Rafehi et al., Supplementary Tables 1 - 3
Table 1: The 20 most up and down regulated genes in keratinocyte cells treated with hydroxytyrosol at 20 µM
UP
Refseq ID
Fold
Gene
Description
Change
1
NM_002133
15.46
HMOX1
heme oxygenase (decycling) 1
Location
Family
Diseases
Cytoplasm
enzyme
Atherosclerosis,
Carcinoma, DNA damage,
Diabetes, Wounds [1-5]
Carcinoma, Neoplasms
[6,7]
Carcinoma, DNA damage
[8,9]
Carcinoma [10]
Carcinoma, Inflammation
[11,12]
Prostatic Neoplasms [13]
2
NM_005980
10.59
S100P
S100 calcium binding protein P
Cytoplasm
other
3
NM_004864
8.78
GDF15
growth differentiation factor 15
Extracellular Space
growth factor
4
5
NM_004753
NM_005564
6.67
6.20
DHRS3
LCN2
dehydrogenase/reductase (SDR family) member 3
lipocalin 2
Cytoplasm
Extracellular Space
enzyme
transporter
6
NR_033343
5.76
prostate stem cell antigen
Plasma Membrane
other
7
8
NM_014059
NM_001012964
5.31
4.42
PSCA (includes
EG:8000)*
C13ORF15
KLK6*
chromosome 13 open reading frame 15
kallikrein-related peptidase 6
Cytoplasm
Extracellular Space
other
peptidase
9
10
NM_199001
NM_003841
4.32
4.27
C9ORF169
TNFRSF10C
unknown
Plasma Membrane
11
NM_002032
4.20
FTH1
chromosome 9 open reading frame 169
tumor necrosis factor receptor superfamily, member
10c, decoy without an intracellular domain
ferritin, heavy polypeptide 1
Cytoplasm
other
transmembrane
receptor
enzyme
12
NR_003070
4.16
small nucleolar RNA, C/D box 89
unknown
other
13
14
15
16
NR_002201
NM_004878
NM_020169
NM_005420
4.00
3.88
3.67
3.58
SNORD89
(includes
EG:692205)
FTHL3
PTGES
LXN
SULT1E1
unknown
Cytoplasm
Cytoplasm
Cytoplasm
other
enzyme
other
enzyme
17
18
NM_001498
NR_000010
3.57
3.56
ferritin, heavy polypeptide-like 3
prostaglandin E synthase
latexin
sulfotransferase family 1E, estrogen-preferring,
member 1
glutamate-cysteine ligase, catalytic subunit
small nucleolar RNA, C/D box 4A
Cytoplasm
unknown
enzyme
other
19
20
NR_002562
NM_003662
3.56
3.53
small nucleolar RNA, C/D box 28
pirin (iron-binding nuclear protein)
unknown
Nucleus
other
transcription
GCLC
SNORD4A
(includes
EG:26773)
SNORD28
PIR*
Neoplasms [14]
Neoplasms, Carcinoma
[15,16]
Diabetes, Neoplasms
[17,18]
Infections, Neoplasms
[19,20]
Carcinoma [20,21]
Carcinoma, Neoplasms
[22,23]
Diabetes [24]
regulator
DOWN
1
NR_030635
2
NR_030386
3
NR_002592
-5.05
-4.67
-3.59
4
NM_004625
-3.58
MIR939
MIR663
SNORD96A
(includes
EG:619571)
WNT7A
5
NM_005947
-3.45
MT1B
6
7
NR_031735
NR_002312
-3.37
-3.27
8
9
10
11
NM_000933
NM_001013653
NR_003286
NM_000598
-3.24
-3.21
-3.19
-2.86
12
NM_001168682
-2.85
13
NR_002591
-2.81
14
15
NR_030290
NR_004392
-2.81
-2.81
16
NM_000916
17
18
19
20
NM_001850
NR_001445
NR_003285
NM_018670
microRNA 939
microRNA 663
small nucleolar RNA, C/D box 96A
unknown
unknown
unknown
microRNA
microRNA
other
wingless-type MMTV integration site family, member
7A
metallothionein 1B
Extracellular Space
other
Wounds [25]
Cytoplasm
other
Diabetes, LeukemiaLymphoma, Adult T-Cell,
Prostatic Neoplasms [2628]
MIR1914
RPPH1 (includes
EG:85495)
PLCB4*
LRRC26
RN18S1
IGFBP3*
microRNA 1914
ribonuclease P RNA component H1
unknown
unknown
microRNA
other
phospholipase C, beta 4
leucine rich repeat containing 26
RNA, 18S ribosomal 1
insulin-like growth factor binding protein 3
Cytoplasm
Cytoplasm
unknown
Extracellular Space
enzyme
other
other
other
SAP25 (includes
EG:100316904)
SNORD95
(includes
EG:619570)
MIR564
RNY3 (includes
EG:6085)
sin3A-binding protein 25
unknown
other
small nucleolar RNA, C/D box 95
unknown
other
microRNA 564
RNA, Ro-associated Y3
unknown
unknown
microRNA
other
-2.80
OXTR
oxytocin receptor
Plasma Membrane
G-protein coupled
receptor
-2.73
-2.72
-2.71
-2.65
COL8A1*
RN7SK
RN5-8S1
MESP1
collagen, type VIII, alpha 1
RNA, 7SK small nuclear
RNA, 5.8S ribosomal 1
mesoderm posterior 1 homolog (mouse)
Extracellular Space
Nucleus
unknown
unknown
other
other
other
other
Atherosclerosis,
Carcinoma [29,30]
Lung Neoplasms,
Prostatic Neoplasms
[28,31]
Lung Neoplasms, NonSmall-Cell Lung
Carcinoma, Hyperplasia
