GO ENRICHMENT ANALYSIS OF CLOCK GENES USING DIFFERENTIALLY METHYLATED BACKGROUND

<br>SUMMARYThis script performs Gene Ontology (GO) enrichment analysis on a set of clock-related CpGs in <i>Nasonia vitripennis</i>, using a background of differentially methylated genes. It identifies over-represented GO terms, applies FDR correction, and visualizes significant terms using semantic similarity metrics.<br>ORIGINAdapted from code by Alun Jones (see Bebane et al., 2019).<br>KEY STEPS1. Load GO annotations for the background gene set (differentially methylated genes).2. Create GOFrame and GeneSetCollection objects compatible with GOstats.3. Load a user-defined list of clock genes.4. Filter gene list to those with GO annotations.5. Run a hypergeometric test for enrichment across BP, CC, and MF ontologies.6. Apply FDR correction (Benjamini-Hochberg).7. Visualize enriched Biological Process terms using: - Treemap - Scatter plot - Heatmap - Word cloud<br>INPUT FILES- diff_backgroundGOannotations.csv (GO annotations for differentially methylated genes)- clock_genes.csv (list of clock-related CpGs)<br>OUTPUT FILES- `supplementary_tables_pnas.xlsx` → Sheet: Table_S4_GOterms (FDR-filtered GO terms)- `diff_erin_methylated_clock_genes_GO_treemap.png` → Treemap of reduced GO terms<br>SOFTWARE REQUIREMENTS- R packages: GOstats, GSEABase, treemap, readr, dplyr, rrvgo, openxlsx, org.Dm.eg.dbNOTES- Uses Drosophila GO database for semantic similarity.- Focuses on over-representation in the Biological Process ontology.<br>CITATIONBebane, P. et al. (2019). "Neonics and bumblebees." [Insert DOI]<br>CONTACTEamonn [e-mail]<br>