· web viewtable s2. genes commonly down-regulated by stat5a and hp1alpha illumina id gene symbol...

Table S2. Genes commonly down-regulated by STAT5A and HP1alpha

Illumina ID

Gene Symbol

Control HP1alpha

STAT5A[Y964F]

sh-STAT5A

sh-HP1a

Gene Descriptioin Over-expressed in cancer

Relevance to human cancer

Reference

1240440 TXNIP 2616.25 217.8 264.5 4256.413175

10003.30882

Thioredoxin-interacting protein ? Promotes inflammation Zhou, et al., 2010

6270138 TACSTD2

2742.55 340.8 582.9 4078.00689

4705.645339

Tumor-associated calcium signal transducer-2

Yes Prognostic marker and target of colon cancer

Wang, et al., 2008; Muhlmann et al., 2009

1510424 S100P 3710.35 474.9 550.8 6053.138973

8690.578097

S-100 family protein Yes Promotes pancreatic cancer; Over-expressed in colon-liver metastasis

Logsdon et al., 2005; Lin et al., 2011

1340021 AGR2 4817.75 734.2 1621.1 8208.388584

5962.52231

Metastasis-Associated Anterior Gradient 2

Yes Prognostic marker of breast, pancreatic cancer

Barraclough, 2009; Ramachandran, 2008

4640086 FOXQ1 3851.3 631.2 1124.9 6306.30252

6186.511655

Forkhead box Q1 Yes Over-expressed in and promotes colorectal cancer

Kaneda et al., 2010

2680110 TM4SF1 2746.05 479.7 698.5 3131.045788

3811.964873

Transmembrane-4-L-six-family-1 Yes Required for tumor angiogenesis

Shih et al., 2009

7510132 OLR1 946.15 175 272.2 869.6248265

1170.29178

Opioid Receptor-Like 1 No

540377 CXCL5 3166.95 589.4 1191.6 3593.136362

4262.250238

C-X-C motif chemokine 5 Yes Over-expressed in gastric cancer; promotes prostate cancer; pro-angiogenic

Begley et al., 2008; Park et al., 2007; Kawamura, 2012

5570139 QPCT 2265.9 440.8 624.9 3808.232068

4050.82885

Glutaminyl-peptide cyclotransferase Yes Over-expressed in thyroid and lung cancer

Jarząb et al., 2005; da Silveira Mitteldorf et al., 2011

7650358 TGFBI 2308.95 461.2 785.7 2567.239322

4978.541734

Transforming growth factor beta induced Yes Promotes colon cancer metastasis; overexpresed in renal, gastrointestinal and brain tumors

Ma et al., 2008; Ivanov et al., 2008

830056 FOXA1 2319.9 471.8 659.5 2977.765497

3187.048437

Forkhead-box A1 Yes Prognostic marker (favorable) for breast cancer; antagonizes epithelial-to-mesenchymal transition in pancreatic cancer

Badve et al., 2007; Song et al., 2010

2940291 QPRT 883.55 201.2 380 1063.627687

1822.760376

Quinolate phosphoribosyltransferase Yes Biomarker for thyroid cancer subtyping; bladder cancer risk variant SNP

Hinsch et al., 2009; Menashe et al., 2012

1850674 TRIM31 450.6 103.4 142.7 481.9197309

891.096861

Tripartite motif-containing protein 31 Yes Over-expressed in gastric cancer; down-regulated in squamous cell carcinoma cancer stem-like cells

Sugiura et al., 2008; Geng et al., 2012

7050673 CDH17 915 214.1 401.9 1172.36008

2208.071102

Cadherin 17 Yes Prognostic marker for gastric cancer; hepatocellular carcinoma liver cancer risk factor SNP variant

Lee et al., 2010; Wang et al., 2006

1110180 RORA 428.1 100.2 142.7 458.0942675

437.5196873

RAR-related orphan receptor A ? Differentially DNA methylated in gastric cancer; Prognostic marker for bladder cancer

Watanabe et al., 2009; Compérat et al., 2009

4560543 TSPAN8 1481.25 354.3 547.3 1823.621812

2268.836344

Tetraspanin-8 (also D6.1A/CO-029) Yes Over-expressed in invasive melanoma; prognostic marker for gastrointestinal

Berthier-Vergnes et al., 2011; Gesierich et al., 2006

cancer and regulates pancreatic tumor angiogenesis

380010 CXCL5 738.5 177.4 321.5 775.7212243

902.1961109

C-X-C motif chemokine 5 Yes Over-expressed in gastric cancer; promotes prostate cancer; pro-angiogenic

Begley et al., 2008; Park et al., 2007; Kawamura, 2012

1070189 AXIN2 3564.6 867.3 1349.7 3910.49477

4371.946747

Axis inhibition protein 2 (also Axin-like protein, Axil)

? Mutations cause colorectal cancer predisposition; regulates epithelial-to-mesenchymal transition in breast cancer cells

Liu et al., 2000; Yook et al., 2006

2190184 PRSS23 2036.2 500.7 620.8 3062.391835

2785.798194

Serine protease 23 Yes Over-expressed in ERα breast cancer, colon cancer

Chan et al., 2012; Hein et al., 2011

6480471 LOC645553

431.15 108.9 145.8 477.2270992

719.9546756

LOC645553 No

5390121 GDPD3 445.7 113.5 154.3 474.6174405

614.1639881

Glycerophosphodiester phosphodiesterase domain-containing protein 3

No

1570661 CYP2J2 1345.05 345.4 435.6 1379.633471

1495.735124

Cytochrome P450 2J2 Yes Over-expressed in esophageal, lung, breast, stomach, liver, colon carcinoma tissue; drug inhibition reduces proliferation in tongue squamous cell, alveolar basal epithelial, hepatoma, cervical carcinoma cells

Jiang et al., 2005; Chen et al., 2009

2600397 RPESP 687.2 180.2 245 849.3123642

881.6637351

RPE-spondin ? Down-regulated in prostate cancer; over-exressed in Keloid dermal fibroproliferative tumor

Zhang et al., 2005; Seifert et al., 2008

7200435 ASCL2 1186.6 313.3 677.4 1873.528663

2015.50029

Achaete-scute complex homolog 2 (also HASH2)

Yes Over-expressed in colorectal cancer; correlated with colorectal cancer metastasizing to the liver

Jubb et al., 2006; Stange et al., 2010

4150600 EIF1AY 808.15 216.7 262 1019.321203

997.4003165

Eukaryotic translation initiation factor 1A Yes Over-expressed in prostate, colon cancer; breast cancer of parous women

Dasari et al., 2001; Balough et al., 2007

3400097 MUC20 299.1 80.5 114.8 339.9888052

494.2072121

Mucin-20 Yes Amplification in salivary gland cancer

Vékony et al., 2009

4780072 TCEAL3 356.15 99 114.7 448.2702648

486.7141548

Transccription elongation factor A (SII)-like 3

No

7570484 TFF3 635.3 178.4 285.4 615.899176

1233.3381

Trefoil factor 3 Yes Over-expressed in gastric cancer; Over-expressed in prostate cancer

Leung et al., 2002; Garraway et al., 2004

4570255 LEF1 471.4 134.6 224.1 766.5112528

649.1033008

Lymphoid enhancer-binding factor-1 Yes Over-expressed in colorectal cancer and malignant melanoma; Over-expressed in highly metastatic lung adenocarcinoma

Conacci-Sorrell et al., 2002; Nguyen et al., 2009

110181 KIAA1199

1350.9 389.9 613.5 1154.910235

1383.885655

KIAA1199 Yes Over-expressed in gastric cancer; Over-expressed in colorectal adenoma

Matsuzaki et al., 2009; Sabates-Bellver et al., 2007

5260343 SCG5 821.4 237.3 332 1314.24 2504.991 Secretogranin V Yes colorectal cancer increase Jaeger et al., 2007;

874 risk SNP association; over-expressed lymph node metastatic cancer compared to primary breast tumor

Ellsworth et al., 2009

2060450 NNT 386 113.2 127.7 608.9993329

557.7558372

Nicotinamide nucleotide (NAD(P)) transhydroenase

Yes Prognostic marker for cervical cancer, increased copy number and over-expression; prognostic marker, over-expressed in progressed, metastatic, hormone independent prostate cancer cell line compared to LNCaP early disease line

Scotto et al., 2008; Liu et al., 2004

6520598 SLC2A10 436.5 129.7 180.5 531.7430497

797.9823083

Solute carrier family 2, facilitated glucose transporter member 10

Yes Prognostic marker for late stage prostate cancer; prognostic marker in breast cancer

Dozmorov et al., 2010; Dairkee et al., 2009

50168 GRHL3 282.05 84.4 106.5 338.7463452

395.7290355

Grainyhead-like 3 Yes Pro-angiogenic functions in breast cancer cell; tumor suppressor functions in murine squamous cell carcinoma model

Guardiola-Serrano et al., 2008; Darido et al., 2011

5080576 KIT 297 89.9 137.9 302.0748576

338.8071603

c-Kit (also CD117) Yes Prognostic marker, gain of function mutations in testicular, ovarian, extragonadal samples; prognostic marker, over-expressed in small cell lung solid tumor

Tian et al., 1999; Matsuda et al., 1993

5340017 H19 294.65 90.6 101 389.5009865

303.5231568

H19 imprinted maternally expressed transcript

Yes loss of imprinting hypomethylation and over-expression in colorectal and esophageal cancer; loss of imprinting hypomethylation of paternal allele associated with bladder cancer

Hibi et al., 1996; Takai et al., 2001

5560369 ALDH3A1

780.65 245.4 304.7 753.2089697

992.1351818

Aldehyde dehydrogenase 3 family, member A1

Yes Prognostic marker, over-expressed in lung cancer; marker for chemoresistance and metastasis in breast cancer

Patel et al., 2008; Hu et al., 2009

4390398 LCN2 1445.8 461.2 600.2 973.5909652

3568.890137

Lipocalin-2 Yes Prognostic marker, over-expressed in invasive breast cancer tissue; over-expressed in bladder cancer

Yang et al., 2009; Dokun et al., 2008

1980255 RNF39 255.75 82.1 81.6 253.1851719

326.0995702

RING finger protein 39 Yes Over-expressed in colorectal cancer; prognostic marker for invasive breast ductal carcinoma

Camps et al., 2009; Vargas et al., 2012

3450189 HOXA13 638.25 208.8 220.5 828.9211587

1103.834887

Homeobox protein A13 Yes Chromosomal translocation NUP98-fusion protein in acute

Taketani et al., 2002; Chiba et al., 2006

myeloid leukemia; over-expressed in liver cancer stem cells

610437 CD24 3266.1 1072.9 1278.7 4357.816501

2820.171355

Cluster of differentiation 24 ? CD24-/low /CD44+ breast cancer stem cells correlated with invasieness and metastasis; prognosic marker, cytoplasmic expression in poor prognosis epithelial ovarian carcinoma

Sheridan et al., 2006; Kristiansen et al. 2002

4830520 KRT80 676.5 222.8 199.4 746.0424671

711.3852376

Keratin 80 Yes Over-expressed in breast cancer cells; marker for melanoma subtyping

Bateman et al., 2010; Jönsson eet al., 2010

3460014 C4ORF18

594.35 196.6 275.1 807.269652

904.6043501

Chromosome 4 open reading frame 18 ? Over-expressed in melanoma; down-regulated in Non-BRCA1/2 breast cancer subtype

Hoek 2007; Waddell et al., 2010

870376 C9ORF152

325.9 110 139.5 424.1453809

540.0854943

Chromosome 9 open reading frame 152 ? Deletion in non-BRCA1/2 breast cancer, rare germline

Krepischi et al., 2012

5310360 TLE4 280.25 94.8 148.3 320.1716524

427.3612892

Transducin-like enhancer of split 4 No Common deletion, tumor suppressor function in acute myeloid leukemia; homozygous deletion in lung cancer cells

Dayyani et al., 2008; Nagayama et al., 2007

6760037 SYTL2 1258.3 432.1 391 1564.711793

1953.921826

Synaptotagmin-like 2 Yes Prognostic gene set marker (favorable) for ER+ breast cancer patient survival; down-regulated in bladder cancer cells

Kok et al., 2009; Ho et al., 2012

6400564 HS.560343

366 126.7 155 439.0456781

421.813071



2340193 KRT80 254.75 88.8 98.1 302.2146715

301.9853735

Keratin 80 Yes Overexpressed in breast cancer cells; marker for melanoma subtyping

Bateman et al., 2010; Jönsson eet al., 2010

2810601 LEF1 509.75 178.8 272.7 881.0280136

677.9934635

Lymphoid enhancer-binding factor-1 Yes Over-expressed in colorectal cancer and malignant melanoma; Over-expressed in highly metastatic lung adenocarcinoma

Conacci-Sorrell et al., 2002; Nguyen et al., 2009

670754 TMEM30B

317.35 111.7 139 369.6044177

442.6756359

Transmembrane protein 30B No DNA hypermethylated in malignant melanomas; DNA hypermethylated in malignant pleural mesothelioma

Furuta et al., 2006; Goto et al., 2009

3940703 RORA 296.3 104.6 120.2 307.1805246

354.0056393



3170440 BCL11A 267.9 94.8 132.8 301.3645161

304.8580645

B-cel lymphoma/leukemia 11A Yes Translocation and amplification in aggressive B-cell chronic lymphoma; prognostic marker, over-expressed in ERG high

Satterwhite et al., 2001; Marcucci et al, 2005

worse outcome acute myeloid leukemia patients

940504 RUNX2 247.3 88.2 91.3 342.0260234

259.7734649

Run-related transcription factor 2 Yes Over-expressed in breast, prostate cancer cells metastasizing to the bone; regualtes breast cancer metastatic property to the bone

Pratap et al., 2005; Barnes et al., 2003

1710242 C1ORF59

486.15 174.3 226.3 561.3826325

638.0463204

HEN1 methyltransferase homolog 1 No

4730523 IGFL2 271.25 98 93.1 337.7328431

318.2312092

Insulin like growth factor 2 Yes Loss of DNA methylation imprinting, prognostic in colorectal cancer; loss of imprinting, over-expression, prognostic for ovarian cancer

Cui et al., 2003; Murphy et al., 2006

4490544 LY6G6D 178.15 64.5 73.2 255.9848711

237.1304613

Lymphocyte antigen 6 complex, locus G6D

No

1710053 SERP2 200.25 73.4 90.6 193.5815377

258.1087169

Stress-associated endoplasmic reticulum protein family member 2

No

7210632 AKR1C3 666.8 245.8 291.8 969.1243091

792.9766745

Aldo-keto reductase family 1 member C3 Yes Prognostic marker, over-expressed in androgen-independent prostate tumors; SNPs prognostic of bladder cancer risk

