Table 3.

Common pathway categories identified by GSEA of the 3 ovarian endometriosis datasets

Pathway name	Classification	Genes
Up-regulation
PPAR signaling pathway	Endocrine System	26
Cytokine-cytokine receptor interaction	Signaling Molecules and Interaction	84
Cell adhesion molecules (CAMs)	Signaling Molecules and Interaction	68
Complement and coagulation cascades	Immune System	32
Toll-like receptor signaling pathway	Immune System	37
Hematopoietic cell lineage	Immune System	36
Asthma	Immune Disorders	12
Autoimmune thyroid disease	Immune Disorders	16
Systemic lupus erythematosus	Immune Disorders	29
Allograft rejection	Immune Disorders	16
Graft-versus-host disease	Immune Disorders	17
Arachidonic acid metabolism	Lipid Metabolism	19
Metabolism of xenobiotics by cytochrome P450	Xenobiotics Biodegradation and Metabolism	19
Drug metabolism - cytochrome P450	Xenobiotics Biodegradation and Metabolism	20
Type I diabetes mellitus	Metabolic Disorders	19
Olfactory transduction	Sensory System	4
Down-regulation
Fatty acid metabolism	Lipid Metabolism	21
Androgen and estrogen metabolism	Lipid Metabolism	5
Sphingolipid metabolism	Lipid Metabolism	18
Oxidative phosphorylation	Energy Metabolism	44
Citrate cycle (TCA cycle)	Carbohydrate Metabolism	13
Butanoate metabolism	Carbohydrate Metabolism	12
Pyrimidine metabolism	Nucleotide Metabolism	36
Glycosylphosphatidylinositol(GPI)-anchor biosynthesis	Glycan Biosynthesis and Metabolism	10
Lysine degradation	Amino Acid Metabolism	19
Folate biosynthesis	Metabolism of Cofactors and Vitamins	10
DNA polymerase	Replication and Repair	22
Base excision repair	Replication and Repair	16
Nucleotide excision repair	Replication and Repair	19
Mismatch repair	Replication and Repair	13
Homologous recombination	Replication and Repair	10
Cell cycle	Cell Growth and Death	57
Thyroid cancer	Cancers	15
Proteasome	Folding, Sorting and Degradation	13
Ubiquitin mediated proteolysis	Folding, Sorting and Degradation	50

Genes: Number of common genes included in the pathway.