[32,33]
Keratoconus [34]
Table 2: The 20 most up and down regulated genes in K562 cells treated with hydroxytyrosol at 20 µM
UP
Refseq ID
Gene
1
2
NM_016378
NR_003048
3
4
5
6
NR_003704
NR_030754
NR_004424
NR_023317
7
NR_030362
8
9
10
NR_031694
NR_031660
NM_012404
VCX2
SNORD23
(includes
EG:692091)
SNORA84
MIR622
RNU1-7
RNU7 (includes
EG:100147744)
MIR632
(includes
EG:693217)
MIR1281
MIR1259
ANP32D
11
NR_002960
12
13
NR_030377
NR_003051
14
15
16
17
NM_080746
NR_002984
NR_024562
NM_205845
SNORA20
(includes
EG:677806)
MIR647
RMRP (includes
EG:6023)
RPL10L
SNORA56
LOC100128675*
AKR1C2*
fold
change
3.95
3.42
Description
Location
Family
variable charge, X-linked 2
small nucleolar RNA, C/D box 23
unknown
unknown
other
other
3.34
3.28
3.19
3.19
small nucleolar RNA, H/ACA box 84
microRNA 622
RNA, U1 small nuclear 7
RNA, U7 small nuclear
unknown
unknown
unknown
unknown
other
microRNA
other
other
2.73
microRNA 632
unknown
microRNA
2.50
2.28
2.28
microRNA 1281
microRNA 1259
acidic (leucine-rich) nuclear
phosphoprotein 32 family, member D
small nucleolar RNA, H/ACA box 20
unknown
unknown
unknown
microRNA
microRNA
other
unknown
other
microRNA 647
RNA component of mitochondrial RNA
processing endoribonuclease
ribosomal protein L10-like
small nucleolar RNA, H/ACA box 56
hypothetical LOC100128675
aldo-keto reductase family 1, member
C2 (dihydrodiol dehydrogenase 2; bile
acid binding protein; 3-alpha
hydroxysteroid dehydrogenase, type
unknown microRNA
Cytoplasm other
2.21
2.19
2.07
2.01
2.00
1.98
1.97
Nucleus
unknown
unknown
Cytoplasm
other
other
other
enzyme
Disease
Colonic Neoplasms [35]
Anemia [36]
Carcinoma, Neoplasms,
Obesity, Wounds [37-40]
18
NM_001818
AKR1C4
1.97
19
20
DOWN
1
2
NR_003938
SNORD81
1.95
III)
aldo-keto reductase family 1, member
C4 (chlordecone reductase; 3-alpha
hydroxysteroid dehydrogenase, type I;
dihydrodiol dehydrogenase 4)
small nucleolar RNA, C/D box 81
NR_003938
SNORD81
1.95
NR_028373
NR_002957
3
4
NR_002922
NR_002752
RNU6-42
SNORA15
(includes
EG:677803)
SNORA13
RNU6-2
5
6
7
8
NR_004427
NR_030296
NR_003687
NR_003041
9
NR_001456
10
11
12
13
14
NR_004383
NR_003026
NR_002573
NR_031735
NR_002591
15
16
17
Cytoplasm enzyme
unknown
other
small nucleolar RNA, C/D box 81
unknown
other
-2.57
-2.56
RNA, U6 small nuclear 42
small nucleolar RNA, H/ACA box 15
unknown
unknown
other
other
-2.56
-2.50
small nucleolar RNA, H/ACA box 13
RNA, U6 small nuclear 2
unknown
Nucleus
other
other
-2.47
-2.43
-2.38
-2.35
RNA, U1 small nuclear 2
microRNA 570
small nucleolar RNA, C/D box 19B
small nucleolar RNA, C/D box 13
Nucleus
unknown
unknown
unknown
other
microRNA
other
other
-2.33
small nucleolar RNA, C/D box 38A
unknown
other
-2.29
-2.20
-2.20
-2.20
-2.20
small ILF3/NF90-associated RNA G1
small nucleolar RNA, H/ACA box 1
U58 small nucleolar RNA
microRNA 1914
small nucleolar RNA, C/D box 95
unknown
unknown
unknown
unknown
unknown
other
other
other
microRNA
other
NR_002953
NR_004391
RNU1-2
MIR570
SNORD19B
SNORD13
(includes
EG:692084)
SNORD38A
(includes
EG:94162)
SNAR-G1
SNORA1
U58
MIR1914
SNORD95
(includes
EG:619570)
SNORA11
RNY1
-2.10
-2.09
small nucleolar RNA, H/ACA box 11
RNA, Ro-associated Y1
unknown
unknown
other
other
NR_031608
MIR663B
-2.02
microRNA 663b
unknown
microRNA
Breast Neoplasms [41]
Non-Small-Cell Lung
Carcinoma [42]
Lung Neoplasm, Prostatic
Neoplasms [31]
18
19
20
NR_000006
NR_031741
NR_002575
SNORD21
MIR1977
SNORA27
-1.98
-1.95
-1.95
small nucleolar RNA, C/D box 21
microRNA 1977
small nucleolar RNA, H/ACA box 27
unknown
unknown
unknown
Table 3: The 20 most up and down regulated genes in K562 cells treated with hydroxytyrosol at 20 µM
UP Refseq ID
Gene
Fold change
Description
1 NM_019058
DDIT4
13.02
DNA-damage-inducible transcript 4
other
other
other
Location
Cytoplasm
Family
other
aldo-keto reductase family 1, member C4 (chlordecone
reductase; 3-alpha hydroxysteroid dehydrogenase, type
I; dihydrodiol dehydrogenase 4)
aldo-keto reductase family 1, member C2 (dihydrodiol
