Table A1. Genes Differentially Expressed Between the Smoking and Non-Smoking Groups

APPENDIX 1

Table A1. Genes differentially expressed between the smoking and non-smoking groups.

Gene / Description / AffyID / Genomic Location / Fold (S/N) / Raw P value (Mas5.0) / Adjusted P value (Mas5.0) / Raw P value (RMA) / Adjusted P value (RMA) / Raw P value (GCRMA) / Adjusted P value (GCRMA) / Raw P value (dChip) / Adjusted P value (dChip)
HBA1 / hemoglobin, alpha 1 /// hemoglobin, alpha 2 / 217414_x_at / 16p13.3 / -2.97 / 8.78E-03 / 3.57E-02 / 4.50E-03 / 1.71E-02 / 7.36E-03 / 2.64E-02 / 3.67E-03 / 1.50E-02
PPBP / pro-platelet basic protein (chemokine (C-X-C motif) ligand 7) / 214146_s_at / 4q12-q13 / -2.57 / 6.08E-03 / 2.68E-02 / 4.29E-04 / 2.42E-03 / 7.22E-05 / 6.42E-04 / 1.16E-02 / 3.76E-02
HBA2 / hemoglobin, alpha 2 / 214414_x_at / 16p13.3 / -2.50 / 1.43E-03 / 8.59E-03 / 2.66E-03 / 1.10E-02 / 1.45E-03 / 7.27E-03 / 3.47E-03 / 1.43E-02
MYH11 / myosin, heavy chain 11, smooth muscle / 207961_x_at / 16p13.11 / -2.35 / 8.11E-06 / 1.46E-04 / 1.12E-07 / 2.22E-06 / 3.25E-05 / 3.39E-04 / 1.23E-06 / 1.44E-05
NRGN / neurogranin (protein kinase C substrate, RC3) / 204081_at / 11q24 / -2.26 / 4.68E-04 / 3.56E-03 / 2.76E-03 / 1.14E-02 / 5.96E-03 / 2.23E-02 / 1.20E-03 / 5.87E-03
HAB1 / B1 for mucin / 215778_x_at / chr7 / -2.25 / 4.44E-15 / 4.58E-12 / 7.31E-14 / 1.21E-11 / 1.44E-13 / 4.73E-11 / 4.82E-14 / 4.02E-12
HBA1 / hemoglobin, alpha 1 /// hemoglobin, alpha 2 / 211699_x_at / 16p13.3 / -2.23 / 2.70E-03 / 1.41E-02 / 2.66E-03 / 1.10E-02 / 4.09E-03 / 1.67E-02 / 4.71E-03 / 1.82E-02
TRPV6 / transient receptor potential cation channel, subfamily V, member 6 / 206827_s_at / 7q33-q34 / -2.17 / 5.14E-07 / 1.71E-05 / 5.81E-07 / 8.68E-06 / 1.69E-05 / 1.99E-04 / 3.31E-13 / 2.12E-11
KCNF1 / potassium voltage-gated channel, subfamily F, member 1 / 210263_at / 2p25 / -2.12 / 3.40E-11 / 7.21E-09 / 2.75E-14 / 6.85E-12 / 1.81E-08 / 6.97E-07 / 1.27E-14 / 1.26E-12
CCR1 / chemokine (C-C motif) receptor 1 / 205099_s_at / 3p21 / -2.10 / 6.55E-11 / 1.31E-08 / 7.81E-05 / 5.95E-04 / 1.85E-05 / 2.15E-04 / 1.97E-03 / 9.01E-03
DSPP / dentin sialophosphoprotein / 221681_s_at / 4q21.3 / -2.09 / 3.41E-10 / 4.92E-08 / 6.20E-14 / 1.15E-11 / 1.46E-09 / 8.13E-08 / 2.61E-12 / 1.24E-10
PAGE4 / P antigen family, member 4 (prostate associated) / 205564_at / Xp11.23 / -2.06 / 2.16E-08 / 1.45E-06 / 5.74E-07 / 8.61E-06 / 1.71E-03 / 8.29E-03 / 3.24E-11 / 1.22E-09
HBA1 / hemoglobin, alpha 1 / 211745_x_at / 16p13.3 / -2.05 / 5.24E-03 / 2.39E-02 / 5.29E-03 / 1.95E-02 / 5.07E-03 / 1.97E-02 / 6.18E-03 / 2.25E-02
HBB / hemoglobin, beta / 211696_x_at / 11p15.5 / -2.03 / 3.65E-03 / 1.80E-02 / 4.53E-03 / 1.72E-02 / 1.14E-03 / 5.95E-03 / 5.37E-03 / 2.03E-02
HBA1 / hemoglobin, alpha 1 /// hemoglobin, alpha 2 / 204018_x_at / 16p13.3 / -2.01 / 1.23E-02 / 4.64E-02 / 5.28E-03 / 1.95E-02 / 7.66E-03 / 2.73E-02 / 5.79E-03 / 2.14E-02
SKI / V-ski sarcoma viral oncogene homolog (avian) / 213755_s_at / 1q22-q24 / -1.98 / 1.54E-05 / 2.42E-04 / 1.15E-09 / 4.81E-08 / 3.11E-05 / 3.27E-04 / 3.89E-03 / 1.57E-02
TBC1D25 / TBC1 domain family, member 25 / 213789_at / Xp11 / -1.97 / 2.14E-03 / 1.18E-02 / 8.88E-08 / 1.84E-06 / 1.06E-02 / 3.50E-02 / 2.04E-08 / 4.02E-07
HNRNPU / heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A) / 221639_x_at / 1q44 / -1.95 / 6.98E-07 / 2.13E-05 / 3.15E-03 / 1.27E-02 / 1.09E-08 / 4.56E-07 / 4.44E-15 / 5.13E-13
