Table 3.

Network and Gene Analysis of Differentially Expressed mRNA, from RNA-Seq of Endometriotic Stromal and Epithelial Samples, by Ingenuity Pathway Analysis (IPA) and DAVID.

Ingenuity Pathway Analysis
z Score	Function	Genes
Stromal
−2.190	Immune cell trafficking decrease	MYD88 upstream
−2.366	Antigen-presenting cell movement decrease	C3, CXCL12, IL15, MYD88, PLXND1, PTGDS, SELE
−2.000	Mast cell migration decrease	C3, CXCL12, IL15, PIK3R1
−2.216	Macrophage cell movement decrease	C3, CXCL12, IL15, PLXND1, PTGDS
−2.177	Phagocyte maturation decrease	CSF3, IL-15, MYD88, PIK3R1, SERPINA1
−2.219	Inflammatory disease decrease	C3, CXCL12, DLL4, MYD88, PIK3R1
2.321	Cell morphology increases cell size	CBS, DEPTOR, PIM2, PLCB1, UCN2, IGFBP2
2.186	Muscle cell migration increase	IGFBP2, MMP7, MYOCD, POSTN, SERPINA1
Epithelial
2.268	Cancer increase	TGFβ1 upstream
2.537	Tumor cell proliferation increase	AXL, CST6, IL1RN, MMP2, NOS2, PTGS2 (COX2), ZEB1
2.420	Vascularization increase	ADAMTS1, ALOX5, FGF2, IGF2, IL1B, NOS2, NRP2, SPARC
2.803	Cell migration increase	ALOX5, AXL, CDK6, CHST10, CXCL5, FGF2, FMOD, GCNT1, HEY1, IGF2, IL1B, NOS2, NQO1, NRP2, RAP1GAP, SPARC, SPDEF, TGM2
2.608	Leukocyte migration increase	ALOX5, AQP9, CXCL5, FGF2, GCNT1, IGF2, IL1B, NOS2, NQO1, NRP2, RAP1GAP, SPARC, SPDEF, TGM2
DAVID
Function	Gene Number	Enrichment	P Value	Benjamini
Stromal	150 genes
Signal	64	8.34	2.3 × 10−13	5.9 × 10−11
Extracellular region	29	5.03	4.9 × 10−8	4.6 × 10−6
Cell adhesion	17	3.54	4.5 × 10−4	7.4 × 10−2
Vasculature development	12	2.66	1.4 × 10−5	4.2 × 10−3
EGF-like region	10	2.17	7.5 × 10−4	1.5 × 10−1
Neuropeptide signal	7	1.88	1.7 × 10−4	4.1 × 10−2
Carbohydrate binding	11	1.83	7.2 × 10−4	1.2 × 10−1
Hormone regulation	8	1.78	3.9 × 10−4	7.4 × 10−2
Epithelial	213 genes
Extracellular	35	5.41	8.1 × 10−8	1.9 × 10−5
Signal	48	5.37	1.6 × 10−9	5.6 × 10−7
Vasculature development	11	2.44	1.1 × 10−3	1.3 × 10−1
Oxidoreductase	19	2.27	4.7 × 10−5	3.3 × 10−3