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Table 3 Estimates and enriched categories of differentially a regulated non-common genes

From: Genome-wide expressions in autologous eutopic and ectopic endometrium of fertile women with endometriosis

Specific analysis Nature of differential change [Number of genes] Top enriched pathways [Gene symbol(s) of major candidate(s)] (p-value)
Pooled Up-regulated [50] WNT signaling [NRCAM, WNT16] (0)
   DNA damage-induced responses and apoptosis [CHEK1] (<0.01)
   Role of 14-3-3 proteins in cell cycle regulation [CHEK1] (<0.02)
   Cadherins mediated cell adhesion [CHP] (<0.03)
   Endothelial cell contacts by non-junctional mechanisms [CHP] (<0.03)
   Role of SCF complex in cell cycle regulation [CHEK1] (<0.03)
   ATM/ATR regulation of cell cycle [CHEK1] (<0.04)
   nNOS signaling in neuronal synapses [RASD1] (<0.03)
   Activation of astroglial cell proliferation by ACM3 [ERBB3] (<0.04)
   G-protein signaling in RhoA regulation pathway [ARHGAP26] (<0.04)
   CDK5 in apoptosis and survival [ERBB3] (<0.04)
   ERBB-family signaling [ERBB3] (<0.05)
   Regulation of ElF2 activity associated with translation [CSNK1G1] (<0.05)
   Ligand-independent activation of ESR1 and ESR2 [ERBB3] (<0.05)
   Non-genomic action of androgen receptor [WNT16] (<0.05)
  Down-regulated [41] Regulation of glucose and lipid metabolism [APOE] (0)
   GDNF signaling [ITGB1] (<0.04)
   Immune response involving antigen presentation by MHC class I [HLA-C] (0.05)
   Chemotaxis involving CCR4-induced leukocyte adhesion [ITGB1] (<0.05)
Stage 3 Up-regulated [4] No specific enriched category identified   
  Down-regulated [48] Cytoskeleton remodeling involving RalB and RalA regulation pathway [RALGDS] (<0.01)
   Clathrin coated vesicle formation [MYO1D] (<0.02)
   Transcriptional silencing involving HP1 family [PFDN5] (<0.02)
   G-protein signaling involving interaction among Ras-family GTPases and K-RAS/N-RAS/H_RAS regulation pathway [RALGDS] (<0.03)
Stage 4 Up-regulated [31] Cell contraction involving relaxin and GPCRs [ADCY6, EDNRA, RXFP1] (0)
   Development involving endothelin-1/EDNRA signaling [ADCY6, EDNRA] (0)
   DNA damage induced apoptosis and DNA repair [NBN] (<0.01)
   Beta-2 adrenergic dependent CFTR expression [ADCY6] (<0.01)
   Regulation of lipid metabolism [PPARA] (<0.02)
   Alpha-1 adrenergic receptor signaling [ADCY6] (<0.02)
   Mu- and kappa-type opioid receptor mediated physiological process [ADCY6] (<0.03)
   Mucin expression via IL-6, IL-17 signaling pathways [TRAF3IP2] (<0.04)
   G-protein signaling [ADCY6] (<0.04)
  Down-regulated [3] Transport from Golgi and ER to the apical membrane [PPIA] (0)
   Intracellular cholesterol and sphingolipids transport [PPIA] (<0.01)
Proliferative phase Up-regulated [109] RAS regulation pathway [BCR, RASGRF1] (0)
   TC21 regulation pathway [BCR, RASGRF1] (0)
   Regulation of CDC42 activity [BCR, FGFR1] (<0.01)
   Sin3 and NuRD mediated transcription regulation [CHD3, SIN3A] (<0.01)
   GDNF family signaling [GFRA2, NRTN] (<0.01)
   Phospholipid metabolism [GPD2, NRTN] (<0.02)
   Immune response involving CD40 signaling [IRF1, TRAF3IP2] (<0.02)