CX3CR1 / chemokine (C-X3-C motif) receptor 1 / 205898_at / 3p21.3 / -1.95 / 9.02E-03 / 3.63E-02 / 6.67E-04 / 3.53E-03 / 1.51E-03 / 7.47E-03 / 1.05E-02 / 3.50E-02
HBA1 / hemoglobin, alpha 1 /// hemoglobin, alpha 2 / 209458_x_at / 16p13.3 / -1.95 / 9.86E-03 / 3.90E-02 / 5.83E-03 / 2.12E-02 / 1.19E-02 / 3.82E-02 / 8.34E-03 / 2.90E-02
CLU / clusterin / 208792_s_at / 8p21-p12 / -1.94 / 2.83E-05 / 4.05E-04 / 2.67E-05 / 2.35E-04 / 5.72E-05 / 5.32E-04 / 7.33E-15 / 8.21E-13
RANBP3 / RAN binding protein 3 / 202639_s_at / 19p13.3 / -1.91 / 2.01E-07 / 7.86E-06 / 2.29E-07 / 3.93E-06 / 4.07E-03 / 1.67E-02 / 2.78E-03 / 1.19E-02
METTL5 / methyltransferase like 5 / 220839_at / 2q31.1 / -1.90 / 3.74E-10 / 5.18E-08 / 2.86E-09 / 1.03E-07 / 9.75E-11 / 8.58E-09 / 9.97E-10 / 2.61E-08
TUT1 / terminal uridylyl transferase 1, U6 snRNA-specific / 218965_s_at / 11q12.2 / -1.90 / 2.98E-06 / 6.57E-05 / 1.30E-10 / 7.29E-09 / 5.75E-10 / 3.57E-08 / 7.27E-05 / 5.25E-04
DALRD3 / DALR anticodon binding domain containing 3 / 218808_at / 3p21.31 / -1.89 / 3.53E-07 / 1.28E-05 / 2.73E-11 / 1.95E-09 / 1.88E-12 / 3.39E-10 / 4.27E-13 / 2.59E-11
ADRA2C / adrenergic, alpha-2C-, receptor / 206128_at / 4p16 / -1.89 / 1.33E-05 / 2.17E-04 / 7.55E-07 / 1.09E-05 / 1.44E-04 / 1.13E-03 / <1.00E-17 / <1.00E-17
DUSP6 / dual specificity phosphatase 6 / 208891_at / 12q22-q23 / -1.89 / 6.39E-04 / 4.57E-03 / 3.04E-04 / 1.82E-03 / 3.79E-05 / 3.80E-04 / 2.19E-03 / 9.82E-03
LILRA1 / leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1 / 210660_at / 19q13.4 / -1.88 / 2.87E-05 / 4.08E-04 / 2.18E-03 / 9.39E-03 / 1.20E-02 / 3.85E-02 / 6.93E-04 / 3.67E-03
PRX / periaxin / 220024_s_at / 19q13 / -1.87 / 1.50E-06 / 3.79E-05 / 7.82E-04 / 4.02E-03 / 3.64E-05 / 3.71E-04 / 1.85E-10 / 5.83E-09
LRRC61 / leucine rich repeat containing 61 / 218907_s_at / 7q31-q35 / -1.84 / 6.08E-05 / 7.22E-04 / 1.73E-04 / 1.15E-03 / 1.82E-04 / 1.37E-03 / 3.74E-06 / 3.89E-05
COMT / catechol-O-methyltransferase / 213981_at / 22q11 / -1.83 / 6.96E-07 / 2.13E-05 / 4.74E-05 / 3.85E-04 / 5.05E-04 / 3.11E-03 / 1.33E-02 / 4.22E-02
GRIN1 / glutamate receptor, ionotropic, N-methyl D-aspartate 1 / 210782_x_at / 9q34.3 / -1.83 / 9.49E-06 / 1.66E-04 / 1.25E-03 / 5.96E-03 / 1.28E-02 / 4.07E-02 / 1.10E-04 / 7.41E-04
RAB2A / RAB2A, member RAS oncogene family / 208730_x_at / 8q12.1 / -1.82 / 3.55E-15 / 4.27E-12 / 4.09E-14 / 8.93E-12 / 8.24E-14 / 2.97E-11 / 1.42E-14 / 1.40E-12
SPARC / secreted protein, acidic, cysteine-rich (osteonectin) / 200665_s_at / 5q31.3-q32 / -1.81 / 1.85E-04 / 1.71E-03 / 3.21E-04 / 1.91E-03 / 9.83E-03 / 3.31E-02 / 6.98E-07 / 8.84E-06
G0S2 / G0/G1switch 2 / 213524_s_at / 1q32.2 / -1.80 / 6.35E-06 / 1.20E-04 / 1.94E-07 / 3.43E-06 / 9.15E-07 / 1.83E-05 / 1.58E-10 / 5.09E-09
LILRA4 / leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4 / 210313_at / 19q13.4 / -1.76 / 6.82E-08 / 3.57E-06 / 1.29E-05 / 1.27E-04 / 1.01E-05 / 1.31E-04 / 5.17E-04 / 2.86E-03
MUC5AC / mucin 5AC, oligomeric mucus/gel-forming / 217182_at / 11p15.5 / -1.75 / 1.73E-08 / 1.21E-06 / 8.15E-09 / 2.45E-07 / 6.01E-08 / 1.92E-06 / 4.42E-10 / 1.29E-08
HOXB1 / homeobox B1 / 208224_at / 17q21.3 / -1.74 / 4.51E-06 / 9.24E-05 / 8.31E-03 / 2.80E-02 / 1.45E-03 / 7.25E-03 / 1.67E-04 / 1.07E-03
HAMP / hepcidin antimicrobial peptide / 220491_at / 19q13.1 / -1.74 / 3.45E-09 / 3.27E-07 / 5.06E-12 / 4.51E-10 / 3.95E-07 / 9.10E-06 / 2.00E-15 / 2.98E-13
