Supplemental Table 3. NFκB-regulated and inflammation-related differentially expressed in FTEb(S) samples (n=4) relative to remaining luteal phase FTE samples (n=8).

Probe Set ID Title Gene Symbol Fold Change* p-value

Increased in FTEb(S) samples (186 probe sets) 209959_at nuclear receptor subfamily 4, group A, member 3 NR4A3 19.83 8.4826275E-4 217738_at nicotinamide phosphoribosyltransferase NAMPT 12.34 0.003273 215078_at superoxide dismutase 2, mitochondrial SOD2 11.14 0.010432 206552_s_at tachykinin, precursor 1 TAC1 9.84 0.007360 201348_at glutathione peroxidase 3 (plasma) GPX3 9.70 0.014476 217739_s_at nicotinamide phosphoribosyltransferase NAMPT 8.26 0.004631 202859_x_at 8 IL8 7.93 0.043747 236495_at nicotinamide phosphoribosyltransferase NAMPT 7.89 0.001434 myeloid/lymphoid or mixed-lineage leukemia (trithorax 211071_s_at homolog, Drosophila); translocated to, 11 MLLT11 7.55 0.009800 207466_at galanin prepropeptide GAL 7.55 0.039294 243296_at G0S9 mRNA, instability elements NAMPT 7.54 0.003790 221477_s_at superoxide dismutase 2, mitochondrial SOD2 7.53 0.012492 209875_s_at secreted phosphoprotein 1 SPP1 6.92 0.019227 214091_s_at glutathione peroxidase 3 (plasma) GPX3 6.01 0.027464 210538_s_at baculoviral IAP repeat-containing 3 BIRC3 5.67 0.010586 CD55 molecule, decay accelerating factor for 201925_s_at complement (Cromer blood group) CD55 5.34 0.001130 218541_s_at 8 open reading frame 4 C8orf4 5.32 0.046228 244536_at tumor binding protein, 2 TP53BP2 5.20 0.008577 -related cell adhesion molecule 1 209498_at (biliary glycoprotein) CEACAM1 4.74 0.005984 CD55 molecule, decay accelerating factor for 241615_x_at complement (Cromer blood group) CD55 4.72 0.014010 205758_at CD8a molecule CD8A 4.70 0.014737 204440_at CD83 molecule CD83 4.68 0.036789 CD55 molecule, decay accelerating factor for 243395_at complement (Cromer blood group) CD55 4.46 0.034940 203561_at Fc fragment of IgG, low affinity IIa, receptor (CD32) FCGR2A 4.16 0.035934 Fc fragment of IgE, high affinity I, receptor for; gamma 1554899_s_at polypeptide FCER1G 4.16 0.002125 210845_s_at plasminogen activator, PLAUR 4.10 8.392256E-4 transglutaminase 2 (C polypeptide, protein-glutamine- 201042_at gamma-glutamyltransferase) TGM2 4.03 0.046188 serpin peptidase inhibitor, clade B (ovalbumin), 242814_at member 9 SERPINB9 4.01 0.004845 212587_s_at protein tyrosine phosphatase, receptor type, C PTPRC 3.88 0.020730 serpin peptidase inhibitor, clade A (alpha-1 antiprotein- 202833_s_at ase, antitrypsin), member 1 SERPINA1 3.85 0.006534 215049_x_at CD163 molecule CD163 3.66 0.027666 226342_at , beta, non-erythrocytic 1 SPTBN1 3.59 0.024181 222528_s_at solute carrier family 25, member 37 SLC25A37 3.55 0.028280 Fc fragment of IgE, high affinity I, receptor for; gamma 204232_at polypeptide FCER1G 3.53 0.004663 217546_at metallothionein 1M MT1M 3.38 0.010239 239045_at endoplasmic reticulum to nucleus signaling 1 ERN1 3.36 0.007162 203508_at receptor superfamily, member 1B TNFRSF1B 3.36 0.004415 serpin peptidase inhibitor, clade A (alpha-1 antiprotein- 211429_s_at ase, antitrypsin), member 1 SERPINA1 3.24 0.005363 Probe Set ID Gene Title Gene Symbol Fold Change* p-value 1556346_at