Supplemental Table 2. NFκB-regulated and -related differentially expressed in FTEb(S) samples (n=4) relative to remaining FTE samples (n=20).

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

Increased in FTEb(S) samples (93 probe sets) 201348_at glutathione peroxidase 3 (plasma) GPX3 28.73 0.000035 209875_s_at secreted phosphoprotein 1 SPP1 22.38 1.1121641E-4 215078_at superoxide dismutase 2, mitochondrial SOD2 20.85 1.2667075E-4 214091_s_at glutathione peroxidase 3 (plasma) GPX3 15.48 4.945755E-4 217738_at nicotinamide phosphoribosyltransferase NAMPT 13.46 1.2322652E-5 206552_s_at tachykinin, precursor 1 TAC1 13.10 4.205674E-6 221477_s_at superoxide dismutase 2, mitochondrial SOD2 12.37 2.2633802E-5 216841_s_at superoxide dismutase 2, mitochondrial SOD2 11.97 7.4213964E-4 210538_s_at baculoviral IAP repeat-containing 3 BIRC3 11.32 1.5022882E-4 217739_s_at nicotinamide phosphoribosyltransferase NAMPT 9.97 5.0427465E-5 243296_at G0S9 mRNA, instability elements NAMPT 9.75 1.7093652E-4 202859_x_at interleukin 8 IL8 9.66 0.001903 -related adhesion molecule 1 209498_at (biliary glycoprotein) CEACAM1 8.65 5.363363E-5 208607_s_at serum amyloid A2 SAA2 8.34 0.002072 207466_at galanin prepropeptide GAL 8.28 5.717648E-4 236495_at nicotinamide phosphoribosyltransferase NAMPT 7.96 4.3827233E-5 Fc fragment of IgE, high affinity I, receptor for; gamma 1554899_s_at polypeptide FCER1G 7.37 1.9141025E-5 Fc fragment of IgE, high affinity I, receptor for; gamma 204232_at polypeptide FCER1G 7.04 3.8488844E-4 CD55 molecule, decay accelerating factor for 201925_s_at complement (Cromer blood group) CD55 5.54 2.50206E-4 244536_at tumor p53 binding protein, 2 TP53BP2 5.20 2.596663E-4