GNL1 / guanine nucleotide binding protein-like 1 / 203307_at / 6p21.3 / -1.72 / 1.05E-10 / 1.90E-08 / 8.66E-09 / 2.55E-07 / 4.61E-08 / 1.57E-06 / 1.95E-12 / 9.63E-11
REM1 / RAS (RAD and GEM)-like GTP-binding 1 / 210300_at / 20q11.21 / -1.71 / 3.35E-06 / 7.29E-05 / 1.31E-03 / 6.17E-03 / 2.73E-04 / 1.89E-03 / 1.15E-02 / 3.73E-02
CACNA1S / calcium channel, voltage-dependent, L type, alpha 1S subunit / 217515_s_at / 1q32 / -1.70 / 8.02E-06 / 1.45E-04 / 7.86E-08 / 1.65E-06 / 2.10E-05 / 2.38E-04 / 1.42E-02 / 4.45E-02
LILRB2 / leukocyte immunoglobulin-like receptor, subfamily B, member 2 / 210146_x_at / 19q13.4 / -1.70 / 7.65E-03 / 3.20E-02 / 4.31E-04 / 2.43E-03 / 1.88E-03 / 8.98E-03 / 1.89E-10 / 5.93E-09
EIF5A / Eukaryotic translation initiation factor 5A / 213757_at / 17p13-p12 / -1.70 / 6.95E-07 / 2.13E-05 / 3.48E-07 / 5.58E-06 / 1.41E-06 / 2.63E-05 / 9.95E-05 / 6.82E-04
CLTA / Clathrin, light chain (Lca) / 216293_at / 9p13 / -1.69 / 3.76E-05 / 4.93E-04 / 2.74E-04 / 1.67E-03 / 1.92E-03 / 9.12E-03 / 2.61E-04 / 1.55E-03
ICOSLG / inducible T-cell co-stimulator ligand / 211197_s_at / 21q22.3 / -1.68 / 3.28E-05 / 4.48E-04 / 6.92E-03 / 2.43E-02 / 6.68E-04 / 3.89E-03 / 1.98E-09 / 4.90E-08
MRC2 / mannose receptor, C type 2 / 209280_at / 17q23.2 / -1.67 / 1.31E-07 / 5.64E-06 / 4.99E-09 / 1.65E-07 / 1.24E-07 / 3.53E-06 / 1.56E-12 / 7.93E-11
CLTCL1 / clathrin, heavy chain-like 1 / 205944_s_at / 22q11 / -1.67 / 1.06E-04 / 1.11E-03 / 2.11E-05 / 1.93E-04 / 1.99E-05 / 2.28E-04 / 1.42E-07 / 2.15E-06
PAFAH1B3 / platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit 29kDa / 203228_at / 19q13.1 / -1.66 / 6.24E-05 / 7.39E-04 / 6.34E-05 / 4.98E-04 / 4.70E-05 / 4.53E-04 / 2.57E-09 / 6.25E-08
SLC34A1 / solute carrier family 34 (sodium phosphate), member 1 / 208177_at / 5q35 / -1.65 / 1.12E-05 / 1.90E-04 / 2.31E-06 / 2.92E-05 / 2.76E-04 / 1.90E-03 / 8.65E-11 / 2.98E-09
GPR4 / G protein-coupled receptor 4 / 206236_at / 19q13.3 / -1.64 / 3.31E-04 / 2.74E-03 / 3.18E-03 / 1.28E-02 / 2.99E-07 / 7.25E-06 / 3.60E-03 / 1.47E-02
RRM2 / ribonucleotide reductase M2 polypeptide / 209773_s_at / 2p25-p24 / -1.64 / 7.91E-04 / 5.39E-03 / 1.37E-03 / 6.39E-03 / 9.52E-03 / 3.23E-02 / 6.45E-04 / 3.47E-03
SPDEF / SAM pointed domain containing ets transcription factor / 214403_x_at / 6p21.3 / -1.62 / 9.90E-08 / 4.58E-06 / 4.77E-04 / 2.64E-03 / 2.67E-08 / 9.81E-07 / 1.43E-06 / 1.64E-05
NPPA / natriuretic peptide precursor A / 209957_s_at / 1p36.21 / -1.61 / 3.78E-06 / 8.07E-05 / 6.02E-05 / 4.76E-04 / 1.49E-04 / 1.15E-03 / 1.41E-06 / 1.63E-05
GPR27 / G protein-coupled receptor 27 / 221306_at / 3p21-p14 / -1.61 / 3.08E-08 / 1.92E-06 / 2.10E-04 / 1.34E-03 / 1.67E-05 / 1.97E-04 / 9.86E-05 / 6.77E-04
EPHB3 / EPH receptor B3 / 204600_at / 3q21 / -1.61 / 2.83E-04 / 2.42E-03 / 5.03E-05 / 4.05E-04 / 1.35E-05 / 1.65E-04 / 4.50E-03 / 1.76E-02
RNF5 / ring finger protein 5 / 216018_at / 6p21.3 / -1.61 / 1.59E-05 / 2.48E-04 / 4.42E-06 / 5.02E-05 / 7.57E-06 / 1.05E-04 / 4.13E-10 / 1.22E-08
EBP / emopamil binding protein (sterol isomerase) / 202735_at / Xp11 / -1.60 / <1.00E-17 / <1.00E-17 / 6.22E-15 / 2.36E-12 / 3.57E-13 / 8.95E-11 / 7.17E-14 / 5.65E-12
MAP3K12 / mitogen-activated protein kinase kinase kinase 12 / 205448_s_at / 12q13 / -1.60 / 2.69E-08 / 1.73E-06 / 2.70E-11 / 1.95E-09 / 2.07E-08 / 7.81E-07 / 7.44E-06 / 7.14E-05
USP33 / ubiquitin specific peptidase 33 / 217441_at / 1p31.1 / -1.60 / 3.14E-05 / 4.33E-04 / 4.58E-06 / 5.16E-05 / 1.05E-04 / 8.78E-04 / 2.09E-05 / 1.75E-04