dehydrogenase 2; bile acid binding protein; 3-alpha
hydroxysteroid dehydrogenase, type III)
aldo-keto reductase family 1, member C1 (dihydrodiol
dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid
dehydrogenase)
brain expressed X-linked 2
Cytoplasm
enzyme
Cytoplasm
enzyme
Cytoplasm
enzyme
Nucleus
other
2
NM_001818
AKR1C4
9.38
3
NM_205845
AKR1C2*
8.78
4
NM_001353
AKR1C1
8.49
5
NM_032621
BEX2*
7.42
6
NM_003739
AKR1C3
6.76
aldo-keto reductase family 1, member C3 (3-alpha
hydroxysteroid dehydrogenase, type II)
Cytoplasm
enzyme
7
8
NM_031479
NM_014331
INHBE
SLC7A11
6.59
6.27
Extracellular Space
Plasma Membrane
growth factor
transporter
9
NR_004424
RNU1-7
5.62
inhibin, beta E
solute carrier family 7, (cationic amino acid transporter,
y+ system) member 11
RNA, U1 small nuclear 7
unknown
other
10
11
12
NM_006623
NM_031459
NM_002089
PHGDH
SESN2
CXCL2
5.35
5.30
5.23
phosphoglycerate dehydrogenase
sestrin 2
chemokine (C-X-C motif) ligand 2
Cytoplasm
Cytoplasm
Extracellular Space
enzyme
other
cytokine
13
NM_004864
GDF15
5.14
growth differentiation factor 15
Extracellular Space
growth factor
14
15
NR_004402
NM_052966
RNU1-8
FAM129A
5.11
4.98
RNA, U1 small nuclear 8
family with sequence similarity 129, member A
unknown
unknown
other
other
Disease
Carcinoma, Neoplasms
[43,44]
Breast Neoplasms [41]
Carcinoma,
Neoplasms, Wounds
[37-39]
Carcinoma,
Neoplasms, Obesity
[45,46,40]
Leukaemia, Neoplasms
[47,48]
Carcinoma, Leukaemia,
Neoplasms, Metabolic
disorders [49-52]
Pancreatic ductal
carcinoma [53]
Tubercolosis [54]
Breast Neoplasms [55]
Neoplasms, Metastasis
[56,57]
Carcinoma, DNA damage
[8,9]
Neoplasms [58]
16
17
18
NM_001902
NM_002966
NM_002090
CTH*
S100A10
CXCL3
Cytoplasm
Cytoplasm
Extracellular
Space
unknown
Extracellular
Space
enzyme
other
cytokine
19
20
NR_031671
NM_000584
MIR1267
IL8
NM_021066
HIST1H2AJ
-3.65
histone cluster 1, H2aj
Nucleus
other
2
NM_001130964
PLCD1*
-3.15
phospholipase C, delta 1
Cytoplasm
enzyme
3
NM_004925
AQP3
-2.99
aquaporin 3 (Gill blood group)
Plasma Membrane
transporter
4
NR_031706
MIR1306
(includes
EG:100302197)
CRYAB
-2.94
microRNA 1306
unknown
microRNA
5
NM_001885
-2.81
crystallin, alpha B
Nucleus
other
6
NR_029683
-2.80
microRNA 142
unknown
microRNA
NM_033334
MIR142
(includes
EG:406934)
NR6A1*
7
-2.79
nuclear receptor subfamily 6, group A, member 1
Nucleus
8
NM_015086
DDN
-2.77
dendrin
Plasma Membrane
liganddependent
nuclear
receptor
other
9
NM_001010865
EME2
-2.76
essential meiotic endonuclease 1 homolog 2 (S. pombe)
unknown
other
10
11
NR_001453
NM_001018016
SNORD14C
MUC1*
-2.72
-2.72
small nucleolar RNA, C/D box 14C
mucin 1, cell surface associated
unknown
Plasma Membrane
other
other
12
13
NR_003703
NR_027709
SCARNA27
C10ORF110*
-2.69
-2.69
small Cajal body-specific RNA 27
chromosome 10 open reading frame 110
unknown
unknown
other
other
DOWN
1
4.88
4.84
4.66
cystathionase (cystathionine gamma-lyase)
S100 calcium binding protein A10
chemokine (C-X-C motif) ligand 3
4.60
4.56
microRNA 1267
interleukin 8
Hypertension [59]
microRNA
cytokine
Major Depressive
Disorder [60]
Carcinoma,
Neoplasms, Bipolar
disorder [61-63]
Carcinoma, Neoplasms
Inflammation [64,65]
Carcinoma,
Neoplasms, Dilated
Cardiomyopathy [6668]
Choriocarcinoma [69]
Nephrotic Syndrome
[70]
Colorectal Neoplasms
[71]
Carcinoma, DNA
damage, Inflammation,
Wounds [72-75]
14
15
NR_004383
NM_004104
SNAR-G1
FASN
-2.67
-2.63
small ILF3/NF90-associated RNA G1
fatty acid synthase
unknown
Cytoplasm
other
enzyme
16
NM_001142621
TGFBRAP1*
-2.62
Cytoplasm
other
17
18
19
NR_002560
NR_028373
NM_001927
SNORD31
RNU6-42
DES
-2.61
-2.53
-2.52
transforming growth factor, beta receptor associated
protein 1
small nucleolar RNA, C/D box 31
RNA, U6 small nuclear 42
desmin
unknown
unknown
Cytoplasm
other
other
other
20
NR_002963
SNORA24
(includes
EG:677809)
-2.52
small nucleolar RNA, H/ACA box 24
unknown
other
DNA Damage
Carcinoma,
Neoplasms, Obesity
[76-79]
Chronic Hepatitis C
[80]
Neoplasms,
Cardiomyopathies
[81,82]
References