major histocompatibility complex, class II, DR beta 1 /// major histocompatibility complex, class II, DR beta 2 HLA-DRB1 /// (pseudogene) /// major histocompatibility complex, HLA-DRB2 /// class II, DR beta 3 /// major histocompatibility complex, HLA-DRB3 /// class II, DR beta 4 /// major histocompatibility complex, HLA-DRB4 /// 209312_x_at class II, DR beta 5 HLA-DRB5 5.16 0.002286 210029_at indoleamine 2,3-dioxygenase 1 IDO1 5.09 9.548861E-4 CD74 molecule, major histocompatibility complex, class II 1567628_at invariant chain CD74 4.89 5.591996E-4 205758_at CD8a molecule CD8A 4.73 9.566794E-4 215049_x_at CD163 molecule CD163 4.59 5.8961805E-4 serpin peptidase inhibitor, clade B (ovalbumin), 242814_at member 9 SERPINB9 4.13 8.8773394E-4 MHC class II HLA-DRB3 mRNA (HLA-DRB3*01012 208306_x_at allele) HLA-DRB1 3.90 0.002387 203561_at Fc fragment of IgG, low affinity IIa, receptor (CD32) FCGR2A 3.76 0.002388 201859_at serglycin SRGN 3.72 4.3516807E-4 212587_s_at protein tyrosine phosphatase, receptor type, C PTPRC 3.65 0.002275 , beta 2 ( receptor 3 202803_s_at and 4 subunit) ITGB2 3.62 0.002321 210845_s_at plasminogen activator, PLAUR 3.61 9.875576E-5 220491_at hepcidin antimicrobial peptide HAMP 3.58 2.2351372E-4 203508_at tumor necrosis factor receptor superfamily, member 1B TNFRSF1B 3.53 5.538238E-4 204924_at toll-like receptor 2 TLR2 3.50 7.6501985E-4 212501_at CCAAT/enhancer binding protein (C/EBP), beta CEBPB 3.46 1.967901E-5 Probe Set ID Gene Title Gene Symbol Fold Change* p-value 212588_at protein tyrosine phosphatase, receptor type, C PTPRC 3.43 0.001470 1556346_at coactosin-like 1 (Dictyostelium) COTL1 3.43 5.160742E-4 201858_s_at serglycin SRGN 3.35 0.001321 223377_x_at cytokine inducible SH2-containing protein CISH 3.30 9.758455E-4 221059_s_at coactosin-like 1 (Dictyostelium) COTL1 3.28 9.714586E-4 209016_s_at keratin 7 KRT7 3.19 0.001996 200798_x_at myeloid cell leukemia sequence 1 (BCL2-related) MCL1 3.06 1.4892804E-4 serpin peptidase inhibitor, clade A (alpha-1 antiprotein- 202833_s_at ase, antitrypsin), member 1 SERPINA1 3.01 0.001995 CD74 molecule, major histocompatibility complex, class II 209619_at invariant chain CD74 3.00 0.001562 211924_s_at plasminogen activator, urokinase receptor PLAUR 2.99 4.3188655E-5 221223_x_at cytokine inducible SH2-containing protein CISH 2.90 0.001630 201743_at CD14 molecule CD14 2.84 2.7645347E-4 serpin peptidase inhibitor, clade B (ovalbumin), 209723_at member 9 SERPINB9 2.76 4.6121113E-5 carcinoembryonic antigen-related molecule 1 206576_s_at (biliary glycoprotein) CEACAM1 2.70 5.729606E-4 206118_at signal transducer and activator of transcription 4 STAT4 2.67 3.368644E-4 213076_at inositol 1,4,5-trisphosphate 3-kinase C ITPKC 2.65 8.8357905E-5 203645_s_at CD163 molecule CD163 2.63 4.7350605E-4 214240_at galanin prepropeptide GAL 2.57 8.464188E-5 integrin, beta 2 (complement component 3 receptor 3 1555349_a_at and 4 subunit) ITGB2 2.55 0.001448 201667_at protein, alpha 1, 43kDa GJA1 2.52 1.1176099E-4 37152_at peroxisome proliferator-activated receptor delta PPARD 2.48 0.001346 240798_at cut-like homeobox 1 CUX1 2.42 0.001730 203922_s_at cytochrome b-245, beta polypeptide CYBB 2.41 1.1826403E-6 223961_s_at cytokine inducible SH2-containing protein CISH 2.38 5.24332E-5 v-rel reticuloendotheliosis viral oncogene homolog 206036_s_at (avian) REL 2.36 0.001192 204881_s_at UDP-glucose ceramide glucosyltransferase UGCG 2.28 1.4784404E-5 219386_s_at SLAM family member 8 SLAMF8 2.21 9.197912E-4 208075_s_at chemokine (C-C motif) ligand 7 CCL7 2.14 0.001080 218136_s_at solute carrier family 25, member 37 SLC25A37 2.14 1.1050079E-4 202820_at aryl hydrocarbon receptor AHR 2.12 5.367252E-4 221905_at cylindromatosis (turban tumor syndrome) CYLD 2.10 0.001923 mucosa associated lymphoid tissue lymphoma 210017_at translocation gene 1 MALT1 2.09 7.9169526E-4 222529_at solute carrier family 25, member 37 SLC25A37 2.09 0.001483 protein kinase, AMP-activated, beta 1 non-catalytic 201834_at subunit PRKAB1 2.07 0.001882 214533_at chymase 1, mast cell CMA1 2.01 2.881116E-5 221920_s_at solute carrier family 25, member 37 SLC25A37 2.01 0.002119 nuclear factor of kappa polypeptide gene enhancer 209239_at in B-cells 1 NFKB1 1.99 0.001417 206337_at chemokine (C-C motif) receptor 7 CCR7 1.96 2.9847243E-7 209752_at regenerating islet-derived 1 alpha REG1A 1.94 1.4872196E-4 202963_at regulatory factor X, 5 (influences HLA class II expression) RFX5 1.93 1.6902457E-4 221577_x_at growth differentiation factor 15 GDF15 1.87 0.001258 204103_at chemokine (C-C motif) ligand 4 CCL4 1.73 0.002399 207539_s_at interleukin 4 IL4 1.66 6.159569E-5 solute carrier family 40 (iron-regulated transporter), 223044_at member 1 SLC40A1 1.65 1.7114203E-4 Probe Set ID Gene Title Gene Symbol Fold Change* p-value signal transducer and activator of transcription 6, 201332_s_at interleukin-4 induced STAT6 1.64 6.239914E-4 207643_s_at tumor necrosis factor receptor superfamily, member 1A TNFRSF1A 1.61 0.002220 229120_s_at CDC42 small effector 1 CDC42SE1 1.56 5.1123864E-4 209295_at tumor necrosis factor receptor superfamily, member 10b TNFRSF10B 1.52 2.8548867E-4 207275_s_at acyl-CoA synthetase long-chain family member 1 ACSL1 1.50 0.001191 TAF8 RNA polymerase II, TATA box binding protein 229412_at (TBP)-associated factor, 43kDa TAF8 1.49 0.002246 219385_at SLAM family member 8 SLAMF8 1.37 0.001731 inhibitor of kappa light polypeptide gene enhancer in 211027_s_at B-cells, kinase beta IKBKB 1.36 8.4468396E-4 sphingomyelin phosphodiesterase 3, neutral membrane 231732_at (neutral sphingomyelinase II) SMPD3 1.35 1.0776003E-4 transglutaminase 2 (C polypeptide, protein-glutamine- 211573_x_at gamma-glutamyltransferase) TGM2 1.34 9.92243E-4 1554442_at BEST1 1.34 2.8173975E-4 protein kinase, AMP-activated, beta 1 non-catalytic 201835_s_at subunit PRKAB1 1.25 0.002137 211108_s_at Janus kinase 3 (a protein tyrosine kinase, leukocyte) JAK3 1.21 8.574884E-5