APOBEC3A / apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A / 210873_x_at / 22q13 / -1.59 / 3.81E-03 / 1.87E-02 / 3.78E-03 / 1.48E-02 / 4.59E-03 / 1.83E-02 / <1.00E-17 / <1.00E-17
CIB2 / calcium and integrin binding family member 2 / 205008_s_at / 15q24 / -1.59 / 1.25E-06 / 3.25E-05 / 1.08E-08 / 3.01E-07 / 3.60E-06 / 5.79E-05 / 4.30E-03 / 1.70E-02
TGM5 / transglutaminase 5 / 207911_s_at / 15q15.2 / -1.58 / 4.31E-04 / 3.34E-03 / 3.73E-03 / 1.47E-02 / 4.24E-04 / 2.69E-03 / 2.13E-03 / 9.60E-03
PRB1 / proline-rich protein BstNI subfamily 1 /// proline-rich protein BstNI subfamily 2 / 210597_x_at / 12p13.2 / -1.58 / 1.63E-06 / 4.04E-05 / 4.12E-06 / 4.76E-05 / 1.00E-06 / 1.98E-05 / 5.50E-05 / 4.16E-04
SOX4 / SRY (sex determining region Y)-box 4 / 201417_at / 6p22.3 / -1.57 / 5.27E-09 / 4.48E-07 / 7.65E-06 / 8.03E-05 / 1.77E-04 / 1.34E-03 / 1.97E-03 / 9.03E-03
CEBPE / CCAAT/enhancer binding protein (C/EBP), epsilon / 214523_at / 14q11.2 / -1.57 / 5.24E-07 / 1.73E-05 / 9.35E-05 / 6.83E-04 / 1.09E-05 / 1.38E-04 / <1.00E-17 / <1.00E-17
IGHA1 / Immunoglobulin heavy constant alpha 1 / 216318_at / 14q32.33 / -1.57 / 9.46E-08 / 4.43E-06 / 9.57E-09 / 2.74E-07 / 7.94E-07 / 1.65E-05 / 4.44E-15 / 5.13E-13
FADS2 / fatty acid desaturase 2 / 202218_s_at / 11q12-q13 / -1.57 / 3.69E-04 / 3.00E-03 / 8.27E-08 / 1.72E-06 / 2.60E-03 / 1.16E-02 / 8.26E-08 / 1.35E-06
FANCA / Fanconi anemia, complementation group A / 215530_at / 16q24.3 / -1.57 / 1.71E-06 / 4.20E-05 / 8.48E-06 / 8.79E-05 / 2.65E-07 / 6.57E-06 / 1.11E-15 / 1.81E-13
IL13 / interleukin 13 / 207844_at / 5q31 / -1.56 / 1.28E-07 / 5.60E-06 / 1.69E-05 / 1.60E-04 / 1.29E-04 / 1.02E-03 / 5.93E-12 / 2.64E-10
DNAH7 / dynein, axonemal, heavy chain 7 / 214222_at / 2q32.3 / -1.56 / 4.59E-07 / 1.58E-05 / 3.95E-07 / 6.27E-06 / 7.14E-06 / 9.97E-05 / 4.07E-09 / 9.49E-08
TCF3 / Transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47) / 216647_at / 19p13.3 / -1.56 / 3.54E-07 / 1.28E-05 / 2.30E-03 / 9.76E-03 / 1.83E-04 / 1.38E-03 / 8.55E-05 / 5.99E-04
EFNB3 / ephrin-B3 / 210883_x_at / 17p13 / -1.55 / 2.31E-05 / 3.44E-04 / 9.12E-03 / 3.02E-02 / 6.12E-04 / 3.63E-03 / 5.21E-04 / 2.88E-03
ATN1 / atrophin 1 / 208871_at / 12p13.31 / -1.55 / 1.24E-02 / 4.65E-02 / 1.61E-06 / 2.12E-05 / 2.19E-04 / 1.58E-03 / 8.78E-11 / 3.01E-09
EIF4B / eukaryotic translation initiation factor 4B / 219599_at / 12q13.13 / -1.54 / 5.80E-14 / 2.22E-11 / 1.64E-14 / 4.74E-12 / 4.40E-11 / 4.41E-09 / 8.12E-11 / 2.81E-09
CC2D1A / coiled-coil and C2 domain containing 1A / 58994_at / 19p13.12 / -1.54 / 7.07E-09 / 5.73E-07 / 2.16E-10 / 1.13E-08 / 2.49E-07 / 6.28E-06 / 8.51E-03 / 2.94E-02
HRASLS2 / HRAS-like suppressor 2 / 221122_at / 11q12.3 / -1.54 / 8.79E-05 / 9.58E-04 / 2.32E-07 / 3.97E-06 / 3.64E-05 / 3.71E-04 / 1.03E-06 / 1.24E-05
DNAJC4 / DnaJ (Hsp40) homolog, subfamily C, member 4 / 206781_at / 11q13 / -1.54 / 1.33E-07 / 5.73E-06 / 2.45E-11 / 1.81E-09 / 1.68E-06 / 3.10E-05 / 2.11E-03 / 9.52E-03
CEBPD / CCAAT/enhancer binding protein (C/EBP), delta / 203973_s_at / 8p11 / -1.53 / 2.40E-04 / 2.10E-03 / 3.21E-05 / 2.76E-04 / 1.43E-02 / 4.40E-02 / 9.13E-03 / 3.11E-02
ZMYND8 / zinc finger, MYND-type containing 8 / 209049_s_at / 20q13.12 / -1.53 / 1.16E-10 / 2.00E-08 / 1.54E-09 / 6.06E-08 / 2.53E-09 / 1.32E-07 / 2.71E-08 / 5.21E-07
DDX54 / DEAD (Asp-Glu-Ala-Asp) box polypeptide 54 / 219111_s_at / 12q24.13 / -1.52 / 1.81E-07 / 7.31E-06 / 7.62E-05 / 5.82E-04 / 1.28E-04 / 1.02E-03 / 3.73E-03 / 1.52E-02