coactosin-like 1 (Dictyostelium) COTL1 3.22 0.017314 202068_s_at low density lipoprotein receptor LDLR 3.17 0.036231 201859_at serglycin SRGN 3.15 8.588452E-4 233627_at megakaryoblastic leukemia (translocation) 1 MKL1 3.14 6.398543E-4 P59fyn(T)=OKT3-induced calcium influx regulator 1559101_at [human, Jurkat J6 T cell line, mRNA Partial, 1605 nt] FYN 3.11 0.004810 CD55 molecule, decay accelerating factor for 201926_s_at complement (Cromer blood group) CD55 2.97 0.027754 244035_at B-cell CLL/lymphoma 2 BCL2 2.91 0.046942 235745_at endoplasmic reticulum to nucleus signaling 1 ERN1 2.90 0.006626 208763_s_at TSC22 domain family, member 3 TSC22D3 2.83 0.013059 212501_at CCAAT/enhancer binding protein (C/EBP), beta CEBPB 2.79 0.002550 200798_x_at myeloid cell leukemia sequence 1 (BCL2-related) MCL1 2.77 0.003726 242106_at mitogen-activated protein kinase 1 MAPK1 2.62 0.013185 211924_s_at plasminogen activator, urokinase receptor PLAUR 2.60 0.005440 213076_at inositol 1,4,5-trisphosphate 3-kinase C ITPKC 2.59 0.003654 211919_s_at (C-X-C motif) receptor 4 CXCR4 2.59 0.001906 220491_at hepcidin antimicrobial peptide HAMP 2.54 0.040021 serpin peptidase inhibitor, clade B (ovalbumin), 209723_at member 9 SERPINB9 2.52 0.001842 212588_at protein tyrosine phosphatase, receptor type, C PTPRC 2.48 0.030983 CD74 molecule, major histocompatibility complex, class 1567628_at II invariant chain CD74 2.47 0.013567 1566243_at cut-like homeobox 1 CUX1 2.47 0.007385 209201_x_at chemokine (C-X-C motif) receptor 4 CXCR4 2.45 0.006723 224583_at coactosin-like 1 (Dictyostelium) COTL1 2.45 0.039919 201858_s_at serglycin SRGN 2.44 0.021120 206118_at signal transducer and activator of transcription 4 STAT4 2.44 0.018549 229799_s_at neural cell adhesion molecule 1 NCAM1 2.41 0.029896 214240_at galanin prepropeptide GAL 2.41 0.016115 222529_at solute carrier family 25, member 37 SLC25A37 2.35 0.001384 carcinoembryonic antigen-related cell adhesion molecule 1 206576_s_at (biliary glycoprotein) CEACAM1 2.34 0.035600 204924_at toll-like receptor 2 TLR2 2.33 0.029449 218136_s_at solute carrier family 25, member 37 SLC25A37 2.33 3.6045845E-4 37152_at peroxisome proliferator-activated receptor delta PPARD 2.29 0.004995 221059_s_at coactosin-like 1 (Dictyostelium) COTL1 2.27 0.010840 211745_x_at hemoglobin, alpha 1 /// hemoglobin, alpha 2 HBA1 /// HBA2 2.24 0.032968 1561762_s_at UPF2 regulator of nonsense transcripts homolog (yeast) UPF2 2.23 0.009737 203645_s_at CD163 molecule CD163 2.19 0.030180 214866_at plasminogen activator, urokinase receptor PLAUR 2.17 0.012954 221920_s_at solute carrier family 25, member 37 SLC25A37 2.16 0.025933 231771_at protein, beta 6, 30kDa GJB6 2.16 0.039615 209681_at solute carrier family 19 (thiamine transporter), member 2 SLC19A2 2.14 0.018404 208075_s_at chemokine (C-C motif) ligand 7 CCL7 2.13 0.045802 201667_at gap junction protein, alpha 1, 43kDa GJA1 2.12 0.006631 206337_at chemokine (C-C motif) receptor 7 CCR7 2.11 2.7350875E-4 v-rel reticuloendotheliosis viral oncogene homolog 206036_s_at (avian) REL 2.11 0.021887 221905_at cylindromatosis (turban tumor syndrome) CYLD 2.08 0.025454 238643_at C1ORF15-NBL1 read-through transcript C1orf15-NBL1 