  Down-regulated [20] Cytoskeleton remodeling involving α-1A adrenergic receptor   
   Dependent inhibition of PI3K and regulation of actin by Rho GTPases [LAMB1, MYL12B] (<0.01)
   Cell contraction involving δ-type opioid receptor, S1P2 receptor, ACM [MYL12B] (<0.01)
   Development associated MAG dependent inhibition of neurite outgrowth [MYL12B] (<0.01)
   Development associated with TGF-beta dependent induction of EMT via RhoA, PI3K and ILK [TPM1] (<0.01)
   Cell adhesion involving histamine H1 receptor [MYL12B] (<0.01)
   Cell adhesion and chemotaxis involving integrin [LAMB1, MYL12B] (<0.01)
   Chemotaxis involving inhibitory action of lipoxins on IL-8 and leukotriene B4-induced neutrophil migration [MYL12B] (<0.01)
   GPCRs in platelet aggregation [MYL12B] (<0.02)
   Immune response involving CCR3 signaling in eosinophils [MYL12B] (<0.02)
   Oxidative phosphorylation [UQCR11] (<0.03)
Secretory phase Up-regulated [17] Transport involving RAN regulation pathway [TNPO1] (<0.01)
   Immune response involving MIF-JAB1 signaling [PGR] (<0.01)
   nNOS signaling in neuronal synapses and circadian rhythm [RASD1] (<0.02)
   Cell cycle associated spindle assembly and chromosome separation [TNPO1] (<0.02)
   Regulation of lipid metabolism [TNPO1] (<0.02)
   Regulation of glycogen metabolism [AGL] (<0.02)
   Progesterone mediated maturation [PGR] (<0.02)
   Cell adhesion associated ECM remodeling [MME] (<0.03)
   TGF-beta receptor signaling in development [TNPO1] (<0.03)
  Down-regulated [122] Cell contraction involving δ-type opioid receptor [MYL9] (0)
   Development associated Slit-Robo signaling [DPYSL2, ROBO3] (<0)
   Insulin mediated regulation of translation [ElF4EBP1, PPP1CC] (<0.01)
   Leukotriene 4 biosynthesis and metabolism [GGT5, LTA4H] (<0.01)
   Chemotaxis involving inhibitory action of lipoxins on IL-8 and leukotriene B4-induced neutrophil migration [MYL9, RAC2) (<0.01)
   Endoplasmic reticulum stress response pathway [ATF4, PPP1CC] (<0.01)
   Immune response involving CCR3 signaling in eosinophils [MYL9, RAC2] (<0.03)
   GTP-XTP metabolism [GUK1, NME3, POLR3H] (<0.03)
   Cytoskeleton remodeling via RalB regulation pathway [RALGDS] (<0.04)
Eutopic Up-regulated [182] Cytoskeleton remodeling involving ACM3 and ACM4 [CHRM4, GNAQ] (0)
   G-protein signaling involving regulation of cAMP levels by ACM [CHRM4, GNAQ] (0)
   Transcription involving Tubby signaling and HP1 family [GNAQ] (0)
   Regulation of lipid metabolism involving G-alpha(q) regulation [GNAQ, PTGS2] (0)
   Cell contacts by non-junctional mechanisms [ITGA5, MAG1, PECAM1] (<0.01)
   NMDA –dependent neurophysiological process [GNAQ, GRIN2A] (<0.01)
   Cell cycle at metaphase check point [CBX3, INCENP] (<0.01)
   G-protein signaling involving Rap1A regulation pathways [MAGI1, RAPGEF1] (<0.02)
   Regulation of translation through EIF4F activity [EIF4A2] (<0.03)
   Regulation of translation by alpha-1 adrenergic receptors [EIF4A2, GNAQ] (<0.03)
   Development involving endothelin-1/EDNRA signaling [GNAQ, NPPB] (<0.03)
   Cytoskeleton remodeling via FAK signalin [GNAQ, RAPGEF1] (<0.04)
