrichment for genes associated with brain related cell types and processes in the list of DE genes that have significant differential expression beween the UHR samples compared to the HBR samples?

### What is gage?
The Generally Applicable Gene-set Enrichment tool ([GAGE](https://bioconductor.org/packages/release/bioc/html/gage.html)) is a popular bioconductor package used to perform gene-set enrichment and pathway analysis. The package works independent of sample sizes, experimental designs, assay platforms, and is applicable to both microarray and RNAseq data sets. In this section we will use [GAGE](https://bioconductor.org/packages/release/bioc/html/gage.html) and gene sets from the "Gene Ontology" ([GO](http://www.geneontology.org/)) and the [MSigDB](https://www.gsea-msigdb.org/gsea/msigdb) databases to perform pathway analysis.
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