2.04 0.011016 223961_s_at inducible SH2-containing protein CISH 2.04 0.015802 240798_at cut-like homeobox 1 CUX1 2.03 0.032234 209795_at CD69 molecule CD69 2.02 0.042785 Probe Set ID Gene Title Gene Symbol Fold Change* p-value 207075_at NLR family, pyrin domain containing 3 NLRP3 2.01 0.003692 204286_s_at phorbol-12-myristate-13-acetate-induced protein 1 PMAIP1 2.00 0.040890 201743_at CD14 molecule CD14 1.99 0.004482 206461_x_at metallothionein 1H MT1H 1.98 0.030181 mucosa associated lymphoid tissue lymphoma 210017_at translocation gene 1 MALT1 1.98 0.014663 238760_at tyrosyl-tRNA synthetase YARS 1.96 0.016669 229063_s_at coiled-coil domain containing 107 CCDC107 1.96 0.009146 218012_at TSPY-like 2 TSPYL2 1.94 0.003847 202963_at regulatory factor X, 5 (influences HLA class II expression) RFX5 1.93 0.003992 202067_s_at low density lipoprotein receptor LDLR 1.91 0.003633 204881_s_at UDP-glucose ceramide glucosyltransferase UGCG 1.89 0.002327 203320_at SH2B adaptor protein 3 SH2B3 1.86 0.025850 221577_x_at growth differentiation factor 15 GDF15 1.86 0.048176 213988_s_at spermidine/spermine N1-acetyltransferase 1 SAT1 1.84 0.040285 228635_at protocadherin 10 PCDH10 1.84 0.010591 signal transducer (gp130, 204864_s_at receptor) IL6ST 1.84 6.112349E-4 203455_s_at spermidine/spermine N1-acetyltransferase 1 SAT1 1.82 0.049387 1552480_s_at protein tyrosine phosphatase, receptor type, C PTPRC 1.81 0.010091 214533_at chymase 1, mast cell CMA1 1.80 0.003060 protein kinase, AMP-activated, beta 1 non-catalytic 201834_at subunit PRKAB1 1.80 0.023147 1558924_s_at CAP-GLY domain containing linker protein 1 CLIP1 1.77 0.016763 227660_at anthrax toxin receptor 1 ANTXR1 1.76 1.9182866E-4 201587_s_at interleukin-1 receptor-associated kinase 1 IRAK1 1.75 0.023572 CD74 molecule, major histocompatibility complex, class 209619_at II invariant chain CD74 1.75 0.006791 203922_s_at cytochrome b-245, beta polypeptide CYBB 1.73 0.017394 209752_at regenerating islet-derived 1 alpha REG1A 1.70 0.013211 224694_at anthrax toxin receptor 1 ANTXR1 1.70 0.032156 237568_at solute carrier family 25, member 37 SLC25A37 1.68 0.003973 225258_at binding LIM protein 1 FBLIM1 1.67 0.033067 226275_at MAX dimerization protein 1 MXD1 1.67 0.015822 229120_s_at CDC42 small effector 1 CDC42SE1 1.66 8.729772E-4 242218_at peroxisome proliferator-activated receptor delta PPARD 1.66 0.031294 215868_x_at SRY (sex determining region Y)-box 5 SOX5 1.65 0.002135 218603_at headcase homolog (Drosophila) HECA 1.64 0.048368 202820_at aryl hydrocarbon receptor AHR 1.63 0.043736 nuclear factor of kappa polypeptide gene enhancer 209239_at in B-cells 1 NFKB1 1.63 0.045093 207539_s_at IL4 1.62 0.002696 220093_at anthrax toxin receptor 1 ANTXR1 1.62 0.010835 218157_x_at CDC42 small effector 1 CDC42SE1 1.62 0.004822 207275_s_at acyl-CoA synthetase long-chain family member 1 ACSL1 1.60 0.002658 216979_at nuclear receptor subfamily 4, group A, member 3 NR4A3 1.60 0.049994 203751_x_at jun D proto-oncogene JUND 1.59 0.013422 212089_at A/C LMNA 1.59 0.038807 212549_at signal transducer and activator of transcription 5B STAT5B 1.59 0.010713 207667_s_at mitogen-activated protein kinase kinase 3 MAP2K3 1.59 