Stanbrough et al., 2006; Figueroa et al., 2008

730156 ICAM2 227.1 84 102 268.2378178

326.45625

Intercellular adhesion molecule 2 No Ectopic expression reduces tumorigeneicity of gastric carcinoma cells and inhibits metastasis in mice; Ezrin over-expressed in pancreatic adenocarcinoma with metastatic potential binds to inhibit ICAM-2

Tanaka et al., 2004; Akisawa et al., 1999

5810278 SYTL2 412.05 155.2 168.1 441.7472973

565.7335135

Synaptotagmin-like 2 Yes Prognostic gene set marker (favorable) for ER+ breast cancer patient survival; down-regulated in bladder cancer cells

Kok et al., 2009; Ho et al., 2012

3460296 HDGFRP3

197.45 74.5 97.6 247.1958154

248.8994392

Hepatoma-derived growth factor related protein 3

Yes Over-expressed in Erα+ breast cancer; down-regulated in some non-small cell lung cancer

Abba et al., 2005; Suzuki et al., 2008

730739 TCEAL3 159.35 60.2 73.6 169.8515759

197.4752865

Transccription elongation factor A (SII)-like 3

No

5810494 LOC100129195

309.65 118.3 172 313.2123451

380.074823

LOC100129195 No

6020575 NNT 201.8 77.5 88.8 293.780023

222.1885189

Nicotinamide nucleotide (NAD(P)) transhydroenase

Yes Prognostic marker for cervical cancer, increased copy number and over-expression; prognostic marker, over-expressed in progressed, metastatic, hormone independent prostate cancer cell line compared to LNCaP early disease line

Scotto et al., 2008; Liu et al., 2004

3140463 AGR2 225 87.6 110.1 288.5341 269.1097 Anterior gradient homolog 2 Yes Metastasis-Associated Prognostic marker of

727 122 Anterior Gradient 2 breast, pancreatic cancer630243 PRR15L 283.45 110.4 124.5 338.6151

108377.6343

354Proline rich 15-like Yes Marker set of basal-like

breast cancer subtyping; Over-expressed in the APC gene mutation colorectal cancer subtype

Krijgsman et al., 2011; Meunier et al., 2011

6200148 PCP4 218.65 86.6 94.5 236.4349282

302.3437799

Purkinje cell protein 4 No Deletion in ERG rearranged prostate cancer; down-regulated in bladder cancer

Demichelis et al., 2009; Lu et al., 2010

2260731 ERAP2 500.95 198.5 227.1 579.5989315

680.531727

Endoplasmic reticulum aminopeptidase 2 No Down-regulated in neuroblastoma; down-regulated, variable in melanoma cells

Giacomini et al., 2010; Kamphausen et al., 2010

3420452 TSPAN13

1167.5 463.6 502.8 1560.992831

1283.554052

Tetraspanin 13 Yes Over-expressed in prostate cancer; over-expressed in breast cancer fibroblast microenvironment

Arencibia et al., 2009; Mercier et al., 2008

6940270 MUC13 268.95 108.1 133.2 339.7483645

530.778271

Mucin 13 Yes Prognostic marker, over-expressed in gastric cancer; over-expressed in ovarian cancer

Shimamura et al., 2005; Chauhan et al., 2009

4150270 ANKRD22

579.85 234.5 280.4 903.7192195

746.0428452

Ankyrin repeat domain 22 Yes Over-expressed in pancreatic cancer; deletion n metastatic melanoma

Baine et al., 2011; Dutton‐Regester 2012

130324 TMPRSS2

333.8 135.6 125 393.8301613

447.668871

Transmembrane protease, serine 2 Yes Oncogenic chromosomal rearrangement common in prostate cancer; oncogenic rearrangement prognostic, associated with lethal prostate cancer subtype

Tomlins et al., 2005; Demichelis et al., 2007

5670475 GCHFR 550.7 225.2 279.2 722.4815073

726.9009421

GTP cyclohydrolase 1 feedback regulator Yes Prognostic marker, over-expressed in recurring hepatocellular carcinoma; altered expression upon bradykinin antagonist antiproliferative treatment of ovarian cancer clear cell carcinoma

Matoba et al., 2005; Jutras et al., 2010

3440491 GALC 438.75 179.9 173.3 477.7179276

718.020148

Galactosylceramidase Yes Commonly expressed intestinal differentiation marker, serves as biomarker for gastric cancer subtyping, over-expressed in the intestinal-type; biomarker for esophagael cancer subtyping, marker set for pre-cancer Barrett's esophagus

Hippo e al., 2002; Greenawalt et al., 2007

6330608 PTK6 306.25 127.2 147.3 305.2205882

457.0588235

Tyrosine-protein kinase 6 Yes Over-expressed in primary breast cancer, prognostic marker for long-term survival; biomarker for ovarian cancer subtyping, over-expressed in the mucinous epithelial type

Aubele et al., 2008; Heinzelmann-Schwarz et al., 2006

7400537 GSTT1 267.95 111.5 125.8 335.8478018

390.03753

Glutathione S-transferase theta-1 No Null genotype signficantly associated with colorectal cancer cases; null genotype associated with slight increase in bladder cancer risk

Deakin et al., 1996; Kempkes et al., 1996

7550292 SELENBP1

346.7 150 187.5 413.3352482

1014.773688

Selenium binding protein 1 Yes Prognostic marker for patients with unfavorable survival, down-regulated in invasive ovarian cancer; predictive marker in colorectal cancer, reduction associated with poor survival

Huang et al., 2006; Kim et al., 2006

2600465 SH3GL2 221.95 96.5 112.6 237.0064645

320.6141261

SH3-domain GRB2-like 2 No Deletions, down-regulation in early onset type of breast carcinoma, proposed tumor suppressor; regulates apoptosis in laryngeal carcinoma cells

Sinha et al., 2008; Shang et al., 2010

4860537 SLC7A8 379.05 166.5 213.3 396.3282509

517.2760071

Solute carrier family 7 No

130181 ANKRD22

398.15 175.5 213.1 548.082786

468.9758073

Ankyrin repeat domain 22 Yes Over-expressed in pancreatic cancer; deletion n metastatic melanoma

Baine et al., 2011; Dutton‐Regester 2012

7210326 PSMB8 254.85 112.5 132.2 393.7328338

471.5072207

Proteasome subunit beta type-8 Yes Over-expressed in basal medullary breast cancer; Over-expressed in LNCaP prostate cancer cells expressing NF-kB2/p52

Bertucci et al., 2006; Nadiminty et al., 2010

6900053 PPFIBP2 419.25 186.9 211.1 552.1503819

679.9802673

PTPRF interacting protein binding protein 2

Yes Prognostic marker, over-expressed in endometrial cancer

Colas et al., 2011

3420632 PSMB8 168 75.4 97.5 215.9194631

229.4496644

Proteasome subunit beta type-8 Yes Over-expressed in basal medullary breast cancer; Over-expressed in LNCaP prostate cancer cells expressing NF-kB2/p52

Bertucci et al., 2006; Nadiminty et al., 2010

1090326 TIMP4 188.05 84.5 93 195.4419025

275.8658019

Metalloproteinase inhibitor 4 No Inhibits breast cancer cell growth and metastasis; down-regulated in prostate cancer patient tissues

Wang et al., 1997; Riddick et al., 2005

3360669 PODXL2 159.95 72.9 97.2 185.9791304

225.1221739

Podocalyxin-like 2 Yes Prognostic marker, over-expressed in poor survival invasive breast carcinoma; increases migration and invasion in breast cancer cell line

Somasiri et al., 2004; Sizemore et al., 2007

3420739 SNTB1 421.25 192.9 230.4 730.6446809

559.993617

Beta-1-syntrophin Yes Genomic copy number gain in recurring breast cancer; over-expressed in ovarian serous adenocarcinoma cell line

Hwang et al., 2008; Cho et al., 2008

6590445 RIN2 288.35 134 141.5 359.9244217

474.0843416

Ras and Rab interactor 2 Yes Associated with breast tumors resistant to chemotherapy

Folgueira et al., 2005

4830632 SLC7A7 227.4 106.3 88.4 218.792674

297.0915751

Y+L amino acid transporter 1 Yes Over-expressed in pancreatic carcinoma cell lines

Missiaglia et al., 2004

3170594 MAL2 1430.15 692 730.8 2315.62797

946.1298747

Four-transmembrane protein of the MAL family

Yes Prognostic marker, over-expressed in ovarian carcinoma

Byrne et al., 2010

730040 LAMB3 662.85 324.3 292.5 917.4024214

907.5469626

Lamin beta 3 subunit (also laminin-5 β3) Yes Over-expressed in malignant esophageal tissue; polymorphisms associated with cervical cancer

Kita et al., 2008; Zhou et al., 2010

6220189 HOXB6 408.95 203.2 182.6 423.7371666

633.9088619

Homeobox protein B6 Yes Prognostic marker, over-expressed in colorectal cancer cells; prognostic marker, over-expressed in ovarian cancer

Vider et al., 2000; Stone et al., 2003

1090390 OAS1 169 84.3 84.8 200.4028369

301.3234043

2'-5'-oligoadenylate synthetase 1 Yes Prognostic marker, over-expressed in node-positive metastatic colon cancer; polymorphism predictive of prostate cancer, low-enzyme-activity associated with higher risk

Bertucci et al., 2004; Mandal et al., 2011

3940673 LOC728285

546.05 272.7 175.6 535.3840552

576.8884926

Keratin associated protein 2-3, 2-4 No Up-regulated with CAPE treatment to suppress tumorigeneicity in prostate cancer

Lin et al., 2012

1110373 C15ORF48

235.9 119.5 124.3 262.6925466

409.2142857

Chromosome 15 open reading frame 48 Yes Prognostic marker, subtyping set, over-expressed in low compared to high grade bladder tumors; prognostic marker, over-expressed in squamous cell carcinoma compared to normal tissue

Mengual et al., 2009; Ra et al., 2011

1230048 ABCB1 413.3 218.2 283.8 430.9341333

713.3558 ATP-binding cassette, sub-family B (MDR/TAP), member 1

Yes Over-expressed in paclitaxel treatment-resistant ovarian cancer; polymorphism dictates susceptibility to irinotecan treatment outcome in advanced non-small cell lung cancer patients

Duan et al., 2004; Han et al., 2007

2710278 TCEAL1 203.9 110.9 121.4 289.1181448

341.9118247

Transcription elongation factor A (SII)-like 1

No Prognostic marker, down-regulated in esophageal squamous tissue compared to matched control; correlated with chemotherapeutic breast tumor reduction

Makino et al., 2005; Ikeda et al., 2007

2650564 RARRES3

201.9 113.6 115.9 232.5087464

427.0508746

Retinoic acid receptor responder protein 3 Yes Prognostic marker, over-expressed in well-differentiated colorectal cancer; over-expressed in cervical cancer tissue

Shyu et al., 2003; Ahn et al., 2004

2120053 CYP1B1 596.15 336.7 304.5 640.5293951

1040.538318

Cytochrome P450 1B1 Yes Prognostic marker, over-expressed in primary and metastatic ovarian cancer;

McFadyen et al., 2001; McKay et al., 1995

over-expressed in breast cancer

5700753 CEACAM1

230.55 133.2 151.2 268.6326251

430.6022961

Carcinoembryonic antigen-related cell adhesion molecule 1

Yes Prognostic marker, rngiogenic, promotes non-small cell lung cancer progression; Over-expressed in colon liver metastasis.

Sienel et al., 2003; Lin et al., 2011

5490240 MAP1LC3A

178.65 104.6 89.2 175.5226477

305.5032276

Microtubule-associated proteins 1A/1B light chain 3A

Yes Over-expressed in breast carcinoma tissues;

Othman et al., 2009;

4120193 PROM2 259.4 153.2 140.6 676.2928571

160.6181583

Prominin 2 Yes Prognostic marker, over-expressed in chromophobe renal cell carcinoma compared to benign oncocytoma

Rohan et al., 2006

6100411 FKBP14 698.7 422 455.4 1326.223079

964.9097266

FK506 binding protein 14 Yes Associated with resistance to erlotinib in adult glioblastoma;

Halatsch et al., 2008

6550026 TICAM2 498.35 304.1 206.9 705.1983752

669.4967873

Toll-like receptor adaptor molecule 2 No

3800168 SLC2A3 342.3 210.6 245 829.1922414

366.497069

Solute carrier family 2 (facilitated glucose transporter), member 3

Yes Prognostic, over-expressed in breast cancer; up-regulated by hypoxia by HIF-1alpha in small cell lung cancer cells

Sternlicht et al., 2006; Wan et al., 2009

1170220 AHSA2 430.25 277.1 158.5 406.970364

490.7770536

Activator of heat shock 90kDa protein ATPase homolog 2

Yes Prognostic marker set, involved in estrogen responsiveness of ER+ tumor; over-expressed in colon liver metastasis

Rody et al., 2008; Lin et al., 2011

460202 KLK3 149.95 97.5 84.1 196.5308245

260.2200384

Kallikrein-related peptidase 3 (or Prostate-specific antigen)

Yes Prognostic marker, over-expressed in prostate cancer, increased Androgen Receptor response promoter polymorphism associated with susceptibility

Lai et al., 2006

1940487 STAT5A 147.45 96.7 210.6 38.95479876

161.1450464

Signal transducer and activator of transcription 5A

N.A. Prognostic marker, gradual loss of activity, but not expression during breast cancer progression and metastasis, activation is a favorable marker for survival; Increased constitutive activation in transformed compared with normal head and neck squamous cells

Nevalainen et al., 2004; Leong et al., 2002

5290674 KRT20 543.45 358 300.3 446.4766844

1320.124153

Keratin 20 Yes Over-expressed in colon liver metastasis; Prognostic marker, over-expressed bladder cancer

Birkenkamp-Demtroder et al., 2005; Mengual et al., 2006

1440324 PPARG 350 234.9 197 336.1554476

662.5954198

Peroxisome proliferator-activated receptor gamma

? Anti-proliferative effects with pathway activation in colorectal cancer cells; induce terminal differentiation of malignant breast epithelial cells,

Lin et al., 2011; Mueller et al., 1998

potential therapeutics3120370 CD68 674.8 463.7 285.3 866.4393

768897.0252

125Cluster of Differentiation 68 ? Prognostic marker,

increased CD68 labeled Tumor-associated macrophages improved survival of primary colon carcinoma patients; prognostic marker, high CD68+Tumor-associated macrophage index prostate cancer cells correlates with higher Gleason grade