1. Schillinger M, Exner M, Mlekusch W, Domanovits H, Huber K, Mannhalter C, Wagner O, Minar E (2002) Heme oxygenase-1 gene promoter polymorphism
is associated with abdominal aortic aneurysm. Thromb Res 106 (2):131-136. doi:S0049384802001007 [pii]
2. Chang KW, Lee TC, Yeh WI, Chung MY, Liu CJ, Chi LY, Lin SC (2004) Polymorphism in heme oxygenase-1 (HO-1) promoter is related to the risk of oral
squamous cell carcinoma occurring on male areca chewers. Br J Cancer 91 (8):1551-1555. doi:10.1038/sj.bjc.6602186
6602186 [pii]
3. Mazza F, Goodman A, Lombardo G, Vanella A, Abraham NG (2003) Heme oxygenase-1 gene expression attenuates angiotensin II-mediated DNA damage
in endothelial cells. Exp Biol Med (Maywood) 228 (5):576-583
4. Arredondo M, Jorquera D, Carrasco E, Albala C, Hertrampf E (2007) Microsatellite polymorphism in the heme oxygenase-1 gene promoter is associated
with iron status in persons with type 2 diabetes mellitus. Am J Clin Nutr 86 (5):1347-1353. doi:86/5/1347 [pii]
5. Grosser N, Abate A, Oberle S, Vreman HJ, Dennery PA, Becker JC, Pohle T, Seidman DS, Schroder H (2003) Heme oxygenase-1 induction may explain the
antioxidant profile of aspirin. Biochem Biophys Res Commun 308 (4):956-960. doi:S0006291X03015043 [pii]
6. Jakubickova L, Barathova M, Pastorekova S, Pastorek J, Gibadulinova A (2005) Expression of S100P gene in cervical carcinoma cells is independent of E7
human papillomavirus oncogene. Acta Virol 49 (2):133-137
7. Austermann J, Nazmi AR, Muller-Tidow C, Gerke V (2008) Characterization of the Ca2+ -regulated ezrin-S100P interaction and its role in tumor cell
migration. J Biol Chem 283 (43):29331-29340. doi:M806145200 [pii]
10.1074/jbc.M806145200
8. Graichen R, Liu D, Sun Y, Lee KO, Lobie PE (2002) Autocrine human growth hormone inhibits placental transforming growth factor-beta gene transcription
to prevent apoptosis and allow cell cycle progression of human mammary carcinoma cells. J Biol Chem 277 (29):26662-26672. doi:10.1074/jbc.M109931200
M109931200 [pii]
9. Wong J, Li PX, Klamut HJ (2002) A novel p53 transcriptional repressor element (p53TRE) and the asymmetrical contribution of two p53 binding sites
modulate the response of the placental transforming growth factor-beta promoter to p53. J Biol Chem 277 (29):26699-26707. doi:10.1074/jbc.M203020200
M203020200 [pii]
10. Oler G, Camacho CP, Hojaij FC, Michaluart P, Jr., Riggins GJ, Cerutti JM (2008) Gene expression profiling of papillary thyroid carcinoma identifies
transcripts correlated with BRAF mutational status and lymph node metastasis. Clin Cancer Res 14 (15):4735-4742. doi:14/15/4735 [pii]
10.1158/1078-0432.CCR-07-4372
11. Fang WK, Xu LY, Lu XF, Liao LD, Cai WJ, Shen ZY, Li EM (2007) A novel alternative spliced variant of neutrophil gelatinase-associated lipocalin receptor in
oesophageal carcinoma cells. Biochem J 403 (2):297-303. doi:BJ20060836 [pii]
10.1042/BJ20060836
12. Klausen P, Niemann CU, Cowland JB, Krabbe K, Borregaard N (2005) On mouse and man: neutrophil gelatinase associated lipocalin is not involved in
apoptosis or acute response. Eur J Haematol 75 (4):332-340. doi:EJH511 [pii]
10.1111/j.1600-0609.2005.00511.x
13. Reiter RE, Gu Z, Watabe T, Thomas G, Szigeti K, Davis E, Wahl M, Nisitani S, Yamashiro J, Le Beau MM, Loda M, Witte ON (1998) Prostate stem cell
antigen: a cell surface marker overexpressed in prostate cancer. Proc Natl Acad Sci U S A 95 (4):1735-1740
14. Fosbrink M, Cudrici C, Niculescu F, Badea TC, David S, Shamsuddin A, Shin ML, Rus H (2005) Overexpression of RGC-32 in colon cancer and other tumors.
Exp Mol Pathol 78 (2):116-122. doi:S0014-4800(04)00115-7 [pii]
10.1016/j.yexmp.2004.11.001
15. Kountourakis P, Psyrri A, Scorilas A, Camp R, Markakis S, Kowalski D, Diamandis EP, Dimopoulos MA (2008) Prognostic value of kallikrein-related
peptidase 6 protein expression levels in advanced ovarian cancer evaluated by automated quantitative analysis (AQUA). Cancer Sci 99 (11):2224-2229.
