Total bronchoscopy: 110

Adeno: 43

17 Yes vs. 14 No

Male: 15Female: 3

Male: 3Female: 13

Total Surgery: 62

Adeno: 38

8 Yes vs. 23 No

Male: 6Female: 2

Male: 5Female: 18

Microarray data analysis of adeno- samples

Male-adeno-(surgery): smokers (6) vs. nonsmokers (5)

Number of genes(FDR<0.05)

Number of genes(FDR<0.1)

Number of genes(FDR<0.2)

Number of genes(FDR<0.3)

0 0 14 226

Probeset ID Gene Title Gene Symbol p-value FDR Fold-Change206533_at cholinergic receptor, nicotinic, alpha 5 CHRNA5 2.06E-05 0.144267 1.42288214908_s_at transformation/transcription domain-associated protein TRRAP 3.43E-05 0.144267 2.19163201971_s_at ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A ATP6V1A 3.43E-05 0.144267 3.93302210541_s_at tripartite motif-containing 27 TRIM27 4.81E-05 0.144267 3.31249216248_s_at nuclear receptor subfamily 4, group A, member 2 NR4A2 5.20E-05 0.144267 -4.51545217356_s_at phosphoglycerate kinase 1 PGK1 6.32E-05 0.144267 4.7035217140_s_at voltage-dependent anion channel 1 VDAC1 6.59E-05 0.144267 3.14045208698_s_at non-POU domain containing, octamer-binding NONO 9.92E-05 0.184235 2.92198208828_at polymerase (DNA directed), epsilon 3 (p17 subunit) POLE3 1.32E-04 0.192425 3.1702222034_at Guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1 GNB2L1 1.34E-04 0.192425 -1.55282210573_s_at polymerase (RNA) III (DNA directed) polypeptide C (62kD) POLR3C 0.000145155 0.193471 1.49257211793_s_at abl interactor 2 ABI2 0.000202778 0.214716 1.51537205101_at class II, major histocompatibility complex, transactivator CIITA 0.000203113 0.214716 -1.95057209964_s_at ataxin 7 ATXN7 0.000205118 0.214716 -1.91137201251_at pyruvate kinase, muscle PKM2 0.000213253 0.214716 3.18141212143_s_at insulin-like growth factor binding protein 3 IGFBP3 0.000228167 0.214716 3.90624214798_at ATPase, Ca++ transporting, type 2C, member 2 ATP2C2 0.000230135 0.214716 -1.6253215296_at CDC42 binding protein kinase alpha (DMPK-like) CDC42BPA 0.000285032 0.22461 -1.83893

211150_s_atdihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase com DLAT 0.000288861 0.22461 1.74448

213548_s_at CDV3 homolog (mouse) CDV3 0.00029555 0.22461 1.6547214545_s_at proline synthetase co-transcribed homolog (bacterial) PROSC 0.000302347 0.22461 1.71274219949_at leucine rich repeat containing 2 LRRC2 0.000332445 0.22461 -1.16671208750_s_at ADP-ribosylation factor 1 ARF1 0.000336094 0.22461 5.89478201372_s_at cullin 3 CUL3 0.000339728 0.22461 -1.20592202348_s_at torsin family 1, member A (torsin A) TOR1A 0.00034923 0.22461 1.58216

209910_at solute carrier family 25 (mitochondrial carrier; Graves disease autoantigen), me SLC25A16 0.00035937 0.22461 -1.19584212009_s_at stress-induced-phosphoprotein 1 (Hsp70/Hsp90-organizing protein) STIP1 0.000361109 0.22461 3.03001217294_s_at enolase 1, (alpha) ENO1 0.000394764 0.237622 15.5786

26 genes

Male-adeno-(surgery): smokers vs. nonsmokers

Cancer cells generally exhibit increased glycolysis for ATP

generation due in part to mitochondrial respiration injury and hypoxia, which are frequently associated with resistance to therapeutic agents.