Khorana et al., 2003; Shimura et al., 2000

7650441 FGFBP1 1106.9 777.7 569.3 1244.730091

1777.650392

Fibroblast growth factor binding protein 1 Yes Over-expressed in pancreatic adenocarcinoma and colon neoplasia; over-expressed in breast cancer

Tassi et al., 2006; Kagan et al., 2003

4610520 GCNT3 242.15 172.1 131 401.9386364

325.8397727

Glucosaminyl (N-acetyl) transferase 3 Yes Prognostic marker, over-expressed in mucinous epithelial ovarian cancer subtype; prognostic marker, over-expressed in intestinal metaplasia

Heinzelmann-Schwarz et al., 2006; lee et al., 2010

4290148 HIST2H2AA4

291.9 214.3 184.9 860.709244

434.3721446

Histone cluster 2, H2aa4 No

2350537 MMP7 209.05 154.4 108.5 293.1505747

342.4094828

Matrix metalloproteinase-7 Yes Prognostic marker, over-expressed in colorectal cancer, important for early onset; prognostic marker, over-expressed in ovarian cancer, promotes cell invasion

Brabletz et al., 1999; Wang et al., 2005

5570279 HIST1H1C

812.65 627.2 473.7 2938.020137

1150.161314

Histone cluster 1, H1c (Histone H1.2) Yes Up-regulated in breast cancer tumor epithelium compared to normal stromal; up-regulated when treating pancreatic cancer cells with SAHA, a histone deacetylase inhibitor and 5Aza-d

Ma et al., 2009; Kumagai et al., 2008

610451 HIST2H2AA3

271.9 224.8 176.6 752.5822325

337.3282348

Histone cluster 2, H2aa3 (Histone H2A.2) Yes Up-regulated after CAPE treatment to suppress proliferation, colony formation, cell cycle progression in prostate; down-reguated when treating HeLa cells with NASP siRNA, usually expressed in malignant cells

Lin et al., 2012; Alekseev et al., 2009

5910767 TNFRSF6B

7310.35 6155.7 3258.1 10848.86339

20000 Tumor necrosis factor receptor superfamily member 6B

Yes Prognostic marker for poor survival in breast cancer patients; over-expressed in various cancers, anti-apoptotic in hepatocellular carcinoma cells

Fournier et al., 2006; Chen et al., 2010

6580369 DYNLRB1

730.95 618.3 545.8 1786.293297

2059.258389

Dynein light chain roadblock-type 1 (also km23-1)

? Prognostic marker set for bladder cancer

Catto et al., 2010; Pulipati et al., 2011

progression; ectopic expression in human ovarian cancer cells inhibits tumor formation

2640392 TNFRSF6B

1915.6 1756.6 1022.4 2151.501686

5226.054369

Tumor necrosis factor receptor superfamily member 6B

Yes Prognostic marker for poor survival in breast cancer patients; over-expressed in various cancers, anti-apoptotic in hepatocellular carcinoma cells

Fournier et al., 2006; Chen et al., 2010

520682 CPA4 519.5 486.4 241.8 293.8179303

2604.399834

Carboxypeptidase A4 Yes Prognostic, specific SNPs associated with increased early onset prostate cancer risk; induced in prostate cancer by NaBu treatment to induce terminal differentiation and apoptosis

Roess et al., 2009; Huang et al., 1999

830019 PPARG 1272.3 1215.4 932.2 1298.085156

3079.583915

Peroxisome proliferator-activated receptor gamma

? Anti-proliferative effects with pathway activation in colorectal cancer cells; induce terminal differentiation of malignant breast epithelial cells, potential therapeutics

Brockman et al., 1998; Mueller et al., 1998

7210224 DYNLRB1

1529.2 1479.3 1419.7 4347.379678

4232.134739

Dynein light chain roadblock-type 1 (also km23-1)

Yes Prognostic marker set for bladder cancer progression; ectopic expression in human ovarian cancer cells inhibits tumor formation

Catto et al., 2010; Pulipati et al., 2011

6280168 SERPINA3

826.7 808.4 612.1 1068.558681

2112.418884

Serpin peptidase inhibitor, clade A Yes Prognostic marker, subtyping, over-expressed in HLA-positive cervical carcinoma; over-expressed in colon liver metastasis.

Gorter et al., 2008; Lin et al., 2011

Total RNA isolated from DLD-1 cells stably expressing the indicated transgene was subjected to microarray analysis using Illumina HumanHT-12 v4 Expression BeadChips. The data were analyzed with GenePattern software (Broad Institute) and only those genes down-regulated by STAT5A[Y964F] and Hp1alpha, and up-regulated by their knock down are shown. The list correspsond to the upper half of Figure 4c. "Yes" in bold indicates over-expressed or important for colorectal cancer development. N.A.: not applicable due to transgene expression. ?: conflicting reports or not clear. No: relevant reference not found.

References (cited in Table S2):

Abba, M.C., Hu, Y., Sun, H., Drake, J.A., Gaddis, S., Baggerly, K., Sahin, A., and Aldaz, C.M. (2005). Gene expression signature of estrogen receptor alpha status in breast cancer. BMC genomics 6, 37.Adam, L., Vadlamudi, R.K., McCrea, P., and Kumar, R. (2001). Tiam1 overexpression potentiates heregulin-induced lymphoid enhancer factor-1/beta -catenin nuclear signaling in breast cancer cells by modulating the intercellular

stability. The Journal of biological chemistry 276, 28443-28450.Ahn, W.S., Bae, S.M., Lee, J.M., Namkoong, S.E., Han, S.J., Cho, Y.L., Nam, G.H., Seo, J.S., Kim, C.K., and Kim, Y.W. (2004). Searching for pathogenic gene functions to cervical cancer. Gynecologic oncology 93, 41-48.Akisawa, N., Nishimori, I., Iwamura, T., Onishi, S., and Hollingsworth, M.A. (1999). High levels of ezrin expressed by human pancreatic adenocarcinoma cell lines with high metastatic potential. Biochemical and biophysical research

communications 258, 395-400.Alekseev, O.M., Richardson, R.T., Alekseev, O., and O'Rand, M.G. (2009). Analysis of gene expression profiles in HeLa cells in response to overexpression or siRNA-mediated depletion of NASP. Reproductive biology and

endocrinology : RB&E 7, 45.Anderson, M.G., Nakane, M., Ruan, X., Kroeger, P.E., and Wu-Wong, J.R. (2006). Expression of VDR and CYP24A1 mRNA in human tumors. Cancer chemotherapy and pharmacology 57, 234-240.Ando, T., Ishiguro, H., Kimura, M., Mitsui, A., Mori, Y., Sugito, N., Tomoda, K., Mori, R., Harada, K., Katada, T., et al. (2007). The overexpression of caveolin-1 and caveolin-2 correlates with a poor prognosis and tumor progression

in esophageal squamous cell carcinoma. Oncology reports 18, 601-609.Arencibia, J.M., Martin, S., Perez-Rodriguez, F.J., and Bonnin, A. (2009). Gene expression profiling reveals overexpression of TSPAN13 in prostate cancer. International journal of oncology 34, 457-463.Arumugam, T., Simeone, D.M., Van Golen, K., and Logsdon, C.D. (2005). S100P promotes pancreatic cancer growth, survival, and invasion. Clin Cancer Res 11, 5356-5364.Aubele, M., Walch, A.K., Ludyga, N., Braselmann, H., Atkinson, M.J., Luber, B., Auer, G., Tapio, S., Cooke, T., and Bartlett, J.M. (2008). Prognostic value of protein tyrosine kinase 6 (PTK6) for long-term survival of breast cancer

patients. British journal of cancer 99, 1089-1095.

Badve, S., Turbin, D., Thorat, M.A., Morimiya, A., Nielsen, T.O., Perou, C.M., Dunn, S., Huntsman, D.G., and Nakshatri, H. (2007). FOXA1 expression in breast cancer--correlation with luminal subtype A and survival. Clin Cancer Res 13, 4415-4421.

Baine, M.J., Chakraborty, S., Smith, L.M., Mallya, K., Sasson, A.R., Brand, R.E., and Batra, S.K. (2011). Transcriptional profiling of peripheral blood mononuclear cells in pancreatic cancer patients identifies novel genes with potential diagnostic utility. PloS one 6, e17014.

Balogh, G.A., Russo, J., Mailo, D.A., Heulings, R., Russo, P.A., Morrison, P., Sheriff, F., and Russo, I.H. (2007). The breast of parous women without cancer has a different genomic profile compared to those with cancer. International journal of oncology 31, 1165-1175.

Barnes, G.L., Javed, A., Waller, S.M., Kamal, M.H., Hebert, K.E., Hassan, M.Q., Bellahcene, A., Van Wijnen, A.J., Young, M.F., Lian, J.B., et al. (2003). Osteoblast-related transcription factors Runx2 (Cbfa1/AML3) and MSX2 mediate the expression of bone sialoprotein in human metastatic breast cancer cells. Cancer Res 63, 2631-2637.

Barraclough, D.L., Platt-Higgins, A., de Silva Rudland, S., Barraclough, R., Winstanley, J., West, C.R., and Rudland, P.S. (2009). The metastasis-associated anterior gradient 2 protein is correlated with poor survival of breast cancer patients. Am J Pathol 175, 1848-1857.

Bashyam, M.D., Bair, R., Kim, Y.H., Wang, P., Hernandez-Boussard, T., Karikari, C.A., Tibshirani, R., Maitra, A., and Pollack, J.R. (2005). Array-based comparative genomic hybridization identifies localized DNA amplifications and homozygous deletions in pancreatic cancer. Neoplasia 7, 556-562.

Basu, A., Banerjee, H., Rojas, H., Martinez, S.R., Roy, S., Jia, Z., Lilly, M.B., De Leon, M., and Casiano, C.A. (2011). Differential expression of peroxiredoxins in prostate cancer: consistent upregulation of PRDX3 and PRDX4. The Prostate 71, 755-765.

Bateman, N.W., Sun, M., Hood, B.L., Flint, M.S., and Conrads, T.P. (2010). Defining central themes in breast cancer biology by differential proteomics: conserved regulation of cell spreading and focal adhesion kinase. Journal of proteome research 9, 5311-5324.

Begley, L.A., Kasina, S., Mehra, R., Adsule, S., Admon, A.J., Lonigro, R.J., Chinnaiyan, A.M., and Macoska, J.A. (2008). CXCL5 promotes prostate cancer progression. Neoplasia 10, 244-254.Berthier-Vergnes, O., Kharbili, M.E., de la Fouchardiere, A., Pointecouteau, T., Verrando, P., Wierinckx, A., Lachuer, J., Le Naour, F., and Lamartine, J. (2011). Gene expression profiles of human melanoma cells with different

invasive potential reveal TSPAN8 as a novel mediator of invasion. British journal of cancer 104, 155-165.Bertucci, F., Finetti, P., Cervera, N., Charafe-Jauffret, E., Mamessier, E., Adelaide, J., Debono, S., Houvenaeghel, G., Maraninchi, D., Viens, P., et al. (2006). Gene expression profiling shows medullary breast cancer is a subgroup

of basal breast cancers. Cancer Res 66, 4636-4644.Bertucci, F., Salas, S., Eysteries, S., Nasser, V., Finetti, P., Ginestier, C., Charafe-Jauffret, E., Loriod, B., Bachelart, L., Montfort, J., et al. (2004). Gene expression profiling of colon cancer by DNA microarrays and correlation with

histoclinical parameters. Oncogene 23, 1377-1391.Bhadri, V.A., Cowley, M.J., Kaplan, W., Trahair, T.N., and Lock, R.B. (2011). Evaluation of the NOD/SCID xenograft model for glucocorticoid-regulated gene expression in childhood B-cell precursor acute lymphoblastic leukemia.

BMC genomics 12, 565.Birkenkamp-Demtroder, K., Olesen, S.H., Sorensen, F.B., Laurberg, S., Laiho, P., Aaltonen, L.A., and Orntoft, T.F. (2005). Differential gene expression in colon cancer of the caecum versus the sigmoid and rectosigmoid. Gut 54,

374-384.Boss, C.N., Grunebach, F., Brauer, K., Hantschel, M., Mirakaj, V., Weinschenk, T., Stevanovic, S., Rammensee, H.G., and Brossart, P. (2007). Identification and characterization of T-cell epitopes deduced from RGS5, a novel

broadly expressed tumor antigen. Clin Cancer Res 13, 3347-3355.Brabletz, T., Jung, A., Dag, S., Hlubek, F., and Kirchner, T. (1999). beta-catenin regulates the expression of the matrix metalloproteinase-7 in human colorectal cancer. Am J Pathol 155, 1033-1038.Brockman, J.A., Gupta, R.A., and Dubois, R.N. (1998). Activation of PPARgamma leads to inhibition of anchorage-independent growth of human colorectal cancer cells. Gastroenterology 115, 1049-1055.Busch, C., Hanssen, T.A., Wagener, C., and B, O.B. (2002). Down-regulation of CEACAM1 in human prostate cancer: correlation with loss of cell polarity, increased proliferation rate, and Gleason grade 3 to 4 transition. Human

pathology 33, 290-298.Byrne, J.A., Maleki, S., Hardy, J.R., Gloss, B.S., Murali, R., Scurry, J.P., Fanayan, S., Emmanuel, C., Hacker, N.F., Sutherland, R.L., et al. (2010). MAL2 and tumor protein D52 (TPD52) are frequently overexpressed in ovarian

carcinoma, but differentially associated with histological subtype and patient outcome. BMC cancer 10, 497.Camps, J., Nguyen, Q.T., Padilla-Nash, H.M., Knutsen, T., McNeil, N.E., Wangsa, D., Hummon, A.B., Grade, M., Ried, T., and Difilippantonio, M.J. (2009). Integrative genomics reveals mechanisms of copy number alterations

responsible for transcriptional deregulation in colorectal cancer. Genes, chromosomes & cancer 48, 1002-1017.Catto, J.W., Abbod, M.F., Wild, P.J., Linkens, D.A., Pilarsky, C., Rehman, I., Rosario, D.J., Denzinger, S., Burger, M., Stoehr, R., et al. (2010). The application of artificial intelligence to microarray data: identification of a novel gene

signature to identify bladder cancer progression. European urology 57, 398-406.Cermak, V., Kosla, J., Plachy, J., Trejbalova, K., Hejnar, J., and Dvorak, M. (2010). The transcription factor EGR1 regulates metastatic potential of v-src transformed sarcoma cells. Cellular and molecular life sciences : CMLS 67,

3557-3568.Chan, H.S., Chang, S.J., Wang, T.Y., Ko, H.J., Lin, Y.C., Lin, K.T., Chang, K.M., and Chuang, Y.J. (2012). Serine protease PRSS23 is upregulated by estrogen receptor alpha and associated with proliferation of breast cancer cells.