doi:CAS942 [pii]
10.1111/j.1349-7006.2008.00942.x
16. Santin AD, Diamandis EP, Bellone S, Soosaipillai A, Cane S, Palmieri M, Burnett A, Roman JJ, Pecorelli S (2005) Human kallikrein 6: a new potential serum
biomarker for uterine serous papillary cancer. Clin Cancer Res 11 (9):3320-3325. doi:11/9/3320 [pii]
10.1158/1078-0432.CCR-04-2528
17. Akilen R, Tsiami A, Devendra D, Robinson N Glycated haemoglobin and blood pressure-lowering effect of cinnamon in multi-ethnic Type 2 diabetic
patients in the UK: a randomized, placebo-controlled, double-blind clinical trial. Diabet Med 27 (10):1159-1167. doi:10.1111/j.1464-5491.2010.03079.x
18. Sanlioglu AD, Dirice E, Aydin C, Erin N, Koksoy S, Sanlioglu S (2005) Surface TRAIL decoy receptor-4 expression is correlated with TRAIL resistance in
MCF7 breast cancer cells. BMC Cancer 5:54. doi:1471-2407-5-54 [pii]
10.1186/1471-2407-5-54
19. Roberts GT, Perry JL, Al-Jefri A, Scott CS (2005) Intra-leukocytic hemosiderin inclusions detected as pseudoeosinophils by automated depolarization
analysis in a patient with beta-thalassaemia major and immune hemolysis. Blood Cells Mol Dis 34 (2):162-165. doi:S1079-9796(05)00003-3 [pii]
10.1016/j.bcmd.2004.12.005
20. Pietsch EC, Chan JY, Torti FM, Torti SV (2003) Nrf2 mediates the induction of ferritin H in response to xenobiotics and cancer chemopreventive
dithiolethiones. J Biol Chem 278 (4):2361-2369. doi:10.1074/jbc.M210664200
M210664200 [pii]
21. Kojima F, Naraba H, Sasaki Y, Beppu M, Aoki H, Kawai S (2003) Prostaglandin E2 is an enhancer of interleukin-1beta-induced expression of membraneassociated prostaglandin E synthase in rheumatoid synovial fibroblasts. Arthritis Rheum 48 (10):2819-2828. doi:10.1002/art.11261
22. Hudelist G, Wulfing P, Kersting C, Burger H, Mattsson B, Czerwenka K, Kubista E, Gschwantler-Kaulich D, Fink-Retter A, Singer CF (2008) Expression of
aromatase and estrogen sulfotransferase in preinvasive and invasive breast cancer. J Cancer Res Clin Oncol 134 (1):67-73. doi:10.1007/s00432-007-0249-2
23. Choi JY, Lee KM, Park SK, Noh DY, Ahn SH, Chung HW, Han W, Kim JS, Shin SG, Jang IJ, Yoo KY, Hirvonen A, Kang D (2005) Genetic polymorphisms of
SULT1A1 and SULT1E1 and the risk and survival of breast cancer. Cancer Epidemiol Biomarkers Prev 14 (5):1090-1095. doi:14/5/1090 [pii]
10.1158/1055-9965.EPI-04-0688
24. Bekris LM, Shephard C, Janer M, Graham J, McNeney B, Shin J, Zarghami M, Griffith W, Farin F, Kavanagh TJ, Lernmark A (2007) Glutamate cysteine
ligase catalytic subunit promoter polymorphisms and associations with type 1 diabetes age-at-onset and GAD65 autoantibody levels. Exp Clin Endocrinol
Diabetes 115 (4):221-228. doi:10.1055/s-2007-970574
25. Lyu J, Joo CK (2005) Wnt-7a up-regulates matrix metalloproteinase-12 expression and promotes cell proliferation in corneal epithelial cells during
wound healing. J Biol Chem 280 (22):21653-21660. doi:M500374200 [pii]
10.1074/jbc.M500374200
26. Yang L, Li H, Yu T, Zhao H, Cherian MG, Cai L, Liu Y (2008) Polymorphisms in metallothionein-1 and -2 genes associated with the risk of type 2 diabetes
mellitus and its complications. Am J Physiol Endocrinol Metab 294 (5):E987-992. doi:90234.2008 [pii]
10.1152/ajpendo.90234.2008
27. Sun NN, Fastje CD, Wong SS, Sheppard PR, Macdonald SJ, Ridenour G, Hyde JD, Witten ML (2003) Dose-dependent transcriptome changes by metal ores
on a human acute lymphoblastic leukemia cell line. Toxicol Ind Health 19 (7-10):157-163
28. Garrett SH, Sens MA, Shukla D, Flores L, Somji S, Todd JH, Sens DA (2000) Metallothionein isoform 1 and 2 gene expression in the human prostate:
downregulation of MT-1X in advanced prostate cancer. Prostate 43 (2):125-135. doi:10.1002/(SICI)1097-0045(20000501)43:2<125::AID-PROS7>3.0.CO;2-S
[pii]
29. Kawachi S, Takeda N, Sasaki A, Kokubo Y, Takami K, Sarui H, Hayashi M, Yamakita N, Yasuda K (2005) Circulating insulin-like growth factor-1 and insulinlike growth factor binding protein-3 are associated with early carotid atherosclerosis. Arterioscler Thromb Vasc Biol 25 (3):617-621.
doi:01.ATV.0000154486.03017.35 [pii]
10.1161/01.ATV.0000154486.03017.35
30. Yumoto E, Nakatsukasa H, Hanafusa T, Yumoto Y, Nouso K, Matsumoto E, Onishi T, Takuma Y, Tanaka H, Fujikawa T, Suzuki M, Uemura M, Shiratori Y
(2005) IGFBP-3 expression in hepatocellular carcinoma involves abnormalities in TGF-beta and/or Rb signaling pathways. Int J Oncol 27 (5):1223-1230
31. Christov CP, Trivier E, Krude T (2008) Noncoding human Y RNAs are overexpressed in tumours and required for cell proliferation. Br J Cancer 98 (5):981988. doi:6604254 [pii]
10.1038/sj.bjc.6604254
32. Wang X, Chorley BN, Pittman GS, Kleeberger SR, Brothers J, 2nd, Liu G, Spira A, Bell DA Genetic variation and antioxidant response gene expression in
the bronchial airway epithelium of smokers at risk for lung cancer. PLoS One 5 (8):e11934. doi:10.1371/journal.pone.0011934
33. Sendemir E, Herbert Z, Sivukhina E, Zermann DH, Arnold R, Jirikowski GF (2008) Colocalization of androgen binding protein, oxytocin receptor, caveolin 1
and proliferation marker p21 in benign prostate hyperplasia. Anat Histol Embryol 37 (5):325-331. doi:AHE848 [pii]
10.1111/j.1439-0264.2008.00848.x
34. Aldave AJ, Bourla N, Yellore VS, Rayner SA, Khan MA, Salem AK, Sonmez B (2007) Keratoconus is not associated with mutations in COL8A1 and COL8A2.