0.036255 signal transducer and activator of transcription 6, 201332_s_at interleukin-4 induced STAT6 1.57 0.026109 232210_at B-cell CLL/lymphoma 2 BCL2 1.57 0.041141 214974_x_at chemokine (C-X-C motif) ligand 5 CXCL5 1.56 0.042655 Probe Set ID Gene Title Gene Symbol Fold Change* p-value 216006_at WAS/WASL interacting protein family, member 2 WIPF2 1.56 0.047250 209331_s_at MYC associated factor X MAX 1.55 0.022030 204103_at chemokine (C-C motif) ligand 4 CCL4 1.54 0.003444 211339_s_at IL2-inducible T-cell kinase ITK 1.54 0.001877 202123_s_at c-abl oncogene 1, receptor tyrosine kinase ABL1 1.53 0.002332 206143_at solute carrier family 26, member 3 SLC26A3 1.51 0.017088

leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6 /// leukocyte immuno- globulin-like receptor, subfamily B (with TM and ITIM 210784_x_at domains), member 3 LILRA6 /// LILRB3 1.50 0.023399 pescadillo homolog 1, containing BRCT domain 202212_at (zebrafish) PES1 1.50 0.017344 213535_s_at -conjugating E2I (UBC9 homolog, yeast) UBE2I 1.50 0.005547 transglutaminase 2 (C polypeptide, protein-glutamine- 211573_x_at gamma-glutamyltransferase) TGM2 1.49 0.003080 219385_at SLAM family member 8 SLAMF8 1.49 0.022057 219656_at protocadherin 12 PCDH12 1.48 0.017782 209295_at tumor necrosis factor receptor superfamily, member 10b TNFRSF10B 1.46 0.021302 nuclear factor of kappa light polypeptide gene enhancer 1553042_a_at in B-cells inhibitor, delta NFKBID 1.45 0.046838 202076_at baculoviral IAP repeat-containing 2 BIRC2 1.45 0.005404 211395_x_at Fc fragment of IgG, low affinity IIc, receptor for (CD32) FCGR2C 1.44 0.030286 207643_s_at tumor necrosis factor receptor superfamily, member 1A TNFRSF1A 1.42 0.025562 227821_at leucine-rich repeat LGI family, member 4 LGI4 1.40 0.018515 solute carrier family 40 (iron-regulated transporter), 223044_at member 1 SLC40A1 1.38 0.007587 211076_x_at atrophin 1 ATN1 1.38 0.015878 214326_x_at jun D proto-oncogene JUND 1.37 0.017567 TAF8 RNA polymerase II, TATA box binding protein 229412_at (TBP)-associated factor, 43kDa TAF8 1.36 0.046453 1554442_at BEST1 1.36 0.007826 201122_x_at eukaryotic translation initiation factor 5A EIF5A 1.35 0.034802 transglutaminase 2 (C polypeptide, protein-glutamine- 211003_x_at gamma-glutamyltransferase) TGM2 1.35 0.023790 1565776_at ATP-binding cassette, sub-family A (ABC1), member 1 ABCA1 1.35 0.003270 205745_x_at ADAM metallopeptidase domain 17 ADAM17 1.34 0.020652 239645_at cerebral cavernous malformation 2 CCM2 1.34 0.040923 205479_s_at plasminogen activator, urokinase PLAU 1.34 0.034834 210973_s_at fibroblast receptor 1 FGFR1 1.34 0.044220 229438_at family with sequence similarity 20, member C FAM20C 1.33 0.002698 toll-interleukin 1 receptor (TIR) domain containing 1554091_a_at adaptor protein TIRAP 1.33 0.006267 sphingomyelin phosphodiesterase 3, neutral membrane 231732_at (neutral sphingomyelinase II) SMPD3 1.33 0.008108 242020_s_at Z-DNA binding protein 1 ZBP1 1.32 0.015030 214536_at secreted LY6/PLAUR domain containing 1 SLURP1 1.31 0.047118 1552256_a_at scavenger receptor class B, member 1 SCARB1 1.30 0.044671 210405_x_at tumor necrosis factor receptor superfamily, member 10b TNFRSF10B 1.29 0.037524 