PloS one 7, e30397.Chan, S.K., Griffith, O.L., Tai, I.T., and Jones, S.J. (2008). Meta-analysis of colorectal cancer gene expression profiling studies identifies consistently reported candidate biomarkers. Cancer epidemiology, biomarkers & prevention : a

publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 17, 543-552.Chapman, E.J., Williams, S.V., Platt, F.M., Hurst, C.D., Chambers, P., Roberts, P., and Knowles, M.A. (2009). Integrated genomic and transcriptional analysis of the in vitro evolution of telomerase-immortalized urothelial cells

(TERT-NHUC). Genes, chromosomes & cancer 48, 694-710.Chauhan, S.C., Vannatta, K., Ebeling, M.C., Vinayek, N., Watanabe, A., Pandey, K.K., Bell, M.C., Koch, M.D., Aburatani, H., Lio, Y., et al. (2009). Expression and functions of transmembrane mucin MUC13 in ovarian cancer. Cancer

Res 69, 765-774.Chen, C., Li, G., Liao, W., Wu, J., Liu, L., Ma, D., Zhou, J., Elbekai, R.H., Edin, M.L., Zeldin, D.C., et al. (2009). Selective inhibitors of CYP2J2 related to terfenadine exhibit strong activity against human cancers in vitro and in vivo.

The Journal of pharmacology and experimental therapeutics 329, 908-918.Chen, G., Rong, M., and Luo, D. (2010). TNFRSF6B neutralization antibody inhibits proliferation and induces apoptosis in hepatocellular carcinoma cell. Pathol Res Pract 206, 631-641.Chen, Y., Miller, C., Mosher, R., Zhao, X., Deeds, J., Morrissey, M., Bryant, B., Yang, D., Meyer, R., Cronin, F., et al. (2003). Identification of cervical cancer markers by cDNA and tissue microarrays. Cancer Res 63, 1927-1935.Chen, Y., Shi, L., Zhang, L., Li, R., Liang, J., Yu, W., Sun, L., Yang, X., Wang, Y., Zhang, Y., et al. (2008). The molecular mechanism governing the oncogenic potential of SOX2 in breast cancer. The Journal of biological chemistry

283, 17969-17978.Chiba, T., Kita, K., Zheng, Y.W., Yokosuka, O., Saisho, H., Iwama, A., Nakauchi, H., and Taniguchi, H. (2006). Side population purified from hepatocellular carcinoma cells harbors cancer stem cell-like properties. Hepatology 44,

240-251.Cho, H., Kang, E.S., Hong, S.W., Oh, Y.J., Choi, S.M., Kim, S.W., Kim, S.H., Kim, Y.T., Lee, K.S., Choi, Y.K., et al. (2008). Genomic and proteomic characterization of YDOV-157, a newly established human epithelial ovarian cancer

cell line. Molecular and cellular biochemistry 319, 189-201.Choi, M.C., Jong, H.S., Kim, T.Y., Song, S.H., Lee, D.S., Lee, J.W., Kim, T.Y., Kim, N.K., and Bang, Y.J. (2004). AKAP12/Gravin is inactivated by epigenetic mechanism in human gastric carcinoma and shows growth suppressor

activity. Oncogene 23, 7095-7103.Chua, M.S., Sun, H., Cheung, S.T., Mason, V., Higgins, J., Ross, D.T., Fan, S.T., and So, S. (2007). Overexpression of NDRG1 is an indicator of poor prognosis in hepatocellular carcinoma. Modern pathology : an official journal of

the United States and Canadian Academy of Pathology, Inc 20, 76-83.Cimino, D., Fuso, L., Sfiligoi, C., Biglia, N., Ponzone, R., Maggiorotto, F., Russo, G., Cicatiello, L., Weisz, A., Taverna, D., et al. (2008). Identification of new genes associated with breast cancer progression by gene expression

analysis of predefined sets of neoplastic tissues. International journal of cancer Journal international du cancer 123, 1327-1338.

Colas, E., Perez, C., Cabrera, S., Pedrola, N., Monge, M., Castellvi, J., Eyzaguirre, F., Gregorio, J., Ruiz, A., Llaurado, M., et al. (2011). Molecular markers of endometrial carcinoma detected in uterine aspirates. International journal of cancer Journal international du cancer 129, 2435-2444.

Comperat, E., Roupret, M., Conort, P., Chartier-Kastler, E., Bitker, M.O., Richard, F., Capron, F., Haertig, A., Cussenot, O., and Camparo, P. (2009). Aurora-A/STK-15 is differentially expressed in the micropapillary variant of bladder cancer. Urologia internationalis 82, 312-317.

Conacci-Sorrell, M.E., Ben-Yedidia, T., Shtutman, M., Feinstein, E., Einat, P., and Ben-Ze'ev, A. (2002). Nr-CAM is a target gene of the beta-catenin/LEF-1 pathway in melanoma and colon cancer and its expression enhances motility and confers tumorigenesis. Genes & development 16, 2058-2072.

Costello, J.F., Plass, C., Arap, W., Chapman, V.M., Held, W.A., Berger, M.S., Su Huang, H.J., and Cavenee, W.K. (1997). Cyclin-dependent kinase 6 (CDK6) amplification in human gliomas identified using two-dimensional separation of genomic DNA. Cancer Res 57, 1250-1254.

Cover, C.M., Hsieh, S.J., Cram, E.J., Hong, C., Riby, J.E., Bjeldanes, L.F., and Firestone, G.L. (1999). Indole-3-carbinol and tamoxifen cooperate to arrest the cell cycle of MCF-7 human breast cancer cells. Cancer Res 59, 1244-1251.

Critchley-Thorne, R.J., Simons, D.L., Yan, N., Miyahira, A.K., Dirbas, F.M., Johnson, D.L., Swetter, S.M., Carlson, R.W., Fisher, G.A., Koong, A., et al. (2009). Impaired interferon signaling is a common immune defect in human cancer. Proceedings of the National Academy of Sciences of the United States of America 106, 9010-9015.

Cui, H., Cruz-Correa, M., Giardiello, F.M., Hutcheon, D.F., Kafonek, D.R., Brandenburg, S., Wu, Y., He, X., Powe, N.R., and Feinberg, A.P. (2003). Loss of IGF2 imprinting: a potential marker of colorectal cancer risk. Science 299, 1753-1755.

Cui, J., Rohr, L.R., Swanson, G., Speights, V.O., Maxwell, T., and Brothman, A.R. (2001). Hypermethylation of the caveolin-1 gene promoter in prostate cancer. The Prostate 46, 249-256.Curtiss, N.P., Bonifas, J.M., Lauchle, J.O., Balkman, J.D., Kratz, C.P., Emerling, B.M., Green, E.D., Le Beau, M.M., and Shannon, K.M. (2005). Isolation and analysis of candidate myeloid tumor suppressor genes from a commonly

deleted segment of 7q22. Genomics 85, 600-607.Dairkee, S.H., Sayeed, A., Luciani, G., Champion, S., Meng, Z., Jakkula, L.R., Feiler, H.S., Gray, J.W., and Moore, D.H. (2009). Immutable functional attributes of histologic grade revealed by context-independent gene expression in

primary breast cancer cells. Cancer Res 69, 7826-7834.Darido, C., Georgy, S.R., Wilanowski, T., Dworkin, S., Auden, A., Zhao, Q., Rank, G., Srivastava, S., Finlay, M.J., Papenfuss, A.T., et al. (2011). Targeting of the tumor suppressor GRHL3 by a miR-21-dependent proto-oncogenic

network results in PTEN loss and tumorigenesis. Cancer cell 20, 635-648.Dasari, V.K., Goharderakhshan, R.Z., Perinchery, G., Li, L.C., Tanaka, Y., Alonzo, J., and Dahiya, R. (2001). Expression analysis of Y chromosome genes in human prostate cancer. The Journal of urology 165, 1335-1341.Dayyani, F., Wang, J., Yeh, J.R., Ahn, E.Y., Tobey, E., Zhang, D.E., Bernstein, I.D., Peterson, R.T., and Sweetser, D.A. (2008). Loss of TLE1 and TLE4 from the del(9q) commonly deleted region in AML cooperates with AML1-ETO

to affect myeloid cell proliferation and survival. Blood 111, 4338-4347.Deakin, M., Elder, J., Hendrickse, C., Peckham, D., Baldwin, D., Pantin, C., Wild, N., Leopard, P., Bell, D.A., Jones, P., et al. (1996). Glutathione S-transferase GSTT1 genotypes and susceptibility to cancer: studies of interactions

with GSTM1 in lung, oral, gastric and colorectal cancers. Carcinogenesis 17, 881-884.Demichelis, F., Fall, K., Perner, S., Andren, O., Schmidt, F., Setlur, S.R., Hoshida, Y., Mosquera, J.M., Pawitan, Y., Lee, C., et al. (2007). TMPRSS2:ERG gene fusion associated with lethal prostate cancer in a watchful waiting

cohort. Oncogene 26, 4596-4599.Demichelis, F., Setlur, S.R., Beroukhim, R., Perner, S., Korbel, J.O., Lafargue, C.J., Pflueger, D., Pina, C., Hofer, M.D., Sboner, A., et al. (2009). Distinct genomic aberrations associated with ERG rearranged prostate cancer. Genes,

chromosomes & cancer 48, 366-380.Dokun, O.Y., Florl, A.R., Seifert, H.H., Wolff, I., and Schulz, W.A. (2008). Relationship of SNCG, S100A4, S100A9 and LCN2 gene expression and DNA methylation in bladder cancer. International journal of cancer Journal

international du cancer 123, 2798-2807.Dozmorov, M.G., Hurst, R.E., Culkin, D.J., Kropp, B.P., Frank, M.B., Osban, J., Penning, T.M., and Lin, H.K. (2009). Unique patterns of molecular profiling between human prostate cancer LNCaP and PC-3 cells. The Prostate 69,

1077-1090.Duan, Z., Brakora, K.A., and Seiden, M.V. (2004). Inhibition of ABCB1 (MDR1) and ABCB4 (MDR3) expression by small interfering RNA and reversal of paclitaxel resistance in human ovarian cancer cells. Mol Cancer Ther 3, 833-

838.Duffy, M.J., O'Grady, P., Devaney, D., O'Siorain, L., Fennelly, J.J., and Lijnen, H.R. (1988). Tissue-type plasminogen activator, a new prognostic marker in breast cancer. Cancer Res 48, 1348-1349.Dutton-Regester, K., Irwin, D., Hunt, P., Aoude, L.G., Tembe, V., Pupo, G.M., Lanagan, C., Carter, C.D., O'Connor, L., O'Rourke, M., et al. (2012). A high-throughput panel for identifying clinically relevant mutation profiles in

melanoma. Mol Cancer Ther 11, 888-897.Ellsworth, R.E., Seebach, J., Field, L.A., Heckman, C., Kane, J., Hooke, J.A., Love, B., and Shriver, C.D. (2009). A gene expression signature that defines breast cancer metastases. Clinical & experimental metastasis 26, 205-213.Endo, T., Uzawa, K., Suzuki, H., Tanzawa, H., and Ichikawa, T. (2009). Characteristic gene expression profiles of benign prostatic hypertrophy and prostate cancer. International journal of oncology 35, 499-509.Ergun, A., Lawrence, C.A., Kohanski, M.A., Brennan, T.A., and Collins, J.J. (2007). A network biology approach to prostate cancer. Molecular systems biology 3, 82.Figueroa, J.D., Malats, N., Garcia-Closas, M., Real, F.X., Silverman, D., Kogevinas, M., Chanock, S., Welch, R., Dosemeci, M., Lan, Q., et al. (2008). Bladder cancer risk and genetic variation in AKR1C3 and other metabolizing

genes. Carcinogenesis 29, 1955-1962.Finlin, B.S., Gau, C.L., Murphy, G.A., Shao, H., Kimel, T., Seitz, R.S., Chiu, Y.F., Botstein, D., Brown, P.O., Der, C.J., et al. (2001). RERG is a novel ras-related, estrogen-regulated and growth-inhibitory gene in breast cancer. The

Journal of biological chemistry 276, 42259-42267.Fiucci, G., Ravid, D., Reich, R., and Liscovitch, M. (2002). Caveolin-1 inhibits anchorage-independent growth, anoikis and invasiveness in MCF-7 human breast cancer cells. Oncogene 21, 2365-2375.Folgueira, M.A., Carraro, D.M., Brentani, H., Patrao, D.F., Barbosa, E.M., Netto, M.M., Caldeira, J.R., Katayama, M.L., Soares, F.A., Oliveira, C.T., et al. (2005). Gene expression profile associated with response to doxorubicin-

based therapy in breast cancer. Clin Cancer Res 11, 7434-7443.Forloni, M., Albini, S., Limongi, M.Z., Cifaldi, L., Boldrini, R., Nicotra, M.R., Giannini, G., Natali, P.G., Giacomini, P., and Fruci, D. (2010). NF-kappaB, and not MYCN, regulates MHC class I and endoplasmic reticulum

aminopeptidases in human neuroblastoma cells. Cancer Res 70, 916-924.Fournier, M.V., Martin, K.J., Kenny, P.A., Xhaja, K., Bosch, I., Yaswen, P., and Bissell, M.J. (2006). Gene expression signature in organized and growth-arrested mammary acini predicts good outcome in breast cancer. Cancer Res

66, 7095-7102.Fu, Z., Kim, J., Vidrich, A., Sturgill, T.W., and Cohn, S.M. (2009). Intestinal cell kinase, a MAP kinase-related kinase, regulates proliferation and G1 cell cycle progression of intestinal epithelial cells. American journal of physiology

Gastrointestinal and liver physiology 297, G632-640.Fujishita, T., Aoki, M., and Taketo, M.M. (2011). JNK signaling promotes intestinal tumorigenesis through activation of mTOR complex 1 in Apc(Delta716) mice. Gastroenterology 140, 1556-1563 e1556.Furuta, J., Nobeyama, Y., Umebayashi, Y., Otsuka, F., Kikuchi, K., and Ushijima, T. (2006). Silencing of Peroxiredoxin 2 and aberrant methylation of 33 CpG islands in putative promoter regions in human malignant melanomas.