Cornea 26 (8):963-965. doi:10.1097/ICO.0b013e31811dfaf7
00003226-200709000-00013 [pii]
35. Sarver AL, French AJ, Borralho PM, Thayanithy V, Oberg AL, Silverstein KA, Morlan BW, Riska SM, Boardman LA, Cunningham JM, Subramanian S, Wang
L, Smyrk TC, Rodrigues CM, Thibodeau SN, Steer CJ (2009) Human colon cancer profiles show differential microRNA expression depending on mismatch
repair status and are characteristic of undifferentiated proliferative states. BMC Cancer 9:401. doi:1471-2407-9-401 [pii]
10.1186/1471-2407-9-401
36. Graf SA, Calado RT, Kajigaya S, Young NS (2007) RMRP mutations in hematological disorders. Clin Genet 71 (5):468-470. doi:CGE776 [pii]
10.1111/j.1399-0004.2007.00776.x
37. Kazemi-Noureini S, Colonna-Romano S, Ziaee AA, Malboobi MA, Yazdanbod M, Setayeshgar P, Maresca B (2004) Differential gene expression between
squamous cell carcinoma of esophageus and its normal epithelium; altered pattern of mal, akr1c2, and rab11a expression. World J Gastroenterol 10
(12):1716-1721
38. Ji Q, Aoyama C, Nien YD, Liu PI, Chen PK, Chang L, Stanczyk FZ, Stolz A (2004) Selective loss of AKR1C1 and AKR1C2 in breast cancer and their potential
effect on progesterone signaling. Cancer Res 64 (20):7610-7617. doi:64/20/7610 [pii]
10.1158/0008-5472.CAN-04-1608
39. Lou H, Du S, Ji Q, Stolz A (2006) Induction of AKR1C2 by phase II inducers: identification of a distal consensus antioxidant response element regulated by
NRF2. Mol Pharmacol 69 (5):1662-1672. doi:mol.105.019794 [pii]
10.1124/mol.105.019794
40. Blouin K, Blanchette S, Richard C, Dupont P, Luu-The V, Tchernof A (2005) Expression and activity of steroid aldoketoreductases 1C in omental adipose
tissue are positive correlates of adiposity in women. Am J Physiol Endocrinol Metab 288 (2):E398-404. doi:00312.2004 [pii]
10.1152/ajpendo.00312.2004
41. Lord SJ, Mack WJ, Van Den Berg D, Pike MC, Ingles SA, Haiman CA, Wang W, Parisky YR, Hodis HN, Ursin G (2005) Polymorphisms in genes involved in
estrogen and progesterone metabolism and mammographic density changes in women randomized to postmenopausal hormone therapy: results from a
pilot study. Breast Cancer Res 7 (3):R336-344. doi:bcr999 [pii]
10.1186/bcr999
42. Bishop JA, Benjamin H, Cholakh H, Chajut A, Clark DP, Westra WH Accurate classification of non-small cell lung carcinoma using a novel microRNA-based
approach. Clin Cancer Res 16 (2):610-619. doi:1078-0432.CCR-09-2638 [pii]
10.1158/1078-0432.CCR-09-2638
43. Schneider A, Younis RH, Gutkind JS (2008) Hypoxia-induced energy stress inhibits the mTOR pathway by activating an AMPK/REDD1 signaling axis in
head and neck squamous cell carcinoma. Neoplasia 10 (11):1295-1302
44. Ellisen LW (2005) Growth control under stress: mTOR regulation through the REDD1-TSC pathway. Cell Cycle 4 (11):1500-1502. doi:2139 [pii]
45. Yang MD, Wu CC, Chiou SH, Chiu CF, Lin TY, Chiang IP, Chow KC (2003) Reduction of dihydrodiol dehydrogenase expression in resected hepatocellular
carcinoma. Oncol Rep 10 (2):271-276
46. Chow KC, Lu MP, Wu MT (2006) Expression of dihydrodiol dehydrogenase plays important roles in apoptosis- and drug-resistance of A431 squamous cell
carcinoma. J Dermatol Sci 41 (3):205-212. doi:S0923-1811(05)00324-5 [pii]
10.1016/j.jdermsci.2005.11.007
47. Fischer C, Drexler HG, Reinhardt J, Zaborski M, Quentmeier H (2007) Epigenetic regulation of brain expressed X-linked-2, a marker for acute myeloid
leukemia with mixed lineage leukemia rearrangements. Leukemia 21 (2):374-377. doi:2404493 [pii]
10.1038/sj.leu.2404493
48. Naderi A, Teschendorff AE, Beigel J, Cariati M, Ellis IO, Brenton JD, Caldas C (2007) BEX2 is overexpressed in a subset of primary breast cancers and
mediates nerve growth factor/nuclear factor-kappaB inhibition of apoptosis in breast cancer cell lines. Cancer Res 67 (14):6725-6736. doi:67/14/6725 [pii]
10.1158/0008-5472.CAN-06-4394
49. Li S, Hanna E, Breau R, Ratanatharathorn V, Xia X, Suen J (2004) Preferential expression of hPGFS in primary SCCHN and tumour cell lines derived from
respiratory and digestive organs. Br J Cancer 90 (5):1093-1099. doi:10.1038/sj.bjc.6601636
6601636 [pii]
50. Liu CY, Hsu YH, Pan PC, Wu MT, Ho CK, Su L, Xu X, Li Y, Christiani DC (2008) Maternal and offspring genetic variants of AKR1C3 and the risk of childhood
leukemia. Carcinogenesis 29 (5):984-990. doi:bgn071 [pii]
10.1093/carcin/bgn071
51. Rizner TL, Smuc T, Rupreht R, Sinkovec J, Penning TM (2006) AKR1C1 and AKR1C3 may determine progesterone and estrogen ratios in endometrial
cancer. Mol Cell Endocrinol 248 (1-2):126-135. doi:S0303-7207(05)00395-3 [pii]
10.1016/j.mce.2005.10.009
52. Svensson PA, Gabrielsson BG, Jernas M, Gummesson A, Sjoholm K (2008) Regulation of human aldoketoreductase 1C3 (AKR1C3) gene expression in the
adipose tissue. Cell Mol Biol Lett 13 (4):599-613. doi:10.2478/s11658-008-0025-6
53. Lo M, Ling V, Wang YZ, Gout PW (2008) The xc- cystine/glutamate antiporter: a mediator of pancreatic cancer growth with a role in drug resistance. Br J
Cancer 99 (3):464-472. doi:6604485 [pii]
10.1038/sj.bjc.6604485
54. Dey S, Burton RL, Grant GA, Sacchettini JC (2008) Structural analysis of substrate and effector binding in Mycobacterium tuberculosis D-3phosphoglycerate dehydrogenase. Biochemistry 47 (32):8271-8282. doi:10.1021/bi800212b
55. Budanov AV, Shoshani T, Faerman A, Zelin E, Kamer I, Kalinski H, Gorodin S, Fishman A, Chajut A, Einat P, Skaliter R, Gudkov AV, Chumakov PM, Feinstein
E (2002) Identification of a novel stress-responsive gene Hi95 involved in regulation of cell viability. Oncogene 21 (39):6017-6031.