ABI2CDC42BPACHRNA5ENO1GNB2L1IGFBP3NR4A2PGK1PKM2POLE3STIP1TRRAP

Male-adeno-(surgery): smokers vs. nonsmokers

Male-adeno-(surgery): smokers vs. nonsmokers

VDAC1 UBE4B TRRAP TRM27 RPL5 POLR3C

PGK1 ATP6V1A CHRNA5 NR4A2 NONO GNB2L1 POLE4

Male-adeno-(surgery): smokers vs. nonsmokers

Male-adeno-(Bronchoscopy): smokers (15) vs. nonsmokers (3)

Number of genes(FDR<0.05)

Number of genes(FDR<0.1)

Number of genes(FDR<0.2)

Number of genes(FDR<0.3)

0 0 3 7

Probeset ID Gene Title Gene Symbol p-value(Yes vs. No) FDRFold-Change(Yes vs.

No)206994_at cystatin S CST4 2.15E-05 0.179158 -2.38971

213010_atprotein kinase C, delta binding

protein PRKCDBP 2.18E-05 0.179158 -2.35618

219842_at ADP-ribosylation factor-like 15 ARL15 2.41E-05 0.179158 -1.43092209839_at dynamin 3 DNM3 5.65E-05 0.258714 -2.74815

219522_at four jointed box 1 (Drosophila) FJX1 5.81E-05 0.258714 -1.71745

211343_s_at collagen, type XIII, alpha 1 COL13A1 7.87E-05 0.279941 -2.45539

206211_atselectin E (endothelial adhesion

molecule 1) SELE 8.79E-05 0.279941 -2.01722

Male-adeno-(Bronchoscopy): smokers vs. nonsmokers

Male-adeno-(Bronchoscopy): smokers vs. nonsmokers

Male-adeno-(Bronchoscopy): smokers vs. nonsmokers

PRKCDBP FJX1 DNM3

COL13A1 APL15 SELE CST4

Male-adeno-(Bronchoscopy): smokers vs. nonsmokers

Probeset ID Gene Title Gene Symbol p-value(Yes vs. No) Fold-Change(Yes vs. No)

206211_at selectin E (endothelial adhesion molecule 1) SELE 3.46E-06 -1.80541

221031_s_at apolipoprotein L domain containing 1 APOLD1 1.06E-05 -2.19057219371_s_at Kruppel-like factor 2 (lung) KLF2 4.40E-05 -2.08101211343_s_at collagen, type XIII, alpha 1 COL13A1 0.000171 -2.31043

214057_atMyeloid cell leukemia sequence 1 (BCL2-related) MCL1 0.000181 -1.62716

203373_at suppressor of cytokine signaling 2 SOCS2 0.000184 -2.22292205656_at protocadherin 17 PCDH17 0.000586 -2.29517

209967_s_at cAMP responsive element modulator CREM 0.000735 -1.6904202237_at nicotinamide N-methyltransferase NNMT 0.000942 -3.33361

202499_s_atsolute carrier family 2 (facilitated glucose transporter), member 3 SLC2A3 0.001003 -3.03379

220296_at

UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase GALNT10 0.001144 -1.81426

212009_s_atstress-induced-phosphoprotein 1 (Hsp70/Hsp90-organizing protein) STIP1 0.001207 1.89047

202388_at regulator of G-protein signaling 2, 24kDa RGS2 0.001324 -2.55253217140_s_at voltage-dependent anion channel 1 VDAC1 0.001731 2.04997209795_at CD69 molecule CD69 0.001976 -2.26674

Male-adeno-(bronchoscopy+surgery): smokers (21) vs. nonsmokers (8)

Male-adeno-(bronchoscopy+surgery): smokers vs. nonsmokers

Male-adeno-(bronchoscopy+surgery): smokers vs. nonsmokers

Female-adeno-(bronchoscopy): smokers (3) vs. nonsmokers (10)

Probeset ID Gene Title Gene Symbol p-value(Yes vs. No)Fold-Change(Yes vs. No)