Cancer Res 66, 6080-6086.Furuya, M., Nishiyama, M., Kimura, S., Suyama, T., Naya, Y., Ito, H., Nikaido, T., and Ishikura, H. (2004). Expression of regulator of G protein signalling protein 5 (RGS5) in the tumour vasculature of human renal cell carcinoma. The

Journal of pathology 203, 551-558.Garraway, I.P., Seligson, D., Said, J., Horvath, S., and Reiter, R.E. (2004). Trefoil factor 3 is overexpressed in human prostate cancer. The Prostate 61, 209-214.Geng, S., Guo, Y., Wang, Q., Li, L., and Wang, J. (2012). Cancer stem-like cells enriched with CD29 and CD44 markers exhibit molecular characteristics with epithelial-mesenchymal transition in squamous cell carcinoma. Archives

of dermatological research.Gesierich, S., Berezovskiy, I., Ryschich, E., and Zoller, M. (2006). Systemic induction of the angiogenesis switch by the tetraspanin D6.1A/CO-029. Cancer Res 66, 7083-7094.Ghosh, S., Albitar, L., LeBaron, R., Welch, W.R., Samimi, G., Birrer, M.J., Berkowitz, R.S., and Mok, S.C. (2010). Up-regulation of stromal versican expression in advanced stage serous ovarian cancer. Gynecologic oncology 119,

114-120.

Giacomini, E., Remoli, M.E., Scandurra, M., Gafa, V., Pardini, M., Fattorini, L., and Coccia, E.M. (2011). Expression of proinflammatory and regulatory cytokines via NF-kappaB and MAPK-dependent and IFN regulatory factor-3-independent mechanisms in human primary monocytes infected by Mycobacterium tuberculosis. Clinical & developmental immunology 2011, 841346.

Goto, Y., Shinjo, K., Kondo, Y., Shen, L., Toyota, M., Suzuki, H., Gao, W., An, B., Fujii, M., Murakami, H., et al. (2009). Epigenetic profiles distinguish malignant pleural mesothelioma from lung adenocarcinoma. Cancer Res 69, 9073-9082.

Greenawalt, D.M., Duong, C., Smyth, G.K., Ciavarella, M.L., Thompson, N.J., Tiang, T., Murray, W.K., Thomas, R.J., and Phillips, W.A. (2007). Gene expression profiling of esophageal cancer: comparative analysis of Barrett's esophagus, adenocarcinoma, and squamous cell carcinoma. International journal of cancer Journal international du cancer 120, 1914-1921.

Guardiola-Serrano, F., Haendeler, J., Lukosz, M., Sturm, K., Melchner, H., and Altschmied, J. (2008). Gene trapping identifies a putative tumor suppressor and a new inducer of cell migration. Biochemical and biophysical research communications 376, 748-752.

Hahtola, S., Burghart, E., Puputti, M., Karenko, L., Abdel-Rahman, W.M., Vakeva, L., Jeskanen, L., Virolainen, S., Karvonen, J., Salmenkivi, K., et al. (2008). Cutaneous T-cell lymphoma-associated lung cancers show chromosomal aberrations differing from primary lung cancer. Genes, chromosomes & cancer 47, 107-117.

Halatsch, M.E., Low, S., Hielscher, T., Schmidt, U., Unterberg, A., and Vougioukas, V.I. (2008). Epidermal growth factor receptor pathway gene expressions and biological response of glioblastoma multiforme cell lines to erlotinib. Anticancer research 28, 3725-3728.

Han, J.Y., Lim, H.S., Yoo, Y.K., Shin, E.S., Park, Y.H., Lee, S.Y., Lee, J.E., Lee, D.H., Kim, H.T., and Lee, J.S. (2007). Associations of ABCB1, ABCC2, and ABCG2 polymorphisms with irinotecan-pharmacokinetics and clinical outcome in patients with advanced non-small cell lung cancer. Cancer 110, 138-147.

Hatano, H., Kudo, Y., Ogawa, I., Tsunematsu, T., Kikuchi, A., Abiko, Y., and Takata, T. (2008). IFN-induced transmembrane protein 1 promotes invasion at early stage of head and neck cancer progression. Clin Cancer Res 14, 6097-6105.

Heffron, C.C., Gallagher, M.F., Guenther, S., Sherlock, J., Henfrey, R., Martin, C., Sheils, O., and O'Leary, J.J. (2007). Global mRNA analysis to determine a transcriptome profile of cancer stemness in a mouse model. Anticancer research 27, 1319-1324.

Hein, S., Muller, V., Kohler, N., Wikman, H., Krenkel, S., Streichert, T., Schweizer, M., Riethdorf, S., Assmann, V., Ihnen, M., et al. (2011). Biologic role of activated leukocyte cell adhesion molecule overexpression in breast cancer cell lines and clinical tumor tissue. Breast cancer research and treatment 129, 347-360.

Heinzelmann-Schwarz, V.A., Gardiner-Garden, M., Henshall, S.M., Scurry, J.P., Scolyer, R.A., Smith, A.N., Bali, A., Vanden Bergh, P., Baron-Hay, S., Scott, C., et al. (2006). A distinct molecular profile associated with mucinous epithelial ovarian cancer. British journal of cancer 94, 904-913.

Hendriksen, P.J., Dits, N.F., Kokame, K., Veldhoven, A., van Weerden, W.M., Bangma, C.H., Trapman, J., and Jenster, G. (2006). Evolution of the androgen receptor pathway during progression of prostate cancer. Cancer Res 66, 5012-5020.

Hibi, K., Nakamura, H., Hirai, A., Fujikake, Y., Kasai, Y., Akiyama, S., Ito, K., and Takagi, H. (1996). Loss of H19 imprinting in esophageal cancer. Cancer Res 56, 480-482.Hinsch, N., Frank, M., Doring, C., Vorlander, C., and Hansmann, M.L. (2009). QPRT: a potential marker for follicular thyroid carcinoma including minimal invasive variant; a gene expression, RNA and immunohistochemical study.

BMC cancer 9, 93.Hippo, Y., Taniguchi, H., Tsutsumi, S., Machida, N., Chong, J.M., Fukayama, M., Kodama, T., and Aburatani, H. (2002). Global gene expression analysis of gastric cancer by oligonucleotide microarrays. Cancer Res 62, 233-240.Ho, J.R., Chapeaublanc, E., Kirkwood, L., Nicolle, R., Benhamou, S., Lebret, T., Allory, Y., Southgate, J., Radvanyi, F., and Goud, B. (2012). Deregulation of rab and rab effector genes in bladder cancer. PloS one 7, e39469.Hoek, K.S. (2007). DNA microarray analyses of melanoma gene expression: a decade in the mines. Pigment cell research / sponsored by the European Society for Pigment Cell Research and the International Pigment Cell Society

20, 466-484.Holla, V.R., Mann, J.R., Shi, Q., and DuBois, R.N. (2006). Prostaglandin E2 regulates the nuclear receptor NR4A2 in colorectal cancer. The Journal of biological chemistry 281, 2676-2682.Homminga, I., Pieters, R., Langerak, A.W., de Rooi, J.J., Stubbs, A., Verstegen, M., Vuerhard, M., Buijs-Gladdines, J., Kooi, C., Klous, P., et al. (2011). Integrated transcript and genome analyses reveal NKX2-1 and MEF2C as

potential oncogenes in T cell acute lymphoblastic leukemia. Cancer cell 19, 484-497.Hu, G., Chong, R.A., Yang, Q., Wei, Y., Blanco, M.A., Li, F., Reiss, M., Au, J.L., Haffty, B.G., and Kang, Y. (2009a). MTDH activation by 8q22 genomic gain promotes chemoresistance and metastasis of poor-prognosis breast

cancer. Cancer cell 15, 9-20.Hu, Y.C., Yang, Z.H., Zhong, K.J., Niu, L.J., Pan, X.J., Wu, D.C., Sun, X.J., Zhou, P.K., Zhu, M.X., and Huo, Y.Y. (2009b). Alteration of transcriptional profile in human bronchial epithelial cells induced by cigarette smoke condensate.

Toxicology letters 190, 23-31.Huang, H., Reed, C.P., Zhang, J.S., Shridhar, V., Wang, L., and Smith, D.I. (1999). Carboxypeptidase A3 (CPA3): a novel gene highly induced by histone deacetylase inhibitors during differentiation of prostate epithelial cancer cells.

Cancer Res 59, 2981-2988.Hwang, K.T., Han, W., Cho, J., Lee, J.W., Ko, E., Kim, E.K., Jung, S.Y., Jeong, E.M., Bae, J.Y., Kang, J.J., et al. (2008). Genomic copy number alterations as predictive markers of systemic recurrence in breast cancer. International

journal of cancer Journal international du cancer 123, 1807-1815.Ikeda, T., Jinno, H., and Shirane, M. (2007). Chemosensitivity-related genes of breast cancer detected by DNA microarray. Anticancer research 27, 2649-2655.Iqbal, J., Gupta, S., Chen, Q.H., Brody, J.P., and Koduru, P. (2007). Diffuse large B-cell lymphoma with a novel translocation involving BCL6. Cancer genetics and cytogenetics 178, 73-76.Ivanov, S.V., Ivanova, A.V., Salnikow, K., Timofeeva, O., Subramaniam, M., and Lerman, M.I. (2008). Two novel VHL targets, TGFBI (BIGH3) and its transactivator KLF10, are up-regulated in renal clear cell carcinoma and other

tumors. Biochemical and biophysical research communications 370, 536-540.Jaeger, E., Webb, E., Howarth, K., Carvajal-Carmona, L., Rowan, A., Broderick, P., Walther, A., Spain, S., Pittman, A., Kemp, Z., et al. (2008). Common genetic variants at the CRAC1 (HMPS) locus on chromosome 15q13.3

influence colorectal cancer risk. Nature genetics 40, 26-28.Jalali, G.R., An, Q., Konn, Z.J., Worley, H., Wright, S.L., Harrison, C.J., Strefford, J.C., and Martineau, M. (2008). Disruption of ETV6 in intron 2 results in upregulatory and insertional events in childhood acute lymphoblastic

leukaemia. Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, UK 22, 114-123.Jarzab, B., Wiench, M., Fujarewicz, K., Simek, K., Jarzab, M., Oczko-Wojciechowska, M., Wloch, J., Czarniecka, A., Chmielik, E., Lange, D., et al. (2005). Gene expression profile of papillary thyroid cancer: sources of variability and

diagnostic implications. Cancer Res 65, 1587-1597.Jiang, J.G., Ning, Y.G., Chen, C., Ma, D., Liu, Z.J., Yang, S., Zhou, J., Xiao, X., Zhang, X.A., Edin, M.L., et al. (2007). Cytochrome p450 epoxygenase promotes human cancer metastasis. Cancer Res 67, 6665-6674.Joesting, M.S., Perrin, S., Elenbaas, B., Fawell, S.E., Rubin, J.S., Franco, O.E., Hayward, S.W., Cunha, G.R., and Marker, P.C. (2005). Identification of SFRP1 as a candidate mediator of stromal-to-epithelial signaling in prostate

cancer. Cancer Res 65, 10423-10430.Jogi, A., Brennan, D.J., Ryden, L., Magnusson, K., Ferno, M., Stal, O., Borgquist, S., Uhlen, M., Landberg, G., Pahlman, S., et al. (2009). Nuclear expression of the RNA-binding protein RBM3 is associated with an improved clinical

outcome in breast cancer. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 22, 1564-1574.Jonsson, G., Busch, C., Knappskog, S., Geisler, J., Miletic, H., Ringner, M., Lillehaug, J.R., Borg, A., and Lonning, P.E. (2010). Gene expression profiling-based identification of molecular subtypes in stage IV melanomas with

different clinical outcome. Clin Cancer Res 16, 3356-3367.Jonsson, G., Staaf, J., Olsson, E., Heidenblad, M., Vallon-Christersson, J., Osoegawa, K., de Jong, P., Oredsson, S., Ringner, M., Hoglund, M., et al. (2007). High-resolution genomic profiles of breast cancer cell lines assessed by

tiling BAC array comparative genomic hybridization. Genes, chromosomes & cancer 46, 543-558.Ju, H., Lim, B., Kim, M., Noh, S.M., Han, D.S., Yu, H.J., Choi, B.Y., Kim, Y.S., Kim, W.H., Ihm, C., et al. (2010). Genetic variants A1826H and D2937Y in GAG-beta domain of versican influence susceptibility to intestinal-type gastric

cancer. Journal of cancer research and clinical oncology 136, 195-201.Jubb, A.M., Chalasani, S., Frantz, G.D., Smits, R., Grabsch, H.I., Kavi, V., Maughan, N.J., Hillan, K.J., Quirke, P., and Koeppen, H. (2006). Achaete-scute like 2 (ascl2) is a target of Wnt signalling and is upregulated in intestinal

neoplasia. Oncogene 25, 3445-3457.

Jutras, S., Bachvarova, M., Keita, M., Bascands, J.L., Mes-Masson, A.M., Stewart, J.M., Gera, L., and Bachvarov, D. (2010). Strong cytotoxic effect of the bradykinin antagonist BKM-570 in ovarian cancer cells--analysis of the molecular mechanisms of its antiproliferative action. The FEBS journal 277, 5146-5160.

Kagan, B.L., Henke, R.T., Cabal-Manzano, R., Stoica, G.E., Nguyen, Q., Wellstein, A., and Riegel, A.T. (2003). Complex regulation of the fibroblast growth factor-binding protein in MDA- MB-468 breast cancer cells by CCAAT/enhancer-binding protein beta. Cancer Res 63, 1696-1705.

Kamphausen, E., Kellert, C., Abbas, T., Akkad, N., Tenzer, S., Pawelec, G., Schild, H., van Endert, P., and Seliger, B. (2010). Distinct molecular mechanisms leading to deficient expression of ER-resident aminopeptidases in melanoma. Cancer immunology, immunotherapy : CII 59, 1273-1284.

Kandimalla, R., van Tilborg, A.A., Kompier, L.C., Stumpel, D.J., Stam, R.W., Bangma, C.H., and Zwarthoff, E.C. (2012). Genome-wide analysis of CpG island methylation in bladder cancer identified TBX2, TBX3, GATA2, and ZIC4 as pTa-specific prognostic markers. European urology 61, 1245-1256.

Kaneda, H., Arao, T., Tanaka, K., Tamura, D., Aomatsu, K., Kudo, K., Sakai, K., De Velasco, M.A., Matsumoto, K., Fujita, Y., et al. (2010). FOXQ1 is overexpressed in colorectal cancer and enhances tumorigenicity and tumor growth. Cancer Res 70, 2053-2063.