Decreased in FTEb(S) samples (31 probe sets) 1552348_at protease, serine, 33 PRSS33 14.72 0.001919 214633_at SRY (sex determining region Y)-box 3 SOX3 6.93 1.0488592E-5 232406_at jagged 1 JAG1 3.80 1.5996171E-5 219850_s_at ets homologous factor EHF 3.77 6.462096E-4 211110_s_at androgen receptor AR 3.65 4.2062375E-4 244881_at leishmanolysin-like (metallopeptidase M8 family) LMLN 3.40 5.7114434E-5 200598_s_at 90kDa beta (Grp94), member 1 HSP90B1 3.36 0.001392 232360_at ets homologous factor EHF 3.23 5.9433343E-5 202154_x_at tubulin, beta 3 TUBB3 3.13 1.2292826E-5 224189_x_at ets homologous factor EHF 3.03 6.418391E-4 235256_s_at galactose mutarotase (aldose 1-epimerase) GALM 3.03 1.6691868E-6 241397_at ets homologous factor EHF 3.01 1.7670434E-4 231729_s_at calcyphosine CAPS 2.97 1.2334871E-5 232361_s_at ets homologous factor EHF 2.94 9.719221E-5 213476_x_at tubulin, beta 3 TUBB3 2.88 4.4825806E-6 34726_at , voltage-dependent, beta 3 subunit CACNB3 2.77 2.1543915E-6 226424_at calcyphosine CAPS 2.73 3.706328E-5 222434_at enabled homolog (Drosophila) ENAH 2.72 1.3099569E-4 201242_s_at ATPase, Na+/K+ transporting, beta 1 polypeptide ATP1B1 2.71 1.9979072E-5 212971_at cysteinyl-tRNA synthetase CARS 2.47 0.001697 231728_at calcyphosine CAPS 2.43 0.001024 222240_s_at inositol-3-phosphate synthase 1 ISYNA1 2.42 5.475835E-4 205714_s_at zinc finger, MYND-type containing 10 ZMYND10 2.38 1.345836E-4 216449_x_at heat shock protein 90kDa beta (Grp94), member 1 HSP90B1 2.21 3.9395635E-4 200599_s_at heat shock protein 90kDa beta (Grp94), member 1 HSP90B1 2.20 0.002159 220125_at dynein, axonemal, intermediate chain 1 DNAI1 2.08 5.499461E-4 225031_at chromodomain helicase DNA binding protein 6 CHD6 2.01 1.5537896E-4 205512_s_at apoptosis-inducing factor, mitochondrion-associated, 1 AIFM1 1.90 0.001979 208614_s_at filamin B, beta (actin binding protein 278) FLNB 1.87 1.5015664E-4 209530_at calcium channel, voltage-dependent, beta 3 subunit CACNB3 1.71 0.001600 208775_at exportin 1 (CRM1 homolog, yeast) XPO1 1.39 8.380994E-4

* 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 FTE samples (n=20).