SEC22B / SEC22 vesicle trafficking protein homolog B / 214257_s_at / 1q21.1 / -1.52 / 1.36E-12 / 3.93E-10 / 2.70E-12 / 2.53E-10 / 3.09E-14 / 1.31E-11 / 1.00E-13 / 7.64E-12
SPATA5L1 / spermatogenesis associated 5-like 1 / 218933_at / 15q21.1 / -1.52 / 9.44E-05 / 1.02E-03 / 2.80E-04 / 1.70E-03 / 2.72E-04 / 1.89E-03 / 8.95E-07 / 1.10E-05
GATA2 / GATA binding protein 2 / 209710_at / 3q21.3 / -1.52 / 1.05E-07 / 4.81E-06 / 1.50E-06 / 1.98E-05 / 1.38E-08 / 5.49E-07 / 1.71E-10 / 5.47E-09
COL13A1 / collagen, type XIII, alpha 1 / 211809_x_at / 10q22 / -1.51 / 1.18E-06 / 3.12E-05 / 1.97E-04 / 1.28E-03 / 7.00E-04 / 4.05E-03 / 1.56E-13 / 1.12E-11
ZNHIT4 / zinc finger, HIT type 4 / 222093_s_at / 2p13.1 / -1.51 / 2.54E-04 / 2.21E-03 / 6.03E-04 / 3.26E-03 / 1.30E-04 / 1.03E-03 / 7.57E-04 / 3.97E-03
VCAM1 / vascular cell adhesion molecule 1 / 203868_s_at / 1p32-p31 / -1.50 / 2.03E-07 / 7.92E-06 / 3.30E-04 / 1.95E-03 / 4.70E-08 / 1.59E-06 / <1.00E-17 / <1.00E-17
INHBC / inhibin, beta C / 207688_s_at / 12q13.1 / -1.50 / 1.17E-07 / 5.13E-06 / 3.23E-07 / 5.25E-06 / 5.40E-08 / 1.74E-06 / 2.79E-05 / 2.28E-04
CPM / Carboxypeptidase M / 217557_s_at / 12q14.3 / -1.50 / 1.61E-03 / 9.41E-03 / 8.22E-15 / 2.82E-12 / 7.59E-11 / 6.93E-09 / 6.66E-16 / 1.29E-13
ARF6 / ADP-ribosylation factor 6 / 214182_at / 14q21.3 / -1.50 / 2.51E-06 / 5.72E-05 / 3.25E-06 / 3.92E-05 / 2.23E-07 / 5.76E-06 / 2.72E-05 / 2.23E-04
SLC12A4 / solute carrier family 12 (potassium/chloride transporters), member 4 / 211112_at / 16q22.1 / -1.50 / 6.76E-05 / 7.85E-04 / 2.31E-13 / 3.14E-11 / 9.74E-04 / 5.25E-03 / <1.00E-17 / <1.00E-17
MATK / megakaryocyte-associated tyrosine kinase / 206267_s_at / 19p13.3 / -1.50 / 8.96E-04 / 5.95E-03 / 1.50E-02 / 4.47E-02 / 4.55E-04 / 2.86E-03 / 5.79E-03 / 2.14E-02
EPHB2 / EPH receptor B2 / 209588_at / 1p36 / -1.50 / 1.70E-05 / 2.62E-04 / 6.39E-03 / 2.27E-02 / 6.46E-07 / 1.39E-05 / 3.86E-03 / 1.56E-02
POLR2J4 / polymerase (RNA) II (DNA directed) polypeptide J, 13.3kDa pseudogene / 222208_s_at / 7p13 / -1.50 / 8.89E-08 / 4.27E-06 / 1.31E-07 / 2.52E-06 / 7.55E-08 / 2.29E-06 / 2.27E-10 / 6.95E-09
CCNL2 / cyclin L2 /// similar to Cyclin-L2 (Paneth cell-enhanced expression protein) / 221427_s_at / 1p36.33 / 1.51 / 2.99E-09 / 2.88E-07 / 4.10E-07 / 6.44E-06 / 4.84E-05 / 4.65E-04 / 1.34E-08 / 2.72E-07
PLEKHA1 / pleckstrin homology domain containing, family A member 1 / 219024_at / 10q26.13 / 1.51 / 2.85E-05 / 4.08E-04 / 1.61E-07 / 2.96E-06 / 8.67E-05 / 7.47E-04 / 1.30E-09 / 3.30E-08
MTMR1 / myotubularin related protein 1 / 214975_s_at / Xq28 / 1.52 / 4.53E-10 / 6.17E-08 / 4.27E-13 / 5.31E-11 / 6.85E-10 / 4.19E-08 / 4.75E-14 / 4.01E-12
IL9R / interleukin 9 receptor /// similar to Interleukin-9 receptor precursor (IL-9R) (CD129 antigen) / 208164_s_at / 16p13.3 / 1.52 / 4.05E-05 / 5.19E-04 / 7.79E-04 / 4.01E-03 / 7.96E-03 / 2.81E-02 / 6.20E-07 / 8.02E-06
G3BP1 / GTPase activating protein (SH3 domain) binding protein 1 / 201514_s_at / 5q33.1 / 1.52 / 1.56E-09 / 1.82E-07 / 3.15E-06 / 3.83E-05 / 7.29E-04 / 4.18E-03 / 4.64E-03 / 1.80E-02
DDX17 / DEAD (Asp-Glu-Ala-Asp) box polypeptide 17 / 213998_s_at / 22q13.1 / 1.53 / 1.69E-03 / 9.81E-03 / 1.11E-04 / 7.90E-04 / 2.16E-04 / 1.56E-03 / 7.85E-04 / 4.08E-03
DDX3X / DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked / 212514_x_at / Xp11 / 1.53 / 2.22E-16 / 4.01E-13 / 7.84E-14 / 1.23E-11 / 3.11E-12 / 5.22E-10 / 2.10E-13 / 1.41E-11