Ke, N., Claassen, G., Yu, D.H., Albers, A., Fan, W., Tan, P., Grifman, M., Hu, X., Defife, K., Nguy, V., et al. (2004). Nuclear hormone receptor NR4A2 is involved in cell transformation and apoptosis. Cancer Res 64, 8208-8212.Kempkes, M., Golka, K., Reich, S., Reckwitz, T., and Bolt, H.M. (1996). Glutathione S-transferase GSTM1 and GSTT1 null genotypes as potential risk factors for urothelial cancer of the bladder. Archives of toxicology 71, 123-126.Khorana, A.A., Ryan, C.K., Cox, C., Eberly, S., and Sahasrabudhe, D.M. (2003). Vascular endothelial growth factor, CD68, and epidermal growth factor receptor expression and survival in patients with Stage II and Stage III colon

carcinoma: a role for the host response in prognosis. Cancer 97, 960-968.Kim, H., Kang, H.J., You, K.T., Kim, S.H., Lee, K.Y., Kim, T.I., Kim, C., Song, S.Y., Kim, H.J., Lee, C., et al. (2006). Suppression of human selenium-binding protein 1 is a late event in colorectal carcinogenesis and is associated with

poor survival. Proteomics 6, 3466-3476.Kim, H., Scorilas, A., Katsaros, D., Yousef, G.M., Massobrio, M., Fracchioli, S., Piccinno, R., Gordini, G., and Diamandis, E.P. (2001). Human kallikrein gene 5 (KLK5) expression is an indicator of poor prognosis in ovarian cancer.

British journal of cancer 84, 643-650.Kirschmann, D.A., Seftor, E.A., Nieva, D.R., Mariano, E.A., and Hendrix, M.J. (1999). Differentially expressed genes associated with the metastatic phenotype in breast cancer. Breast cancer research and treatment 55, 127-136.Kita, Y., Mimori, K., Tanaka, F., Matsumoto, T., Haraguchi, N., Ishikawa, K., Matsuzaki, S., Fukuyoshi, Y., Inoue, H., Natsugoe, S., et al. (2009). Clinical significance of LAMB3 and COL7A1 mRNA in esophageal squamous cell

carcinoma. European journal of surgical oncology : the journal of the European Society of Surgical Oncology and the British Association of Surgical Oncology 35, 52-58.Kloth, J.N., Gorter, A., Fleuren, G.J., Oosting, J., Uljee, S., ter Haar, N., Dreef, E.J., Kenter, G.G., and Jordanova, E.S. (2008). Elevated expression of SerpinA1 and SerpinA3 in HLA-positive cervical carcinoma. The Journal of

pathology 215, 222-230.Ko, J.M., Chan, P.L., Yau, W.L., Chan, H.K., Chan, K.C., Yu, Z.Y., Kwong, F.M., Miller, L.D., Liu, E.T., Yang, L.C., et al. (2008). Monochromosome transfer and microarray analysis identify a critical tumor-suppressive region mapping

to chromosome 13q14 and THSD1 in esophageal carcinoma. Molecular cancer research : MCR 6, 592-603.Kok, M., Koornstra, R.H., Margarido, T.C., Fles, R., Armstrong, N.J., Linn, S.C., Van't Veer, L.J., and Weigelt, B. (2009). Mammosphere-derived gene set predicts outcome in patients with ER-positive breast cancer. The Journal of

pathology 218, 316-326.Krepischi, A.C., Achatz, M.I., Santos, E.M., Costa, S.S., Lisboa, B.C., Brentani, H., Santos, T.M., Goncalves, A., Nobrega, A.F., Pearson, P.L., et al. (2012). Germline DNA copy number variation in familial and early-onset breast

cancer. Breast cancer research : BCR 14, R24.Krijgsman, O., Roepman, P., Zwart, W., Carroll, J.S., Tian, S., de Snoo, F.A., Bender, R.A., Bernards, R., and Glas, A.M. (2012). A diagnostic gene profile for molecular subtyping of breast cancer associated with treatment

response. Breast cancer research and treatment 133, 37-47.Kristiansen, G., Denkert, C., Schluns, K., Dahl, E., Pilarsky, C., and Hauptmann, S. (2002). CD24 is expressed in ovarian cancer and is a new independent prognostic marker of patient survival. Am J Pathol 161, 1215-1221.Kuijjer, M.L., Rydbeck, H., Kresse, S.H., Buddingh, E.P., Lid, A.B., Roelofs, H., Burger, H., Myklebost, O., Hogendoorn, P.C., Meza-Zepeda, L.A., et al. (2012). Identification of osteosarcoma driver genes by integrative analysis of

copy number and gene expression data. Genes, chromosomes & cancer 51, 696-706.Kumagai, T., Akagi, T., Desmond, J.C., Kawamata, N., Gery, S., Imai, Y., Song, J.H., Gui, D., Said, J., and Koeffler, H.P. (2009). Epigenetic regulation and molecular characterization of C/EBPalpha in pancreatic cancer cells.

International journal of cancer Journal international du cancer 124, 827-833.Kuzuhara, T., Suganuma, M., Kurusu, M., and Fujiki, H. (2007). Helicobacter pylori-secreting protein Tipalpha is a potent inducer of chemokine gene expressions in stomach cancer cells. Journal of cancer research and clinical

oncology 133, 287-296.Kvinlaug, B.T., Chan, W.I., Bullinger, L., Ramaswami, M., Sears, C., Foster, D., Lazic, S.E., Okabe, R., Benner, A., Lee, B.H., et al. (2011). Common and overlapping oncogenic pathways contribute to the evolution of acute myeloid

leukemias. Cancer Res 71, 4117-4129.Lai, J., Kedda, M.A., Hinze, K., Smith, R.L., Yaxley, J., Spurdle, A.B., Morris, C.P., Harris, J., and Clements, J.A. (2007). PSA/KLK3 AREI promoter polymorphism alters androgen receptor binding and is associated with prostate

cancer susceptibility. Carcinogenesis 28, 1032-1039.Lee, H.J., Nam, K.T., Park, H.S., Kim, M.A., Lafleur, B.J., Aburatani, H., Yang, H.K., Kim, W.H., and Goldenring, J.R. (2010). Gene expression profiling of metaplastic lineages identifies CDH17 as a prognostic marker in early stage

gastric cancer. Gastroenterology 139, 213-225 e213.Leong, P.L., Xi, S., Drenning, S.D., Dyer, K.F., Wentzel, A.L., Lerner, E.C., Smithgall, T.E., and Grandis, J.R. (2002). Differential function of STAT5 isoforms in head and neck cancer growth control. Oncogene 21, 2846-2853.Leung, W.K., Yu, J., Chan, F.K., To, K.F., Chan, M.W., Ebert, M.P., Ng, E.K., Chung, S.C., Malfertheiner, P., and Sung, J.J. (2002). Expression of trefoil peptides (TFF1, TFF2, and TFF3) in gastric carcinomas, intestinal metaplasia,

and non-neoplastic gastric tissues. The Journal of pathology 197, 582-588.Li, Y., Elashoff, D., Oh, M., Sinha, U., St John, M.A., Zhou, X., Abemayor, E., and Wong, D.T. (2006). Serum circulating human mRNA profiling and its utility for oral cancer detection. Journal of clinical oncology : official journal of the

American Society of Clinical Oncology 24, 1754-1760.Liedert, B., Materna, V., Schadendorf, D., Thomale, J., and Lage, H. (2003). Overexpression of cMOAT (MRP2/ABCC2) is associated with decreased formation of platinum-DNA adducts and decreased G2-arrest in melanoma cells

resistant to cisplatin. The Journal of investigative dermatology 121, 172-176.Lin, H.P., Jiang, S.S., and Chuu, C.P. (2012). Caffeic acid phenethyl ester causes p21 induction, Akt signaling reduction, and growth inhibition in PC-3 human prostate cancer cells. PloS one 7, e31286.Liu, A.Y., Brubaker, K.D., Goo, Y.A., Quinn, J.E., Kral, S., Sorensen, C.M., Vessella, R.L., Belldegrun, A.S., and Hood, L.E. (2004). Lineage relationship between LNCaP and LNCaP-derived prostate cancer cell lines. The Prostate

60, 98-108.Liu, L., Zhang, Q., Zhang, Y., Wang, S., and Ding, Y. (2006). Lentivirus-mediated silencing of Tiam1 gene influences multiple functions of a human colorectal cancer cell line. Neoplasia 8, 917-924.Liu, W., Dong, X., Mai, M., Seelan, R.S., Taniguchi, K., Krishnadath, K.K., Halling, K.C., Cunningham, J.M., Boardman, L.A., Qian, C., et al. (2000). Mutations in AXIN2 cause colorectal cancer with defective mismatch repair by

activating beta-catenin/TCF signalling. Nature genetics 26, 146-147.Lo, K.C., Rossi, M.R., LaDuca, J., Hicks, D.G., Turpaz, Y., Hawthorn, L., and Cowell, J.K. (2007). Candidate glioblastoma development gene identification using concordance between copy number abnormalities and gene

expression level changes. Genes, chromosomes & cancer 46, 875-894.Lopes, N., Sousa, B., Martins, D., Gomes, M., Vieira, D., Veronese, L.A., Milanezi, F., Paredes, J., Costa, J.L., and Schmitt, F. (2010). Alterations in Vitamin D signalling and metabolic pathways in breast cancer progression: a study

of VDR, CYP27B1 and CYP24A1 expression in benign and malignant breast lesions. BMC cancer 10, 483.Lu, Y., Liu, P., Wen, W., Grubbs, C.J., Townsend, R.R., Malone, J.P., Lubet, R.A., and You, M. (2010). Cross-species comparison of orthologous gene expression in human bladder cancer and carcinogen-induced rodent models.

American journal of translational research 3, 8-27.Lum, A.M., Wang, B.B., Beck-Engeser, G.B., Li, L., Channa, N., and Wabl, M. (2010). Orphan receptor GPR110, an oncogene overexpressed in lung and prostate cancer. BMC cancer 10, 40.Luque-Garcia, J.L., Martinez-Torrecuadrada, J.L., Epifano, C., Canamero, M., Babel, I., and Casal, J.I. (2010). Differential protein expression on the cell surface of colorectal cancer cells associated to tumor metastasis. Proteomics

10, 940-952.

Ma, C., Rong, Y., Radiloff, D.R., Datto, M.B., Centeno, B., Bao, S., Cheng, A.W., Lin, F., Jiang, S., Yeatman, T.J., et al. (2008). Extracellular matrix protein betaig-h3/TGFBI promotes metastasis of colon cancer by enhancing cell extravasation. Genes & development 22, 308-321.

Ma, X.J., Dahiya, S., Richardson, E., Erlander, M., and Sgroi, D.C. (2009). Gene expression profiling of the tumor microenvironment during breast cancer progression. Breast cancer research : BCR 11, R7.Maher, C.A., Kumar-Sinha, C., Cao, X., Kalyana-Sundaram, S., Han, B., Jing, X., Sam, L., Barrette, T., Palanisamy, N., and Chinnaiyan, A.M. (2009). Transcriptome sequencing to detect gene fusions in cancer. Nature 458, 97-101.Majid, S.M., Liss, A.S., You, M., and Bose, H.R. (2006). The suppression of SH3BGRL is important for v-Rel-mediated transformation. Oncogene 25, 756-768.Majumdar, S., and Diamandis, E.P. (1999). The promoter and the enhancer region of the KLK 3 (prostate specific antigen) gene is frequently mutated in breast tumours and in breast carcinoma cell lines. British journal of cancer 79,

1594-1602.Makino, H., Tajiri, T., Miyashita, M., Sasajima, K., Anbazhagan, R., Johnston, J., and Gabrielson, E. (2005). Differential expression of TCEAL1 in esophageal cancers by custom cDNA microarray analysis. Diseases of the

esophagus : official journal of the International Society for Diseases of the Esophagus / ISDE 18, 37-40.Mandal, S., Abebe, F., and Chaudhary, J. (2011). 2'-5' oligoadenylate synthetase 1 polymorphism is associated with prostate cancer. Cancer 117, 5509-5518.Marcato, P., Dean, C.A., Pan, D., Araslanova, R., Gillis, M., Joshi, M., Helyer, L., Pan, L., Leidal, A., Gujar, S., et al. (2011). Aldehyde dehydrogenase activity of breast cancer stem cells is primarily due to isoform ALDH1A3 and its

expression is predictive of metastasis. Stem cells 29, 32-45.Marcucci, G., Baldus, C.D., Ruppert, A.S., Radmacher, M.D., Mrozek, K., Whitman, S.P., Kolitz, J.E., Edwards, C.G., Vardiman, J.W., Powell, B.L., et al. (2005). Overexpression of the ETS-related gene, ERG, predicts a worse

outcome in acute myeloid leukemia with normal karyotype: a Cancer and Leukemia Group B study. Journal of clinical oncology : official journal of the American Society of Clinical Oncology 23, 9234-9242.Maruyama, Y., Ono, M., Kawahara, A., Yokoyama, T., Basaki, Y., Kage, M., Aoyagi, S., Kinoshita, H., and Kuwano, M. (2006). Tumor growth suppression in pancreatic cancer by a putative metastasis suppressor gene

Cap43/NDRG1/Drg-1 through modulation of angiogenesis. Cancer Res 66, 6233-6242.Matoba, K., Iizuka, N., Gondo, T., Ishihara, T., Yamada-Okabe, H., Tamesa, T., Takemoto, N., Hashimoto, K., Sakamoto, K., Miyamoto, T., et al. (2005). Tumor HLA-DR expression linked to early intrahepatic recurrence of

hepatocellular carcinoma. International journal of cancer Journal international du cancer 115, 231-240.Matsuda, R., Takahashi, T., Nakamura, S., Sekido, Y., Nishida, K., Seto, M., Seito, T., Sugiura, T., Ariyoshi, Y., Takahashi, T., et al. (1993). Expression of the c-kit protein in human solid tumors and in corresponding fetal and adult

normal tissues. Am J Pathol 142, 339-346.Matsuura, K., Nakada, C., Mashio, M., Narimatsu, T., Yoshimoto, T., Tanigawa, M., Tsukamoto, Y., Hijiya, N., Takeuchi, I., Nomura, T., et al. (2011). Downregulation of SAV1 plays a role in pathogenesis of high-grade clear cell renal

cell carcinoma. BMC cancer 11, 523.Matsuzaki, S., Tanaka, F., Mimori, K., Tahara, K., Inoue, H., and Mori, M. (2009). Clinicopathologic significance of KIAA1199 overexpression in human gastric cancer. Annals of surgical oncology 16, 2042-2051.McFadyen, M.C., Cruickshank, M.E., Miller, I.D., McLeod, H.L., Melvin, W.T., Haites, N.E., Parkin, D., and Murray, G.I. (2001). Cytochrome P450 CYP1B1 over-expression in primary and metastatic ovarian cancer. British journal of

cancer 85, 242-246.McKay, J.A., Melvin, W.T., Ah-See, A.K., Ewen, S.W., Greenlee, W.F., Marcus, C.B., Burke, M.D., and Murray, G.I. (1995). Expression of cytochrome P450 CYP1B1 in breast cancer. FEBS letters 374, 270-272.Menashe, I., Figueroa, J.D., Garcia-Closas, M., Chatterjee, N., Malats, N., Picornell, A., Maeder, D., Yang, Q., Prokunina-Olsson, L., Wang, Z., et al. (2012). Large-scale pathway-based analysis of bladder cancer genome-wide

association data from five studies of European background. PloS one 7, e29396.Mengual, L., Burset, M., Ars, E., Lozano, J.J., Villavicencio, H., Ribal, M.J., and Alcaraz, A. (2009). DNA microarray expression profiling of bladder cancer allows identification of noninvasive diagnostic markers. The Journal of

urology 182, 741-748.Mengual, L., Burset, M., Ars, E., Ribal, M.J., Lozano, J.J., Minana, B., Sumoy, L., and Alcaraz, A. (2006). Partially degraded RNA from bladder washing is a suitable sample for studying gene expression profiles in bladder cancer.