doi:10.1038/sj.onc.1205877
56. Bachmeier BE, Mohrenz IV, Mirisola V, Schleicher E, Romeo F, Hohneke C, Jochum M, Nerlich AG, Pfeffer U (2008) Curcumin downregulates the
inflammatory cytokines CXCL1 and -2 in breast cancer cells via NFkappaB. Carcinogenesis 29 (4):779-789. doi:bgm248 [pii]
10.1093/carcin/bgm248
57. Wu F, Zikusoka M, Trindade A, Dassopoulos T, Harris ML, Bayless TM, Brant SR, Chakravarti S, Kwon JH (2008) MicroRNAs are differentially expressed in
ulcerative colitis and alter expression of macrophage inflammatory peptide-2 alpha. Gastroenterology 135 (5):1624-1635 e1624. doi:S0016-5085(08)01408X [pii]
10.1053/j.gastro.2008.07.068
58. Matsumoto F, Fujii H, Abe M, Kajino K, Kobayashi T, Matsumoto T, Ikeda K, Hino O (2006) A novel tumor marker, Niban, is expressed in subsets of
thyroid tumors and Hashimoto's thyroiditis. Hum Pathol 37 (12):1592-1600. doi:S0046-8177(06)00377-7 [pii]
10.1016/j.humpath.2006.06.022
59. Li Y, Zhao Q, Liu XL, Wang LY, Lu XF, Li HF, Chen SF, Huang JF, Gu DF (2008) Relationship between cystathionine gamma-lyase gene polymorphism and
essential hypertension in Northern Chinese Han population. Chin Med J (Engl) 121 (8):716-720
60. Shelton RC, Claiborne J, Sidoryk-Wegrzynowicz M, Reddy R, Aschner M, Lewis DA, Mirnics K Altered expression of genes involved in inflammation and
apoptosis in frontal cortex in major depression. Mol Psychiatry. doi:mp201052 [pii]
10.1038/mp.2010.52
61. Fu L, Qin YR, Xie D, Hu L, Kwong DL, Srivastava G, Tsao SW, Guan XY (2007) Characterization of a novel tumor-suppressor gene PLC delta 1 at 3p22 in
esophageal squamous cell carcinoma. Cancer Res 67 (22):10720-10726. doi:67/22/10720 [pii]
10.1158/0008-5472.CAN-07-2411
62. Keshamouni VG, Mattingly RR, Reddy KB (2002) Mechanism of 17-beta-estradiol-induced Erk1/2 activation in breast cancer cells. A role for HER2 AND
PKC-delta. J Biol Chem 277 (25):22558-22565. doi:10.1074/jbc.M202351200
M202351200 [pii]
63. Pandey GN, Dwivedi Y, SridharaRao J, Ren X, Janicak PG, Sharma R (2002) Protein kinase C and phospholipase C activity and expression of their specific
isozymes is decreased and expression of MARCKS is increased in platelets of bipolar but not in unipolar patients. Neuropsychopharmacology 26 (2):216-228.
doi:S0893133X0100327X [pii]
10.1016/S0893-133X(01)00327-X
64. Liu YL, Matsuzaki T, Nakazawa T, Murata S, Nakamura N, Kondo T, Iwashina M, Mochizuki K, Yamane T, Takata K, Katoh R (2007) Expression of
aquaporin 3 (AQP3) in normal and neoplastic lung tissues. Hum Pathol 38 (1):171-178. doi:S0046-8177(06)00485-0 [pii]
10.1016/j.humpath.2006.07.015
65. Tancharoen S, Matsuyama T, Abeyama K, Matsushita K, Kawahara K, Sangalungkarn V, Tokuda M, Hashiguchi T, Maruyama I, Izumi Y (2008) The role of
water channel aquaporin 3 in the mechanism of TNF-alpha-mediated proinflammatory events: Implication in periodontal inflammation. J Cell Physiol 217
(2):338-349. doi:10.1002/jcp.21506
66. Boslooper K, King-Yin Lam A, Gao J, Weinstein S, Johnson N (2008) The clinicopathological roles of alpha-B-crystallin and p53 expression in patients with
head and neck squamous cell carcinoma. Pathology 40 (5):500-504. doi:794748436 [pii]
10.1080/00313020802198010
67. Dimberg A, Rylova S, Dieterich LC, Olsson AK, Schiller P, Wikner C, Bohman S, Botling J, Lukinius A, Wawrousek EF, Claesson-Welsh L (2008) alphaBcrystallin promotes tumor angiogenesis by increasing vascular survival during tube morphogenesis. Blood 111 (4):2015-2023. doi:blood-2007-04-087841
[pii]
10.1182/blood-2007-04-087841
68. Inagaki N, Hayashi T, Arimura T, Koga Y, Takahashi M, Shibata H, Teraoka K, Chikamori T, Yamashina A, Kimura A (2006) Alpha B-crystallin mutation in
dilated cardiomyopathy. Biochem Biophys Res Commun 342 (2):379-386. doi:S0006-291X(06)00238-5 [pii]
10.1016/j.bbrc.2006.01.154
69. Mehta DV, Kim YS, Dixon D, Jetten AM (2002) Characterization of the expression of the retinoid-related, testis-associated receptor (RTR) in trophoblasts.