   Immune response involving PGE2 common pathways [GNAQ, PTGS2] (<0.03)
   Immune response involving IL-17 signaling pathways [CXCL3, PTGS2] (<0.04)
   Cell contraction via oxytocin signaling [GNAQ, PTGS2] (<0.04)
   Transcription via PPAR pathway [MED1, PTGS2] (<0.04)
   Regulation of lipid metabolism through alpha-1 adrenergic receptors signaling via arachidonic acid [GNAQ, PTGS2] (<0.05)
  Down-regulated [48] Cell cycle regulation involving SCF complex [CDC34, NEDD8, UBA52] (0)
   p53 regulation involving SUMO [UBA52] (<0.02)
   Regulation of degradation and traffic of CFTR [DYNLL1, UBA52] (<0.02)
   WNT signaling pathway involving degradation of bete-catenin [UBA52] (<0.03)
   Transcriptional silencing involving HP1 family [PFDN5] (<0.03)
   Immune response involving IL-12 and MIF-JAB1 signaling pathways [UBA52] (<0.03)
   Angiotensin signaling via beta-arrestin [CLTA, UBA52] (<0.03)
   ATM/ATR regulation of G1/S and G2/M checkpoints [UBA52] (<0.04)
   NGF signaling for apoptosis and survival [EPB41L1]  
   and activation of NF-kB [UBA52] (<0.04)
   Neurophysiological process involving GABA-A receptor life cycle [CLTA] (<0.04)
   Regulation of translation initiation [EIF1, RPL7, RPL12, RPL15, RPL21, RPL22, RPL29, RPS3A, RPS10, RPS14, UBA52] (<0.04)
   Transition and termination of DNA replication [UBA52] (<0.04)
   Activin A signaling regulation [UBA52] (<0.05)
Ectopic Up-regulated [665] Beta-2 adrenergic-dependent CFTR expression [ADCY2, ADRB3, CREB1, PRKAR1B, PRKAR2B] (0)
   Mu-type opioid receptor mediated neurophysiological process [ADCY2, ADCY5, CREB1, HPCA, PRKAR1B, PRKAR2B] (0)
   Development involving alpha-1 and beta-adrenergic receptors signaling via cAMP and PIP3 signaling [ADCY2, ADCY5, AKT3, CREB1, FOXO3, GAB1, PRKAR1B, PRKAR2B, YWHAE] (0)
   Cell adhesion involving ephrin signaling [ADAM10, EFNA5, EPHA4, EPHB6] (0)
   Transport involving RAB3 regulation pathway [DMXL2, RAB3B] (0)
   Neurophysiological process involving corticoliberin signaling via CRHR1 [ADCY2, ADCY5, CACNA1C, CREB1, PRKAR2B, IVL] (0)
   Signal transduction involving cAMP and PKA signaling [ADCY2, ADCY5, CACNA1C, CREB1, PRKAR1B, PRKAR2B, PCTK1] (0)
   G-protein signaling involving G-Protein beta/gamma signaling cascades [ADCY2, ADCY5, AKT3, PRKAR1B, PRKAR2B] (0)
   G-protein signaling involving RhoA regulation pathway [ARHGEF2, EFNA5, EPHA4, MCF2L] (0)
   eNOS activity in cell contraction [ADCY5, CACNA1C, PRKAR1B,PRKAR2B, PRKG1] (0)
   MAG-dependent inhibition of neurite outgrowth [NGFR, PSEN2, RASGRF1] (0)
   Neurophysiological process involving delta-type opioid receptor [ADCY2, CREB1, HPCA, PRKAR1B, PRKAR2B] (<0.01)
   Neurophysiological process involving HTR1A receptor signaling [ADCY2, ADCY5, HPCA, HTR1A, PRKAR1B, PRKAR2B] (<0.01)
   Neurophysiological process involving melatonin signaling [ADCY2, ADCY5, CREB1, PRKAR1B, PRKAR2B, RORA] (<0.01)
   Neurophysiological process involving dopamine D2 receptor signaling [ADCY2, ADCY5, CACNA1C, PRKAR1B, PRKAR2B] (<0.01)
   Neurophysiological process in circadian rhythm [ADCAY1, CLOCK, CREB1, CACNA1C, RORA] (<0.01)
   Alpha-2 adrenergic receptor regulation of ion channels [ADCY5, AKT3, CACNA1C, PRKAR1B, PRKAR2B] (<0.01)