European urology 50, 1347-1355; discussion 1355-1346.Mercier, I., Casimiro, M.C., Wang, C., Rosenberg, A.L., Quong, J., Minkeu, A., Allen, K.G., Danilo, C., Sotgia, F., Bonuccelli, G., et al. (2008). Human breast cancer-associated fibroblasts (CAFs) show caveolin-1 downregulation and

RB tumor suppressor functional inactivation: Implications for the response to hormonal therapy. Cancer biology & therapy 7, 1212-1225.Meunier, D., Patra, K., Smits, R., Hagebarth, A., Luttges, A., Jaussi, R., Wieduwilt, M.J., Quintanilla-Fend, L., Himmelbauer, H., Fodde, R., et al. (2011). Expression analysis of proline rich 15 (Prr15) in mouse and human

gastrointestinal tumors. Molecular carcinogenesis 50, 8-15.Missiaglia, E., Blaveri, E., Terris, B., Wang, Y.H., Costello, E., Neoptolemos, J.P., Crnogorac-Jurcevic, T., and Lemoine, N.R. (2004). Analysis of gene expression in cancer cell lines identifies candidate markers for pancreatic

tumorigenesis and metastasis. International journal of cancer Journal international du cancer 112, 100-112.Mueller, E., Sarraf, P., Tontonoz, P., Evans, R.M., Martin, K.J., Zhang, M., Fletcher, C., Singer, S., and Spiegelman, B.M. (1998). Terminal differentiation of human breast cancer through PPAR gamma. Molecular cell 1, 465-470.Muhlmann, G., Spizzo, G., Gostner, J., Zitt, M., Maier, H., Moser, P., Gastl, G., Zitt, M., Muller, H.M., Margreiter, R., et al. (2009). TROP2 expression as prognostic marker for gastric carcinoma. J Clin Pathol 62, 152-158.Murphy, S.K., Huang, Z., Wen, Y., Spillman, M.A., Whitaker, R.S., Simel, L.R., Nichols, T.D., Marks, J.R., and Berchuck, A. (2006). Frequent IGF2/H19 domain epigenetic alterations and elevated IGF2 expression in epithelial

ovarian cancer. Molecular cancer research : MCR 4, 283-292.Nadiminty, N., Dutt, S., Tepper, C., and Gao, A.C. (2010). Microarray analysis reveals potential target genes of NF-kappaB2/p52 in LNCaP prostate cancer cells. The Prostate 70, 276-287.Nagayama, K., Kohno, T., Sato, M., Arai, Y., Minna, J.D., and Yokota, J. (2007). Homozygous deletion scanning of the lung cancer genome at a 100-kb resolution. Genes, chromosomes & cancer 46, 1000-1010.Nallar, S.C., Lin, L., Srivastava, V., Gade, P., Hofmann, E.R., Ahmed, H., Reddy, S.P., and Kalvakolanu, D.V. (2011). GRIM-1, a novel growth suppressor, inhibits rRNA maturation by suppressing small nucleolar RNAs. PloS one 6,

e24082.Narayan, G., Bourdon, V., Chaganti, S., Arias-Pulido, H., Nandula, S.V., Rao, P.H., Gissmann, L., Durst, M., Schneider, A., Pothuri, B., et al. (2007). Gene dosage alterations revealed by cDNA microarray analysis in cervical cancer:

identification of candidate amplified and overexpressed genes. Genes, chromosomes & cancer 46, 373-384.Nevalainen, M.T., Xie, J., Torhorst, J., Bubendorf, L., Haas, P., Kononen, J., Sauter, G., and Rui, H. (2004). Signal transducer and activator of transcription-5 activation and breast cancer prognosis. Journal of clinical oncology :

official journal of the American Society of Clinical Oncology 22, 2053-2060.Nguyen, D.X., Chiang, A.C., Zhang, X.H., Kim, J.Y., Kris, M.G., Ladanyi, M., Gerald, W.L., and Massague, J. (2009). WNT/TCF signaling through LEF1 and HOXB9 mediates lung adenocarcinoma metastasis. Cell 138, 51-62.Nussbaum, J.M., Major, M., and Gunnery, S. (2003). Transcriptional upregulation of interferon-induced protein kinase, PKR, in breast cancer. Cancer letters 196, 207-216.Okudela, K., Woo, T., and Kitamura, H. (2010). KRAS gene mutations in lung cancer: particulars established and issues unresolved. Pathology international 60, 651-660.Osada, H., Tomida, S., Yatabe, Y., Tatematsu, Y., Takeuchi, T., Murakami, H., Kondo, Y., Sekido, Y., and Takahashi, T. (2008). Roles of achaete-scute homologue 1 in DKK1 and E-cadherin repression and neuroendocrine

differentiation in lung cancer. Cancer Res 68, 1647-1655.Othman, E.Q., Kaur, G., Mutee, A.F., Muhammad, T.S., and Tan, M.L. (2009). Immunohistochemical expression of MAP1LC3A and MAP1LC3B protein in breast carcinoma tissues. Journal of clinical laboratory analysis 23, 249-258.Paciucci, R., Tora, M., Diaz, V.M., and Real, F.X. (1998). The plasminogen activator system in pancreas cancer: role of t-PA in the invasive potential in vitro. Oncogene 16, 625-633.Park, J.Y., Park, K.H., Bang, S., Kim, M.H., Lee, J.E., Gang, J., Koh, S.S., and Song, S.Y. (2007). CXCL5 overexpression is associated with late stage gastric cancer. Journal of cancer research and clinical oncology 133, 835-840.Patel, M., Lu, L., Zander, D.S., Sreerama, L., Coco, D., and Moreb, J.S. (2008). ALDH1A1 and ALDH3A1 expression in lung cancers: correlation with histologic type and potential precursors. Lung cancer 59, 340-349.Pio, R., Blanco, D., Pajares, M.J., Aibar, E., Durany, O., Ezponda, T., Agorreta, J., Gomez-Roman, J., Anton, M.A., Rubio, A., et al. (2010). Development of a novel splice array platform and its application in the identification of

alternative splice variants in lung cancer. BMC genomics 11, 352.Pratap, J., Javed, A., Languino, L.R., van Wijnen, A.J., Stein, J.L., Stein, G.S., and Lian, J.B. (2005). The Runx2 osteogenic transcription factor regulates matrix metalloproteinase 9 in bone metastatic cancer cells and controls cell

invasion. Molecular and cellular biology 25, 8581-8591.Pulipati, N.R., Jin, Q., Liu, X., Sun, B., Pandey, M.K., Huber, J.P., Ding, W., and Mulder, K.M. (2011). Overexpression of the dynein light chain km23-1 in human ovarian carcinoma cells inhibits tumor formation in vivo and causes

mitotic delay at prometaphase/metaphase. International journal of cancer Journal international du cancer 129, 553-564.

Ra, S.H., Li, X., and Binder, S. (2011). Molecular discrimination of cutaneous squamous cell carcinoma from actinic keratosis and normal skin. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 24, 963-973.

Ramachandran, V., Arumugam, T., Hwang, R.F., Greenson, J.K., Simeone, D.M., and Logsdon, C.D. (2007). Adrenomedullin is expressed in pancreatic cancer and stimulates cell proliferation and invasion in an autocrine manner via the adrenomedullin receptor, ADMR. Cancer Res 67, 2666-2675.

Ramachandran, V., Arumugam, T., Wang, H., and Logsdon, C.D. (2008). Anterior gradient 2 is expressed and secreted during the development of pancreatic cancer and promotes cancer cell survival. Cancer Res 68, 7811-7818.Reid, J.F., Gariboldi, M., Sokolova, V., Capobianco, P., Lampis, A., Perrone, F., Signoroni, S., Costa, A., Leo, E., Pilotti, S., et al. (2009). Integrative approach for prioritizing cancer genes in sporadic colon cancer. Genes,

chromosomes & cancer 48, 953-962.Rho, J.H., Kang, D.Y., Park, K.J., Choi, H.J., Lee, H.S., Yee, S.B., and Yoo, Y.H. (2005). Doxorubicin induces apoptosis with profile of large-scale DNA fragmentation and without DNA ladder in anaplastic thyroid carcinoma cells via

histone hyperacetylation. International journal of oncology 27, 465-471.Riddick, A.C., Shukla, C.J., Pennington, C.J., Bass, R., Nuttall, R.K., Hogan, A., Sethia, K.K., Ellis, V., Collins, A.T., Maitland, N.J., et al. (2005). Identification of degradome components associated with prostate cancer progression

by expression analysis of human prostatic tissues. British journal of cancer 92, 2171-2180.Robbins, C.M., Tembe, W.A., Baker, A., Sinari, S., Moses, T.Y., Beckstrom-Sternberg, S., Beckstrom-Sternberg, J., Barrett, M., Long, J., Chinnaiyan, A., et al. (2011). Copy number and targeted mutational analysis reveals novel

somatic events in metastatic prostate tumors. Genome research 21, 47-55.Roberts, D., Schick, J., Conway, S., Biade, S., Laub, P.B., Stevenson, J.P., Hamilton, T.C., O'Dwyer, P.J., and Johnson, S.W. (2005). Identification of genes associated with platinum drug sensitivity and resistance in human ovarian

cancer cells. British journal of cancer 92, 1149-1158.Rody, A., Karn, T., Holtrich, U., and Kaufmann, M. (2008). "Stem cell like" breast cancers-a model for the identification of new prognostic/predictive markers in endocrine responsive breast cancer exemplified by Plexin B1. European

journal of obstetrics, gynecology, and reproductive biology 139, 11-15.Rohan, S., Tu, J.J., Kao, J., Mukherjee, P., Campagne, F., Zhou, X.K., Hyjek, E., Alonso, M.A., and Chen, Y.T. (2006). Gene expression profiling separates chromophobe renal cell carcinoma from oncocytoma and identifies

vesicular transport and cell junction proteins as differentially expressed genes. Clin Cancer Res 12, 6937-6945.Romanuik, T.L., Ueda, T., Le, N., Haile, S., Yong, T.M., Thomson, T., Vessella, R.L., and Sadar, M.D. (2009). Novel biomarkers for prostate cancer including noncoding transcripts. Am J Pathol 175, 2264-2276.Ross, A.E., Marchionni, L., Vuica-Ross, M., Cheadle, C., Fan, J., Berman, D.M., and Schaeffer, E.M. (2011). Gene expression pathways of high grade localized prostate cancer. The Prostate.Ross, P.L., Cheng, I., Liu, X., Cicek, M.S., Carroll, P.R., Casey, G., and Witte, J.S. (2009). Carboxypeptidase 4 gene variants and early-onset intermediate-to-high risk prostate cancer. BMC cancer 9, 69.Rozanov, D.V., Savinov, A.Y., Williams, R., Liu, K., Golubkov, V.S., Krajewski, S., and Strongin, A.Y. (2008). Molecular signature of MT1-MMP: transactivation of the downstream universal gene network in cancer. Cancer Res 68,

4086-4096.Saaf, A.M., Halbleib, J.M., Chen, X., Yuen, S.T., Leung, S.Y., Nelson, W.J., and Brown, P.O. (2007). Parallels between global transcriptional programs of polarizing Caco-2 intestinal epithelial cells in vitro and gene expression

programs in normal colon and colon cancer. Molecular biology of the cell 18, 4245-4260.Sabates-Bellver, J., Van der Flier, L.G., de Palo, M., Cattaneo, E., Maake, C., Rehrauer, H., Laczko, E., Kurowski, M.A., Bujnicki, J.M., Menigatti, M., et al. (2007). Transcriptome profile of human colorectal adenomas. Molecular

cancer research : MCR 5, 1263-1275.Sagara, Y., Mimori, K., Yoshinaga, K., Tanaka, F., Nishida, K., Ohno, S., Inoue, H., and Mori, M. (2004). Clinical significance of Caveolin-1, Caveolin-2 and HER2/neu mRNA expression in human breast cancer. British journal of

cancer 91, 959-965.Salipante, S.J., Mealiffe, M.E., Wechsler, J., Krem, M.M., Liu, Y., Namkoong, S., Bhagat, G., Kirchhoff, T., Offit, K., Lynch, H., et al. (2009). Mutations in a gene encoding a midbody kelch protein in familial and sporadic classical

Hodgkin lymphoma lead to binucleated cells. Proceedings of the National Academy of Sciences of the United States of America 106, 14920-14925.Sarrio, D., Rodriguez-Pinilla, S.M., Hardisson, D., Cano, A., Moreno-Bueno, G., and Palacios, J. (2008). Epithelial-mesenchymal transition in breast cancer relates to the basal-like phenotype. Cancer Res 68, 989-997.Satterwhite, E., Sonoki, T., Willis, T.G., Harder, L., Nowak, R., Arriola, E.L., Liu, H., Price, H.P., Gesk, S., Steinemann, D., et al. (2001). The BCL11 gene family: involvement of BCL11A in lymphoid malignancies. Blood 98, 3413-