CBFB / core-binding factor, beta subunit / 206788_s_at / 16q22.1 / 1.53 / <1.00E-17 / <1.00E-17 / 5.67E-05 / 4.52E-04 / 1.66E-10 / 1.34E-08 / 3.51E-03 / 1.45E-02
GGA1 / golgi associated, gamma adaptin ear containing, ARF binding protein 1 / 218114_at / 22q13.31 / 1.53 / 1.35E-07 / 5.73E-06 / 1.53E-03 / 7.02E-03 / 4.74E-03 / 1.88E-02 / 6.46E-07 / 8.30E-06
HIST1H4C / histone cluster 1, H4c / 205967_at / 6p21.3 / 1.54 / 2.12E-10 / 3.32E-08 / 6.95E-14 / 1.20E-11 / 7.77E-15 / 5.21E-12 / 4.22E-15 / 5.04E-13
MGEA5 / meningioma expressed antigen 5 (hyaluronidase) / 200898_s_at / 10q24 / 1.56 / 5.48E-14 / 2.22E-11 / 1.78E-15 / 8.01E-13 / 6.66E-16 / 6.87E-13 / 4.44E-16 / 9.09E-14
NEK9 / NIMA (never in mitosis gene a)- related kinase 9 / 214738_s_at / 14q24.3 / 1.56 / 6.71E-04 / 4.73E-03 / 2.89E-04 / 1.74E-03 / 5.12E-07 / 1.13E-05 / 1.91E-05 / 1.63E-04
LPIN1 / lipin 1 / 212274_at / 2p25.1 / 1.57 / 2.60E-09 / 2.60E-07 / 5.55E-14 / 1.06E-11 / 1.43E-05 / 1.74E-04 / 6.18E-06 / 6.04E-05
IQGAP1 / IQ motif containing GTPase activating protein 1 / 213446_s_at / 15q26.1 / 1.57 / 8.37E-10 / 1.06E-07 / 8.69E-09 / 2.55E-07 / 1.08E-10 / 9.25E-09 / 4.48E-05 / 3.46E-04
FOXO1 / forkhead box O1 / 202723_s_at / 13q14.1 / 1.61 / 4.72E-06 / 9.47E-05 / 3.34E-10 / 1.67E-08 / 1.36E-10 / 1.14E-08 / 9.58E-08 / 1.54E-06
ZC3H11A / zinc finger CCCH-type containing 11A / 205787_x_at / 1q32.1 / 1.61 / 1.31E-14 / 8.59E-12 / 7.57E-14 / 1.21E-11 / 5.55E-12 / 8.34E-10 / 1.13E-13 / 8.49E-12
LAMP1 / lysosomal-associated membrane protein 1 / 201551_s_at / 13q34 / 1.68 / 2.45E-13 / 8.05E-11 / 6.21E-06 / 6.69E-05 / 2.33E-05 / 2.56E-04 / 4.83E-06 / 4.91E-05
ATP2A3 / ATPase, Ca++ transporting, ubiquitous / 207521_s_at / 17p13.3 / 1.70 / 5.63E-03 / 2.53E-02 / 1.64E-04 / 1.09E-03 / 1.99E-03 / 9.36E-03 / 9.31E-04 / 4.72E-03
PDPK1 / 3-phosphoinositide dependent protein kinase-1 / 204524_at / 16p13.3 / 1.70 / 7.12E-11 / 1.39E-08 / 9.13E-14 / 1.32E-11 / 1.99E-11 / 2.35E-09 / 8.66E-15 / 9.13E-13
PIK3CG / phosphoinositide-3-kinase, catalytic, gamma polypeptide / 206369_s_at / 7q22.3 / 1.72 / 1.06E-06 / 2.92E-05 / 7.97E-09 / 2.42E-07 / 5.18E-06 / 7.79E-05 / 2.31E-03 / 1.02E-02
SON / SON DNA binding protein / 201085_s_at / 21q22 / 1.77 / 2.15E-14 / 1.29E-11 / 2.22E-16 / 1.46E-13 / 1.21E-12 / 2.42E-10 / <1.00E-17 / <1.00E-17
ZNF3 / zinc finger protein 3 / 212684_at / 7q22.1 / 1.82 / 7.34E-08 / 3.70E-06 / 1.65E-09 / 6.47E-08 / 1.99E-04 / 1.46E-03 / 1.04E-04 / 7.10E-04
TTC3 / tetratricopeptide repeat domain 3 / 208664_s_at / 21q22.2 / 1.83 / 4.93E-07 / 1.66E-05 / 5.30E-08 / 1.20E-06 / 3.46E-07 / 8.22E-06 / 1.30E-08 / 2.65E-07
NCOA3 / nuclear receptor coactivator 3 / 209062_x_at / 20q12 / 1.95 / 1.90E-13 / 6.75E-11 / 3.33E-14 / 7.75E-12 / 4.04E-12 / 6.34E-10 / 6.49E-05 / 4.77E-04
NADSYN1 / NAD synthetase 1 / 218840_s_at / 11q13.4 / 1.96 / 1.21E-03 / 7.59E-03 / 2.07E-03 / 8.97E-03 / 4.04E-03 / 1.66E-02 / 3.76E-08 / 6.80E-07
CRIP2 / cysteine-rich protein 2 / 208978_at / 14q32.3 / 1.96 / 3.71E-05 / 4.91E-04 / 1.64E-02 / 4.80E-02 / 9.95E-03 / 3.34E-02 / 3.67E-03 / 1.50E-02
GIT2 / G protein-coupled receptor kinase interactor 2 / 209876_at / 12q24.1 / 2.00 / 1.20E-08 / 8.87E-07 / 7.46E-05 / 5.70E-04 / 2.50E-04 / 1.76E-03 / 1.70E-06 / 1.93E-05
CIITA / class II, major histocompatibility complex, transactivator / 211884_s_at / 16p13 / 2.01 / 3.00E-14 / 1.66E-11 / 3.84E-11 / 2.62E-09 / 4.91E-03 / 1.92E-02 / 7.10E-11 / 2.51E-09
