Over Representation Analysis
Over Representation Analysis evaluates whether user-selected reactions are statistically over-represented within GEM subsystems by applying hypergeometric enrichment using GSEApy, enabling pathway-level interpretation of reaction-based perturbations.
Input
A one column CSV File containing reaction names in each row
Workflow
ORA Result Column Descriptions
| Column Name | Intepretations |
|---|---|
| Adjusted P-value | Multiple testing corrected p-value (FDR). Indicates statistical significance after adjusting for false positives. |
| Combined Score | A weighted score combining p-value and enrichment magnitude (from Enrichr/GSEApy formula). Higher = stronger enrichment. |
| Gene_set | Identifier for the gene set or pathway group being tested (e.g., subsystem index). |
| Genes | List of input reactions/genes that overlap with the pathway being tested. |
| Odds Ratio | Measure of enrichment strength; ratio of observed vs expected overlap. >1 suggests over-representation. |
| Overlap | Count of overlapping reactions vs total available in the pathway (e.g., 6/6 = 6 out of 6). |
| P-value | Significance score from hypergeometric test before multiple testing correction. |
| Term | Name of the pathway or subsystem being enriched (e.g., Glycolysis, TCA Cycle). |