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Table 5 Summary of GSEA results for K-mean clusters

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

BROAD gene sets (Set description)  
Cluster identity Number of selection (set identity; p value; qFDR; NES) Total number of genes1; number of genes in classified gene families1,2
C1 (Cytogenetics)
K1 0  
K2 0  
K3 0  
K4 1 (Chr4q12; 0; 0.11; 1.8) 47; 6 (Cgf); 1 (Ong); 2 (Tf)
C2 (Functional)
K1 0  
K2 0  
K3 0  
K4 0  
C3 (Regulatory motif)
K1 1 (RRCCGTTA_UN; 0; 0.25; -1.8); 55; 1 (Cgf); 2 (Cdm); 2 (Ong); 3 (Pk); 11 (Tf)
K2 1 (V$AP4_q6; 0; 0.05; −2.0) 173; 1 (Cdm); 9 (Cgf); 7 (Hdp); 9 (Ong); 11(Pk);
   34 (Tf); 1 (Ts)
K3 0  
K4 1 (GCAAGA,MIR-431; 0; 0.04; 1.9) 39; 1 (Cdm); 2 (Cgf); 1 (Hdp); 2 (Ong); 1 (Pk); 6 (Tf); 2 (Ts)
C4 (Cancer gene neighborhood)
K1 2 (MORF_MYC; (0; 0.00; 2.3) 72; 1 (Cdm); 2 (Cgf); 5 (Hdp); 5 (Onc); 4 (Pk); 14 (Tf)
  (MORF_ESR1; 0; 0.04; 2.0) 160; 3 (Cdm); 7 (Cgf); 7 (Hdp); 8 (Ong); 9 (Pk); 36 (Tf); 3 (Ts)
K2 0  
K3 0  
K4 2 (MORF_RAD23B; 0; 0.18; 1.8) 164; 1 (Cgf); 2 (Ong); 1 (Pk); 8 (Tf); 2 (Ts)
  (GNF2_CCNA2; 0.02; 0.23; 1.8) 62; 1 (Cdm); 6 (Pk); 3 (Tf); 1 (Ts)
C5 (Gene ontology)
K1 0  
K2 0  
K3 0  
K4 2 (PATTERN_ BINDING; 0; 0.07; 2.1) 45; 2 (Cdm); 6 (Cgf); 1 (Tf)
  (POLYSACCHARIDE_BINDING; 0; 0.18; 1.9) 36; 6 (Cgf); 1 (Tf)
  1. 1Archived from GSEA data base [15].
  2. 2Based on common feature in homology and biochemical activities, not necessarily having common origin. FDR ≤0.25, minimally 10 genes in a set and maximum 1000 permutation. NES, Normalized enrichment score. The major gene families in selected gene sets in GSEA are: Cdm, cell differentiation markers (CD6, CD14, CD34, HMMR, NRCAM, PSG1, PVR, PVRL3, TLR2, and TNFSF4); Cgf, cytokines and growth factors (BMP10, CXCL5, FGF8, FGF10, FGF12, GMFB, HBEGF, HDGF, HTN3, IL13, IL16, INHA, LTBP4, MDK, MLN, NLN, NPFF, NPPA, NRG2, NRTN, PDGFRA, PF4, PF4V1, PGF, PPBP, PROK2, STC2, TNFSF4, TOR2A, VEGFA, VGF, and XCL2); Hdp, homeodomain proteins (BARX2, HOXA6, HOXB5, HOXC4, HOXC12, HOXD4, LBX1, LHX8, MSX1, PAX7, PAX8, PITX3, POU6F1, SIX3, and SIX5); Ong, oncogenes (ACT, ARNT, BCL2, BCL11B, BFA2T3, CNBP, ELF4, ERC1, EWSR1, GAS7, LCK, MSI2, MYC, NCKIPSD, NR4A3, PAX7, PAX8, PDGFRA, PICALM, RUNX1, TPM3, and TRIM24); Pk, protein kinases (ADRBK1, AURKA, AURKB, BUB1B, CAMK2G, DAPK2, EPHA2, ERN1, FLT1, GRK4, IKBKE, KSR2, LCK, MAP3K13, MAPK2K4, MAPK6, MELK, MYLK, NRK, OBSCN, PLK1, PRKACA, PRKCQ, PTK7, RPS6KB2, SNG1, STK16, STK17A, TRIM24, TTK, and WEE1); Tf, transcription factors (AFF2, ARNT, ATF7IP, ATRX, BACH1, BARX2, BCL11B, BRD1, CBFA2T3, CBX6, CLOCK, CNBP, COPS5, CREB3L1, EGR3, ELF4, EP400, ESR1, ESRRA, ETB3, EYA1, EYA3, EZH2, EZH2, FOSL1, FOSL2, FOXD3, FOXM1, GATA3, HDSE4, HMGB2, HMGN2, HOXA6, HOXB5, HOXC4, HOXC12, HOXD4, ID1, ID3, ILF3, IRF2, KLF13, LBX1, LHX8, MAZ, MBD4, MGA, MORF4L2, MSX1, MTA1, MYC, NEUROG3, NF1, NFIA, NFIC, NFRKB, NFX1, NR1I2, NR3C2, NR4A3, PAX7, PAX8, PAX9, PAXIP1, PHTF1, PIAS2, PITX3, POU6F1, PTF3L1, REST, RUNX1, RXRG, SART3, SF1 (NR5A1), SIX3, SIX3, SIX5, SMAD4, SMARCA2, SMARCA5, SOX12, SP3, TAF2, TBX15, TBX19, TBX5, TCF7, TFAP4, TFDP2, TRIM24, UBTF, VPS72, WT1, ZBTB22, ZNF133, ZNF134, ZNF146, ZNF157, ZNF238, and ZNF592); Ts, tumor suppressors (BRCA1, BUB1B, GATA3, MAPK2K4, NF1, SDHC, SMAD4, WT1, and XPC). The genes that showed differential expression between eutopic and ectopic samples in the present study are marked by underlines.