HP1BP3 / heterochromatin protein 1, binding protein 3 / 220633_s_at / 1p36.12 / 2.01 / 1.57E-05 / 2.46E-04 / 1.44E-08 / 3.91E-07 / 5.72E-10 / 3.57E-08 / 1.66E-04 / 1.06E-03
GPR15 / G protein-coupled receptor 15 / 208524_at / 3q11.2-q13.1 / 2.04 / 1.26E-11 / 2.93E-09 / <1.00E-17 / <1.00E-17 / 3.88E-06 / 6.17E-05 / 1.34E-03 / 6.49E-03
CAPN3 / calpain 3, (p94) / 211890_x_at / 15q15-q21 / 2.08 / 4.69E-08 / 2.64E-06 / 9.67E-07 / 1.35E-05 / 1.04E-05 / 1.33E-04 / 2.66E-06 / 2.87E-05

Notes:

1)The fold change is ratio of the mean expression value given by Mas5.0 in the smoking to that in the non-smoking group;

2)The adjusted P value was produced by the Benjamini and Hochberg (BH) multiple-testing correction.

Table A2. Detail information of genes in the network categorized by ontological and pathway groups.

Gene Symbol / AffyID / Genomic Location / Fold (S/N) / Description / Molecular Function / Biological Process / Cellular Component / KEGG Pathway
HBA1/
HBA2 / 217414_x_at / 16p13.3 / -2.97 / hemoglobin, alpha 1 /// hemoglobin, alpha 2 / GO:0005344,GO:0019825,GO:0020037-oxygen, heme binding and transporter activity / GO:0015671-oxygen transport / GO:0005833-hemoglobin complex
MYH11 / 207961_x_at / 16p13.11 / -2.35 / myosin, heavy chain 11, smooth muscle / GO:0000166-nucleotide binding / GO:0030241-muscle thick filament assembly / GO:0042470-melanosome
GO:0005516-calmodulin binding
HBA1/
HBA2 / 211699_x_at / 16p13.3 / -2.23 / hemoglobin, alpha 1 /// hemoglobin, alpha 2 / GO:0005344,GO:0019825,GO:0020037-oxygen, heme binding and transporter activity / GO:0015671-oxygen transport / GO:0005833-hemoglobin complex
CCR1 / 205099_s_at / 3p21 / -2.10 / chemokine (C-C motif) receptor 1 / GO:0001584-rhodopsin-like receptor activity / GO:0006955-immune response / GO:0005886-plasma membrane / Cytokine-cytokine receptor interaction
GO:0005515-protein binding
HBA1 / 211745_x_at / 16p13.3 / -2.05 / hemoglobin, alpha 1 / GO:0005344,GO:0019825,GO:0020037-oxygen, heme binding and transporter activity / GO:0015671-oxygen transport / GO:0005833-hemoglobin complex
HBB / 211696_x_at / 11p15.5 / -2.03 / hemoglobin, beta / GO:0005344,GO:0019825,GO:0020037-oxygen, heme binding and transporter activity / GO:0015676-oxygen transport / GO:0005833-hemoglobin complex
GO:0050880-regulation of blood vessel size
GO:0030185-nitric oxide transport
HBA1/
HBA2 / 204018_x_at / 16p13.3 / -2.01 / hemoglobin, alpha 1 /// hemoglobin, alpha 2 / GO:0005344,GO:0019825,GO:0020037-oxygen, heme binding and transporter activity / GO:0015671-oxygen transport / GO:0005833-hemoglobin complex
HBA1/
HBA2 / 209458_x_at / 16p13.3 / -1.95 / hemoglobin, alpha 1 /// hemoglobin, alpha 2 / GO:0005344,GO:0019825,GO:0020037-oxygen, heme binding and transporter activity / GO:0015671-oxygen transport / GO:0005833-hemoglobin complex
GRIN1 / 210782_x_at / 9q34.3 / -1.83 / glutamate receptor, ionotropic, N-methyl D-aspartate 1 / GO:0005515-protein binding / GO:0005886-plasma membrane / Calcium signaling
GO:0030054-cell junction / Neuroactive ligand-receptor interaction
MUC5AC / 217182_at / 11p15.5 / -1.75 / mucin 5AC, oligomeric mucus/gel-forming
HOXB1 / 208224_at / 17q21.3 / -1.74 / homeobox B1
B7H2 (ICOSLG) / 211197_s_at / 21q22.3 / -1.68 / inducible T-cell co-stimulator ligand / GO:0006955-immune response / Cell adhesion molecules (CAMs)
NPPA / 209957_s_at / 1p36.21 / -1.61 / natriuretic peptide precursor A / GO:0050880-regulation of blood vessel size
