Blood Proteome GO Enrichment – Interactive Visualization

Interactive Gene Ontology (GO) enrichment visualizations for the PeptideAtlas human blood proteome.
Open any of the HTML files in results/ directly in a browser — no server needed.

Visualizations

File	Description
results/go_enrichment_network.html	Force-directed network — nodes = GO terms, edges = shared genes. Hover to see term details and gene lists.
results/go_enrichment_interactive.html	Interactive bubble/scatter of enriched GO terms, colored by namespace.
results/go_enrichment_dotplot.html	Dot plot of top enriched terms (size = gene count, color = FDR).

Reproducing the analysis

1. Install dependencies

pip install goatools pandas numpy matplotlib seaborn plotly networkx

2. Run GO enrichment

python peptide_atlas_go_enrichment.py   # computes enrichment → results/go_enrichment_results.tsv

3. Generate interactive HTMLs

python go_network_graph.py   # network graph
python go_enrichment.py      # dotplot + interactive scatter

Data

• data/peptide_atlas_blood.tsv – raw PeptideAtlas blood proteome export
• data/peptide_atlas_unique_genes.tsv – unique gene symbols used as the study set
• Large background files (go-basic.obo, gene2go) are downloaded automatically on first run.

Namespace color coding

Color	Namespace
Blue	Biological Process
Red	Molecular Function
Green	Cellular Component