   NGF signaling pathway in apoptosis and survival [AKT3, CAD, GAB1] (<0.01)
   Transcription involving CREB pathway   (<0.01)
   Role of activin A in cell differentiation and proliferation [ADCY2, ADCY5, CREB1, NR5A1/SF1, PRKAR1B, PRKAR2B] (<0.01)
   GH-RH signaling [ADCY2, ADCY5, CACNA1C, CREB1, PRKAR1B, PRKAR2B] (<0.01)
   ZNF202 in regulation of expression of genes involved in atherosclerosis [ADRB3, APOL2, LPL] (<0.01)
   Regulation of lipid metabolism by niacin and isoprenaline [ADCY2, ADCY5, ADRB3, PRKAR1B, PRKAR2B] (<0.01)
   Ligand-independent activation of ESR1 and ESR2 [ADCY2, ADCY5, AKT3, PRKAR1B, PRKAR2B] (<0.01)
   Relaxin signaling pathway [ADCY5, AKT3, CREB1, PRKAR1B, PRKAR2B] (<0.01)
   Melanocyte development and pigmentation [AKT3, CREB1, PRKAR1B, PRKAR2B, PRKG1] (<0.01)
  Down-regulated [18] Immune response involving antigen presentation by MHC class I [PDIA3] (<0.01)
   Vitamin B6 metabolism [PHPT1] (<0.02)
   Blood coagulation and platelet degranulation [F13A1] (<0.03)
   Cholesterol and sphingolipids intracellular transport [PPIA] (<0.03)
   GSL metabolism   (<0.05)
Eutopic Up-regulated [19] Cell cycle at initiation of mitosis and regulation of G1/S transition [LMNB2, PPP2R3A] (<0.01)
   Dopamine D2 receptor transactivation of PDGF receptor [PPP2R3A] (<0.01)
   Apoptosis and survival involving caspase cascade, FAS signaling cascade and HTR1A signaling and anti-apoptosis by external signals via NF-kB [LMNB2, PPP2R3A] (<0.01)
   G-protein signaling involving regulation CDC42 activity [ARHGAP17] (<0.01)
   Gultamate regulation of Dopamine D1A receptor signaling [PPP2R3A] (<0.01)
   PKA signaling [PPP2R3A] (<0.02)
  Down-regulated [56] Translation involving regulation of ElF2 [PPP1CC] (0)
   DNA damage involving NHEJ mechanisms of DSBs repair [CSNK2A2] (<0.02)
   Cytoskeleton remodeling involving activin A [FNTA] (<0.02)
   Olfactory transduction [OR2H1] (<0.02)
   Cell cycle involving chromosome condensation in prometaphase, sister chromatic cohesion, regulation of S phase and initiation of mitosis [HIST1H1C] (<0.03)
   Cadherin mediated cell adhesion [PTPRF] (<0.03)
   GABA-A receptor mediated neurophysiological process [PPP1C] (<0.03)
   MAG-dependent inhibition of neurite outgrowth [MAG] (<0.05)
   Cell adhesion via PLAU signaling [CSNK2A2] (<0.05)
Ectopic Up-regulated [0]    
  Down-regulated [91] G-protein signaling involving Rap2A regulation pathway and G-protein alpha-s signaling cascade [PRKAR2B, RAPGEF3] (0)
   Glycolysis and gluconeogenesis [ENO2] (0)
   cAMP-Ca+2-dependent signal transduction [PRKAR2B, RAPGEF3] (<0.01)
   G protein mediated regulation of MAPK-ERK signaling [PRKAR2B, RAPGEF3] (<0.01)
   Development involving MAG, PACAP signaling, activin A, A2A and A2B receptor signaling and Hedgehog signaling [MYH14, NANOG, NTF3, PRKAR2B, RAPGEF3] (<0.01)
   Regulation of eNOS activity [PRKAR2B] (<0.01)
   CCR3 signaling in eosinophils [FGR, MYH14] (<0.02)
   NMDA dependent neurophysiological process [PRKAR2B, RAPGEF3] (<0.03)
   CFTR expression, maturation and activity [HSPA6, PRKAR2B] (<0.03)
  1. a > 3-fold at P < 0.01.