EPHB3 / 204600_at / 3q21 / -1.61 / EPH receptor B3 / GO:0000166-nucleotide binding / Axon guidance
GO:0005003-ephrin receptor activity
CIB2 / 205008_s_at / 15q24 / -1.59 / calcium and integrin binding family member 2 / GO:0005515-protein binding
FANCA / 215530_at / 16q24.3 / -1.57 / Fanconi anemia, complementation group A / GO:0005515-protein binding / GO:0005737-cytoplasm
IL13 / 207844_at / 5q31 / -1.56 / interleukin 13 / GO:0005144-interleukin-13 receptor binding / GO:0006955-immune response / Cytokine-cytokine receptor interaction
Jak-STAT signaling
Fc epsilon RI signaling
E2A (TCF3) / 216647_at / 19p13.3 / -1.56 / E2A immunoglobulin enhancer binding factors E12/E47 / GO:0002326-B cell lineage commitment
EFNB3 / 210883_x_at / 17p13 / -1.55 / ephrin-B3 / GO:0005005-transmembrane-ephrin receptor activity / GO:0016198-axon choice point recognition / Axon guidance
EIF4B / 219599_at / 12q13.13 / -1.54 / eukaryotic translation initiation factor 4B
GATA2 / 209710_at / 3q21.3 / -1.52 / GATA binding protein 2 / GO:0005515-protein binding / GO:0006909-phagocytosis
VCAM1 / 203868_s_at / 1p32-p31 / -1.50 / vascular cell adhesion molecule 1 / GO:0005515-protein binding / GO:0005886-plasma membrane / Cell adhesion molecules (CAMs)
Leukocyte transendothelial migration
CPM / 217557_s_at / 12q14.3 / -1.50 / Carboxypeptidase M / GO:0005886-plasma membrane
ARF6 / 214182_at / 14q21.3 / -1.50 / ADP-ribosylation factor 6 / GO:0000166-nucleotide binding / GO:0016192-vesicle-mediated transport / GO:0005886-plasma membrane
GO:0005515-protein binding / GO:0035020-regulation of Rac protein signal transduction / GO:0005737-cytoplasm
GO:0005768-endosome
EPHB2 / 209588_at / 1p36 / -1.50 / EPH receptor B2 / GO:0005005-transmembrane-ephrin receptor activity / Axon guidance
GO:0000166-nucleotide binding
GO:0005003-ephrin receptor activity
GO:0005515-protein binding
IL9R / 208164_s_at / 16p13.3 / 1.52 / interleukin 9 receptor/similar to IL-9R precursor (CD129 antigen)
DDX3X / 212514_x_at / Xp11 / 1.53 / DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked / GO:0004004-ATP-dependent RNA helicase activity / GO:0005737-cytoplasm
GO:0000166-nucleotide binding / GO:0016607-nuclear speck
CBFB / 206788_s_at / 16q22.1 / 1.53 / core-binding factor, beta subunit / GO:0005515-protein binding
IQGAP1 / 213446_s_at / 15q26.1 / 1.57 / IQ motif containing GTPase activating protein 1 / GO:0005516-calmodulin binding / GO:0005886-plasma membrane / Regulation of actin cytoskeleton
GO:0005737-cytoplasm
PDPK1 / 204524_at / 16p13.3 / 1.70 / 3-phosphoinositide dependent protein kinase-1 / GO:0000166-nucleotide binding / GO:0005886-plasma membrane / mTOR signaling
GO:0005515-protein binding / GO:0005737-cytoplasm / PPAR signaling
GO:0004676-3-phosphoinositide dependent protein kinase activity
PIK3CG / 206369_s_at / 7q22.3 / 1.72 / phosphoinositide-3-kinase, catalytic, gamma polypeptide / GO:0005515-protein binding
SON / 201085_s_at / 21q22 / 1.77 / SON DNA binding protein / GO:0005515-protein binding / GO:0016607-nuclear speck
GIT2 / 209876_at / 12q24.1 / 2.00 / G protein-coupled receptor kinase interactor 2 / GO:0005515-protein binding

Notes:

1)The fold change is ratio of the mean expression value given by Mas5.0 in the smoking to that in the non-smoking group;

2)The numericalidentifier of Gene Ontology (GO) term is provided in each principle (Molecular function, biological process, and cellular component).