Placenta 23 (4):281-287. doi:10.1053/plac.2001.0779
S0143400401907799 [pii]
70. Duner F, Patrakka J, Xiao Z, Larsson J, Vlamis-Gardikas A, Pettersson E, Tryggvason K, Hultenby K, Wernerson A (2008) Dendrin expression in
glomerulogenesis and in human minimal change nephrotic syndrome. Nephrol Dial Transplant 23 (8):2504-2511. doi:gfn100 [pii]
10.1093/ndt/gfn100
71. Leary RJ, Lin JC, Cummins J, Boca S, Wood LD, Parsons DW, Jones S, Sjoblom T, Park BH, Parsons R, Willis J, Dawson D, Willson JK, Nikolskaya T, Nikolsky
Y, Kopelovich L, Papadopoulos N, Pennacchio LA, Wang TL, Markowitz SD, Parmigiani G, Kinzler KW, Vogelstein B, Velculescu VE (2008) Integrated analysis
of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proc Natl Acad Sci U S A 105 (42):16224-16229.
doi:0808041105 [pii]
10.1073/pnas.0808041105
72. Silverman HS, Sutton-Smith M, Heal P, Parry S, Palmai-Pallag T, Leir SH, Morris HR, Dell A, Harris A (2002) In vivo glycosylation of MUC1 in airway
epithelial cells. Glycoconj J 19 (6):379-384. doi:10.1023/B:GLYC.0000004009.24191.d3
5254313 [pii]
73. Ren J, Agata N, Chen D, Li Y, Yu WH, Huang L, Raina D, Chen W, Kharbanda S, Kufe D (2004) Human MUC1 carcinoma-associated protein confers
resistance to genotoxic anticancer agents. Cancer Cell 5 (2):163-175. doi:S1535610804000200 [pii]
74. Beatty PL, Plevy SE, Sepulveda AR, Finn OJ (2007) Cutting edge: transgenic expression of human MUC1 in IL-10-/- mice accelerates inflammatory bowel
disease and progression to colon cancer. J Immunol 179 (2):735-739. doi:179/2/735 [pii]
75. Miyazaki E, Nureki S, Ono E, Ando M, Matsuno O, Fukami T, Ueno T, Kumamoto T (2007) Circulating thymus- and activation-regulated chemokine/CCL17
is a useful biomarker for discriminating acute eosinophilic pneumonia from other causes of acute lung injury. Chest 131 (6):1726-1734. doi:131/6/1726 [pii]
10.1378/chest.06-2596
76. Silva SD, Perez DE, Nishimoto IN, Alves FA, Pinto CA, Kowalski LP, Graner E (2008) Fatty acid synthase expression in squamous cell carcinoma of the
tongue: clinicopathological findings. Oral Dis 14 (4):376-382. doi:ODI1395 [pii]
10.1111/j.1601-0825.2007.01395.x
77. Bandyopadhyay S, Pai SK, Watabe M, Gross SC, Hirota S, Hosobe S, Tsukada T, Miura K, Saito K, Markwell SJ, Wang Y, Huggenvik J, Pauza ME, Iiizumi M,
Watabe K (2005) FAS expression inversely correlates with PTEN level in prostate cancer and a PI 3-kinase inhibitor synergizes with FAS siRNA to induce
apoptosis. Oncogene 24 (34):5389-5395. doi:1208555 [pii]
10.1038/sj.onc.1208555
78. Xiao R, Su Y, Simmen RC, Simmen FA (2008) Dietary soy protein inhibits DNA damage and cell survival of colon epithelial cells through attenuated
expression of fatty acid synthase. Am J Physiol Gastrointest Liver Physiol 294 (4):G868-876. doi:00515.2007 [pii]
10.1152/ajpgi.00515.2007
79. Kovacs P, Harper I, Hanson RL, Infante AM, Bogardus C, Tataranni PA, Baier LJ (2004) A novel missense substitution (Val1483Ile) in the fatty acid
synthase gene (FAS) is associated with percentage of body fat and substrate oxidation rates in nondiabetic Pima Indians. Diabetes 53 (7):1915-1919.
doi:53/7/1915 [pii]
80. Hwang Y, Chen EY, Gu ZJ, Chuang WL, Yu ML, Lai MY, Chao YC, Lee CM, Wang JH, Dai CY, Shian-Jy Bey M, Liao YT, Chen PJ, Chen DS (2006) Genetic
predisposition of responsiveness to therapy for chronic hepatitis C. Pharmacogenomics 7 (5):697-709. doi:10.2217/14622416.7.5.697
81. Jiang W, Li X, Rao S, Wang L, Du L, Li C, Wu C, Wang H, Wang Y, Yang B (2008) Constructing disease-specific gene networks using pair-wise relevance
metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements. BMC Syst Biol 2:72. doi:1752-0509-2-72 [pii]
10.1186/1752-0509-2-72
82. Vrabie A, Goldfarb LG, Shatunov A, Nagele A, Fritz P, Kaczmarek I, Goebel HH (2005) The enlarging spectrum of desminopathies: new morphological
findings, eastward geographic spread, novel exon 3 desmin mutation. Acta Neuropathol 109 (4):411-417. doi:10.1007/s00401-005-0980-1