201387_s_at ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) UCHL1 0.000472 7.06813201651_s_at protein kinase C and casein kinase substrate in neurons 2 PACSIN2 0.000578 -2.00301220714_at PR domain containing 14 PRDM14 0.000729 1.34103209784_s_at jagged 2 JAG2 0.000825 -2.41471

220445_s_at CSAG family, member 3A /// CSAG family, member 3BCSAG3A /// CSAG3B 0.001096 3.37814

221484_atUDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5 B4GALT5 0.001759 -2.50862

201625_s_at insulin induced gene 1 INSIG1 0.002003 1.65578206176_at bone morphogenetic protein 6 BMP6 0.002094 1.54374222240_s_at myo-inositol 1-phosphate synthase A1 ISYNA1 0.00272 -1.68393201582_at Sec23 homolog B (S. cerevisiae) SEC23B 0.00277 2.03293

214603_at melanoma antigen family A, 2 /// melanoma antigen family A, 2BMAGEA2 /// MAGEA2B 0.002897 3.33431

203379_at ribosomal protein S6 kinase, 90kDa, polypeptide 1 RPS6KA1 0.003213 -1.68547209881_s_at linker for activation of T cells LAT 0.003815 -1.4298

209870_s_atamyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like) APBA2 0.003853 -1.41295

212717_atpleckstrin homology domain containing, family M (with RUN domain) member 1 PLEKHM1 0.004155 -1.79873

201403_s_at microsomal glutathione S-transferase 3 MGST3 0.00418 2.03199204067_at sulfite oxidase SUOX 0.004289 1.73442

204465_s_at internexin neuronal intermediate filament protein, alpha INA 0.004459 1.96424201690_s_at tumor protein D52 TPD52 0.004683 2.86792217927_at signal peptidase complex subunit 1 homolog (S. cerevisiae) SPCS1 0.004746 1.98047

20 genes

Female-adeno-(bronchoscopy): smokers vs. nonsmokers

Female-adeno-(bronchoscopy): smokers vs. nonsmokers

Female-adeno-(bronchoscopy): smokers vs. nonsmokers

Female-adeno-(Surgery): smokers (2) vs. nonsmokers (18)

Probeset ID Gene Title Gene Symbol p-value(Yes vs. No) Fold-Change(Yes vs. No)

220445_s_atCSAG family, member 3A /// CSAG family, member 3B

CSAG3A /// CSAG3B 0.000215 2.13869

206478_at KIAA0125 KIAA0125 0.000258 2.01833

201938_at CDK2-associated protein 1 CDK2AP1 0.000274 1.79749

214254_at melanoma antigen family A, 4 MAGEA4 0.000331 1.75414

214612_x_at melanoma antigen family A, 6 MAGEA6 0.000345 3.99952

203233_at interleukin 4 receptor IL4R 0.000504 -1.80242

209942_x_at melanoma antigen family A, 3 MAGEA3 0.000708 4.06968

201382_at calcyclin binding protein CACYBP 0.000838 1.18307

210293_s_atSec23 homolog B (S. cerevisiae) SEC23B 0.000854 1.51336

205848_at growth arrest-specific 2 GAS2 0.000884 1.46057

Female-adeno-(bronchoscopy+surgery): smokers (31) vs. nonsmokers (5)

Female-adeno-(bronchoscopy+surgery): smokers vs. nonsmokers

Female-adeno-(bronchoscopy+surgery): smokers vs. nonsmokers

ContrastNumber of genes

(FDR<0.05)Number of genes

(FDR<0.1)Number of genes

(FDR<0.2)

Male-Adeno-Yes vs. Male-Adeno-No(13) (2)

- - -

Female-Adeno-Yes vs. Female-Adeno-No(8) (11)

0 2 23

GSE10072

ContrastNumber of genes

(FDR<0.05)Number of genes

(FDR<0.1)Number of genes

(FDR<0.2)

Male-Adeno-Yes vs. Male-Adeno-No(14) (7)

0 0 0

Female-Adeno-Yes vs. Female-Adeno-No(14) (29)

0 10 448

nm1790