205746_s_at ADAM metallopeptidase domain 17 ADAM17 1.28 0.026865 1564301_a_at RPA interacting protein RPAIN 1.28 0.004475 inhibitor of kappa light polypeptide gene enhancer in 211027_s_at B-cells, kinase beta IKBKB 1.28 0.041157 206877_at MAX dimerization protein 1 MXD1 1.27 0.034408 1565735_at cyclin D2 CCND2 1.26 0.044847 Probe Set ID Gene Title Gene Symbol Fold Change* p-value 207849_at IL2 1.24 0.028749 214576_at 36 KRT36 1.24 0.047042 protein kinase, AMP-activated, beta 1 non-catalytic 201835_s_at subunit PRKAB1 1.23 0.014757 211108_s_at 3 (a protein tyrosine kinase, leukocyte) JAK3 1.21 0.001169 214623_at F-box and WD repeat domain containing 4 pseudogene 1 FBXW4P1 1.19 0.033293 gremlin 1, knot superfamily, homolog (Xenopus 218468_s_at laevis) GREM1 1.19 0.003647 214266_s_at PDZ and LIM domain 7 (enigma) PDLIM7 1.18 0.024371 227365_at ataxia, cerebellar, Cayman type ATCAY 1.15 0.012785 234152_at chromosome 14 open reading frame 43 C14orf43 1.09 0.038208 1556773_at parathyroid -like hormone PTHLH 1.08 0.013283

Decreased in FTEb(S) samples (78 probe sets) 209555_s_at CD36 molecule (thrombospondin receptor) CD36 8.28 0.014401 206488_s_at CD36 molecule (thrombospondin receptor) CD36 6.55 0.018697 206271_at toll-like receptor 3 TLR3 3.93 0.005009 214633_at SRY (sex determining region Y)-box 3 SOX3 3.51 5.093901E-4 232406_at jagged 1 JAG1 3.51 0.004620 244881_at leishmanolysin-like (metallopeptidase M8 family) LMLN 3.38 0.005215 212971_at cysteinyl-tRNA synthetase CARS 2.93 0.019810 235256_s_at galactose mutarotase (aldose 1-epimerase) GALM 2.92 4.515564E-4 219850_s_at ets homologous factor EHF 2.83 0.038894 224189_x_at ets homologous factor EHF 2.78 0.009682 241397_at ets homologous factor EHF 2.72 0.014046 232360_at ets homologous factor EHF 2.68 0.006579 211110_s_at AR 2.65 0.011095 232361_s_at ets homologous factor EHF 2.47 0.009302 202154_x_at , beta 3 TUBB3 2.44 0.003100 34726_at , voltage-dependent, beta 3 subunit CACNB3 2.44 6.583853E-4 222240_s_at inositol-3-phosphate synthase 1 ISYNA1 2.44 0.007828 242901_at SET binding protein 1 SETBP1 2.41 0.037782 222434_at enabled homolog (Drosophila) ENAH 2.38 0.004106 205714_s_at zinc finger, MYND-type containing 10 ZMYND10 2.37 0.001617 226424_at calcyphosine CAPS 2.36 0.005649 231729_s_at calcyphosine CAPS 2.33 0.002302 213476_x_at tubulin, beta 3 TUBB3 2.28 0.002899 205659_at histone deacetylase 9 HDAC9 2.25 0.045200 210947_s_at mutS homolog 3 (E. coli) MSH3 2.21 0.005728 201242_s_at ATPase, Na+/K+ transporting, beta 1 polypeptide ATP1B1 2.17 0.004948 208485_x_at CASP8 and FADD-like apoptosis regulator CFLAR 2.14 0.048023 220125_at , axonemal, intermediate chain 1 DNAI1 2.05 0.010807 220816_at lysophosphatidic acid receptor 3 LPAR3 2.05 0.033002 208614_s_at filamin B, beta ( binding protein 278) FLNB 2.02 0.001381 213373_s_at caspase 8, apoptosis-related cysteine peptidase CASP8 2.01 0.044033 solute carrier family 22 (organic cation/ergothioneine 205896_at transporter), member 4 SLC22A4 1.97 0.013647 225031_at chromodomain helicase DNA binding protein 6 CHD6 1.96 0.006135 208025_s_at high mobility group AT-hook 2 HMGA2 1.90 0.028012 209530_at calcium channel, voltage-dependent, beta 