bio-pathway-go-enrichment

Core Pattern

Goal: Identify enriched Gene Ontology terms in a gene list from differential expression or similar analyses.

Approach: Test for over-representation of GO terms using the hypergeometric test via clusterProfiler enrichGO.

"Run GO enrichment on my gene list" → Test whether biological process, molecular function, or cellular component terms are over-represented among significant genes.

Prepare Gene List from DE Results

Goal: Extract significant gene IDs from differential expression results and convert to the format required by enrichGO.

Approach: Filter DE results by adjusted p-value and fold change, then convert gene symbols to Entrez IDs using bitr.

library(dplyr)

de_results <- read.csv('de_results.csv')

sig_genes <- de_results %>%
    filter(padj < 0.05, abs(log2FoldChange) > 1) %>%
    pull(gene_id)

## ID Conversion with bitr

**Goal:** Convert between gene identifier types (Ensembl, Symbol, Entrez) for compatibility with enrichment tools.

**Approach:** Use clusterProfiler bitr to map between ID types using organism annotation databases.

```r