3 subunit CACNB3 1.85 0.001285 215807_s_at plexin B1 PLXNB1 1.81 0.005972 221599_at chromosome 11 open reading frame 67 C11orf67 1.80 0.018167 205130_at renal tumor antigen RAGE 1.76 0.036996 244023_at spleen tyrosine kinase SYK 1.72 0.015982 Probe Set ID Gene Title Gene Symbol Fold Change* p-value spastic paraplegia 7 (pure and complicated autosomal 214494_s_at recessive) SPG7 1.71 0.048771 230561_s_at chromosome 2 open reading frame 67 C2orf67 1.69 0.013260 1555520_at patched homolog 1 (Drosophila) PTCH1 1.68 0.028589 prostaglandin-endoperoxide synthase 1 (prostaglandin 238669_at G/H synthase and cyclooxygenase) PTGS1 1.68 0.043538 222574_s_at DEAH (Asp-Glu-Ala-His) box polypeptide 40 DHX40 1.67 0.038108 209508_x_at CASP8 and FADD-like apoptosis regulator CFLAR 1.67 0.035357 218277_s_at DEAH (Asp-Glu-Ala-His) box polypeptide 40 DHX40 1.64 0.003383 215178_x_at N-acylethanolamine acid amidase NAAA 1.64 0.013123 205887_x_at mutS homolog 3 (E. coli) MSH3 1.59 0.038910 216449_x_at 90kDa beta (Grp94), member 1 HSP90B1 1.58 0.014468 1560386_at exportin 1 (CRM1 homolog, yeast) XPO1 1.56 0.018875 1553306_at caspase 8, apoptosis-related cysteine peptidase CASP8 1.56 0.028473 220088_at complement component 5a receptor 1 C5AR1 1.55 0.039132 219588_s_at non-SMC condensin II complex, subunit G2 NCAPG2 1.55 0.004980 231825_x_at activating transcription factor 7 interacting protein ATF7IP 1.54 0.008275 211316_x_at CASP8 and FADD-like apoptosis regulator CFLAR 1.53 0.045205 205733_at Bloom syndrome BLM 1.52 0.022254 208864_s_at thioredoxin TXN 1.48 0.043650 200599_s_at heat shock protein 90kDa beta (Grp94), member 1 HSP90B1 1.48 0.047165 208775_at exportin 1 (CRM1 homolog, yeast) XPO1 1.47 9.7516685E-4 201032_at bladder cancer associated protein BLCAP 1.46 0.025663 210586_x_at Rh blood group, CcEe antigens RHCE 1.43 0.006547 201620_at membrane-bound transcription factor peptidase, site 1 MBTPS1 1.41 0.032617 231234_at cathepsin C CTSC 1.37 0.011104 217820_s_at enabled homolog (Drosophila) ENAH 1.37 0.027260 1553685_s_at Sp1 transcription factor SP1 1.36 0.036422 203519_s_at UPF2 regulator of nonsense transcripts homolog (yeast) UPF2 1.35 0.031173 211130_x_at EDA 1.29 0.012126 1555330_at glutamate-cysteine ligase, catalytic subunit GCLC 1.29 0.049608 1554216_at coiled-coil domain containing 132 CCDC132 1.27 0.014119 208592_s_at CD1e molecule CD1E 1.22 0.018428 223000_s_at F11R 1.22 0.028435 pathway inhibitor (lipoprotein-associated 214378_at coagulation inhibitor) TFPI 1.21 0.012680 216066_at ATP-binding cassette, sub-family A (ABC1), member 1 ABCA1 1.18 0.040946 210374_x_at prostaglandin E receptor 3 (subtype EP3) PTGER3 1.17 0.023332 210643_at tumor necrosis factor (ligand) superfamily, member 11 TNFSF11 1.17 0.043887 1558691_a_at dedicator of cytokinesis 4 DOCK4 1.16 0.009972 206485_at CD5 molecule CD5 1.16 0.015110 220860_at purine-rich element binding protein G PURG 1.13 0.014253

* corresponds to the relative expression of the specific probe set in the FTEb samples previously found to group with serous carcinomas according to global (FTEb(S), n=4) relative to the remaining luteal phase FTE samples from both mutation carriers and controls (n=8).