3420.Scotto, L., Narayan, G., Nandula, S.V., Subramaniyam, S., Kaufmann, A.M., Wright, J.D., Pothuri, B., Mansukhani, M., Schneider, A., Arias-Pulido, H., et al. (2008). Integrative genomics analysis of chromosome 5p gain in cervical

cancer reveals target over-expressed genes, including Drosha. Molecular cancer 7, 58.Seifert, O., Bayat, A., Geffers, R., Dienus, K., Buer, J., Lofgren, S., and Matussek, A. (2008). Identification of unique gene expression patterns within different lesional sites of keloids. Wound repair and regeneration : official

publication of the Wound Healing Society [and] the European Tissue Repair Society 16, 254-265.Shang, C., Guo, Y., Fu, S., Fu, W., and Sun, K. (2010). SH3GL2 gene participates in MEK-ERK signal pathway partly by regulating EGFR in the laryngeal carcinoma cell line Hep2. Medical science monitor : international medical

journal of experimental and clinical research 16, BR168-173.Sheridan, C., Kishimoto, H., Fuchs, R.K., Mehrotra, S., Bhat-Nakshatri, P., Turner, C.H., Goulet, R., Jr., Badve, S., and Nakshatri, H. (2006). CD44+/CD24- breast cancer cells exhibit enhanced invasive properties: an early step

necessary for metastasis. Breast cancer research : BCR 8, R59.Shi, Y., Hu, Z., Wu, C., Dai, J., Li, H., Dong, J., Wang, M., Miao, X., Zhou, Y., Lu, F., et al. (2011). A genome-wide association study identifies new susceptibility loci for non-cardia gastric cancer at 3q13.31 and 5p13.1. Nature

genetics 43, 1215-1218.Shih, S.C., Zukauskas, A., Li, D., Liu, G., Ang, L.H., Nagy, J.A., Brown, L.F., and Dvorak, H.F. (2009). The L6 protein TM4SF1 is critical for endothelial cell function and tumor angiogenesis. Cancer Res 69, 3272-3277.Shimamura, T., Ito, H., Shibahara, J., Watanabe, A., Hippo, Y., Taniguchi, H., Chen, Y., Kashima, T., Ohtomo, T., Tanioka, F., et al. (2005). Overexpression of MUC13 is associated with intestinal-type gastric cancer. Cancer science

96, 265-273.Shimura, S., Yang, G., Ebara, S., Wheeler, T.M., Frolov, A., and Thompson, T.C. (2000). Reduced infiltration of tumor-associated macrophages in human prostate cancer: association with cancer progression. Cancer Res 60, 5857-

5861.Shipp, M.A., Ross, K.N., Tamayo, P., Weng, A.P., Kutok, J.L., Aguiar, R.C., Gaasenbeek, M., Angelo, M., Reich, M., Pinkus, G.S., et al. (2002). Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and

supervised machine learning. Nature medicine 8, 68-74.Shpyleva, S.I., Tryndyak, V.P., Kovalchuk, O., Starlard-Davenport, A., Chekhun, V.F., Beland, F.A., and Pogribny, I.P. (2011). Role of ferritin alterations in human breast cancer cells. Breast cancer research and treatment 126, 63-

71.Shyu, R.Y., Jiang, S.Y., Chou, J.M., Shih, Y.L., Lee, M.S., Yu, J.C., Chao, P.C., Hsu, Y.J., and Jao, S.W. (2003). RARRES3 expression positively correlated to tumour differentiation in tissues of colorectal adenocarcinoma. British

journal of cancer 89, 146-151.Sienel, W., Dango, S., Woelfle, U., Morresi-Hauf, A., Wagener, C., Brummer, J., Mutschler, W., Passlick, B., and Pantel, K. (2003). Elevated expression of carcinoembryonic antigen-related cell adhesion molecule 1 promotes

progression of non-small cell lung cancer. Clin Cancer Res 9, 2260-2266.Sinha, S., Chunder, N., Mukherjee, N., Alam, N., Roy, A., Roychoudhury, S., and Kumar Panda, C. (2008). Frequent deletion and methylation in SH3GL2 and CDKN2A loci are associated with early- and late-onset breast carcinoma.

Annals of surgical oncology 15, 1070-1080.Sizemore, S., Cicek, M., Sizemore, N., Ng, K.P., and Casey, G. (2007). Podocalyxin increases the aggressive phenotype of breast and prostate cancer cells in vitro through its interaction with ezrin. Cancer Res 67, 6183-6191.Smith, P.G., Wang, F., Wilkinson, K.N., Savage, K.J., Klein, U., Neuberg, D.S., Bollag, G., Shipp, M.A., and Aguiar, R.C. (2005). The phosphodiesterase PDE4B limits cAMP-associated PI3K/AKT-dependent apoptosis in diffuse

large B-cell lymphoma. Blood 105, 308-316.Somasiri, A., Nielsen, J.S., Makretsov, N., McCoy, M.L., Prentice, L., Gilks, C.B., Chia, S.K., Gelmon, K.A., Kershaw, D.B., Huntsman, D.G., et al. (2004). Overexpression of the anti-adhesin podocalyxin is an independent predictor

of breast cancer progression. Cancer Res 64, 5068-5073.Song, Y., Washington, M.K., and Crawford, H.C. (2010). Loss of FOXA1/2 is essential for the epithelial-to-mesenchymal transition in pancreatic cancer. Cancer Res 70, 2115-2125.

Stanbrough, M., Bubley, G.J., Ross, K., Golub, T.R., Rubin, M.A., Penning, T.M., Febbo, P.G., and Balk, S.P. (2006). Increased expression of genes converting adrenal androgens to testosterone in androgen-independent prostate cancer. Cancer Res 66, 2815-2825.

Stange, D.E., Engel, F., Longerich, T., Koo, B.K., Koch, M., Delhomme, N., Aigner, M., Toedt, G., Schirmacher, P., Lichter, P., et al. (2010). Expression of an ASCL2 related stem cell signature and IGF2 in colorectal cancer liver metastases with 11p15.5 gain. Gut 59, 1236-1244.

Sternlicht, M.D., Dunning, A.M., Moore, D.H., Pharoah, P.D., Ginzinger, D.G., Chin, K., Gray, J.W., Waldman, F.M., Ponder, B.A., and Werb, Z. (2006). Prognostic value of PAI1 in invasive breast cancer: evidence that tumor-specific factors are more important than genetic variation in regulating PAI1 expression. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 15, 2107-2114.

Stone, B., Schummer, M., Paley, P.J., Thompson, L., Stewart, J., Ford, M., Crawford, M., Urban, N., O'Briant, K., and Nelson, B.H. (2003). Serologic analysis of ovarian tumor antigens reveals a bias toward antigens encoded on 17q. International journal of cancer Journal international du cancer 104, 73-84.

Sugiura, T., and Miyamoto, K. (2008). Characterization of TRIM31, upregulated in gastric adenocarcinoma, as a novel RBCC protein. Journal of cellular biochemistry 105, 1081-1091.Suomela, S., Cao, L., Bowcock, A., and Saarialho-Kere, U. (2004). Interferon alpha-inducible protein 27 (IFI27) is upregulated in psoriatic skin and certain epithelial cancers. The Journal of investigative dermatology 122, 717-721.Sureban, S.M., Ramalingam, S., Natarajan, G., May, R., Subramaniam, D., Bishnupuri, K.S., Morrison, A.R., Dieckgraefe, B.K., Brackett, D.J., Postier, R.G., et al. (2008). Translation regulatory factor RBM3 is a proto-oncogene that

prevents mitotic catastrophe. Oncogene 27, 4544-4556.Suzuki, H., Ouchida, M., Yamamoto, H., Yano, M., Toyooka, S., Aoe, M., Shimizu, N., Date, H., and Shimizu, K. (2008). Decreased expression of the SIN3A gene, a candidate tumor suppressor located at the prevalent allelic loss

region 15q23 in non-small cell lung cancer. Lung cancer 59, 24-31.Szczepanek, J., Jarzab, M., Oczko-Wojciechowska, M., Kowalska, M., Tretyn, A., Haus, O., Pogorzala, M., Wysocki, M., Jarzab, B., and Styczynski, J. (2012). Gene expression signatures and ex vivo drug sensitivity profiles in

children with acute lymphoblastic leukemia. Journal of applied genetics 53, 83-91.Tada, M., Kanai, F., Tanaka, Y., Sanada, M., Nannya, Y., Tateishi, K., Ohta, M., Asaoka, Y., Seto, M., Imazeki, F., et al. (2010). Prognostic significance of genetic alterations detected by high-density single nucleotide polymorphism

array in gastric cancer. Cancer science 101, 1261-1269.Takai, D., Gonzales, F.A., Tsai, Y.C., Thayer, M.J., and Jones, P.A. (2001). Large scale mapping of methylcytosines in CTCF-binding sites in the human H19 promoter and aberrant hypomethylation in human bladder cancer. Human

molecular genetics 10, 2619-2626.Taketani, T., Taki, T., Ono, R., Kobayashi, Y., Ida, K., and Hayashi, Y. (2002). The chromosome translocation t(7;11)(p15;p15) in acute myeloid leukemia results in fusion of the NUP98 gene with a HOXA cluster gene, HOXA13, but

not HOXA9. Genes, chromosomes & cancer 34, 437-443.Tanaka, H., Yashiro, M., Sunami, T., Sakate, Y., Kosaka, K., and Hirakawa, K. (2004). ICAM-2 gene therapy for peritoneal dissemination of scirrhous gastric carcinoma. Clin Cancer Res 10, 4885-4892.Tapon, N., Harvey, K.F., Bell, D.W., Wahrer, D.C., Schiripo, T.A., Haber, D.A., and Hariharan, I.K. (2002). salvador Promotes both cell cycle exit and apoptosis in Drosophila and is mutated in human cancer cell lines. Cell 110, 467-

478.Tassi, E., Henke, R.T., Bowden, E.T., Swift, M.R., Kodack, D.P., Kuo, A.H., Maitra, A., and Wellstein, A. (2006). Expression of a fibroblast growth factor-binding protein during the development of adenocarcinoma of the pancreas

and colon. Cancer Res 66, 1191-1198.Thibodeaux, C.A., Liu, X., Disbrow, G.L., Zhang, Y., Rone, J.D., Haddad, B.R., and Schlegel, R. (2009). Immortalization and transformation of human mammary epithelial cells by a tumor-derived Myc mutant. Breast cancer research

and treatment 116, 281-294.Tian, Q., Frierson, H.F., Jr., Krystal, G.W., and Moskaluk, C.A. (1999). Activating c-kit gene mutations in human germ cell tumors. Am J Pathol 154, 1643-1647.Tomlins, S.A., Rhodes, D.R., Perner, S., Dhanasekaran, S.M., Mehra, R., Sun, X.W., Varambally, S., Cao, X., Tchinda, J., Kuefer, R., et al. (2005). Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate

cancer. Science 310, 644-648.Tricoli, J.V., Seibel, N.L., Blair, D.G., Albritton, K., and Hayes-Lattin, B. (2011). Unique characteristics of adolescent and young adult acute lymphoblastic leukemia, breast cancer, and colon cancer. Journal of the National Cancer

Institute 103, 628-635.Tripathi, A., King, C., de la Morenas, A., Perry, V.K., Burke, B., Antoine, G.A., Hirsch, E.F., Kavanah, M., Mendez, J., Stone, M., et al. (2008). Gene expression abnormalities in histologically normal breast epithelium of breast cancer

patients. International journal of cancer Journal international du cancer 122, 1557-1566.Vargas, A.C., Reed, A.E., Waddell, N., Lane, A., Reid, L.E., Smart, C.E., Cocciardi, S., da Silva, L., Song, S., Chenevix-Trench, G., et al. (2012). Gene expression profiling of tumour epithelial and stromal compartments during

breast cancer progression. Breast cancer research and treatment.Vekony, H., Leemans, C.R., Ylstra, B., Meijer, G.A., van der Waal, I., and Bloemena, E. (2009). Salivary gland carcinosarcoma: oligonucleotide array CGH reveals similar genomic profiles in epithelial and mesenchymal components.

Oral oncology 45, 259-265.Vider, B.Z., Zimber, A., Chastre, E., Gespach, C., Halperin, M., Mashiah, P., Yaniv, A., and Gazit, A. (2000). Deregulated expression of homeobox-containing genes, HOXB6, B8, C8, C9, and Cdx-1, in human colon cancer cell lines.

Biochemical and biophysical research communications 272, 513-518.Vilar, E., Mukherjee, B., Kuick, R., Raskin, L., Misek, D.E., Taylor, J.M., Giordano, T.J., Hanash, S.M., Fearon, E.R., Rennert, G., et al. (2009). Gene expression patterns in mismatch repair-deficient colorectal cancers highlight the

potential therapeutic role of inhibitors of the phosphatidylinositol 3-kinase-AKT-mammalian target of rapamycin pathway. Clin Cancer Res 15, 2829-2839.Vui-Kee, K., Mohd Dali, A.Z., Mohamed Rose, I., Ghazali, R., Jamal, R., and Mokhtar, N.M. (2012). Molecular markers associated with nonepithelial ovarian cancer in formalin-fixed, paraffin-embedded specimens by genome wide

expression profiling. The Kaohsiung journal of medical sciences 28, 243-250.Waddell, N., Arnold, J., Cocciardi, S., da Silva, L., Marsh, A., Riley, J., Johnstone, C.N., Orloff, M., Assie, G., Eng, C., et al. (2010). Subtypes of familial breast tumours revealed by expression and copy number profiling. Breast

cancer research and treatment 123, 661-677.Wan, J., Ma, J., Mei, J., and Shan, G. (2009). The effects of HIF-1alpha on gene expression profiles of NCI-H446 human small cell lung cancer cells. Journal of experimental & clinical cancer research : CR 28, 150.Wang, F.Q., So, J., Reierstad, S., and Fishman, D.A. (2005). Matrilysin (MMP-7) promotes invasion of ovarian cancer cells by activation of progelatinase. International journal of cancer Journal international du cancer 114, 19-31.Wang, J., Day, R., Dong, Y., Weintraub, S.J., and Michel, L. (2008). Identification of Trop-2 as an oncogene and an attractive therapeutic target in colon cancers. Mol Cancer Ther 7, 280-285.Wang, M., Liu, Y.E., Greene, J., Sheng, S., Fuchs, A., Rosen, E.M., and Shi, Y.E. (1997). Inhibition of tumor growth and metastasis of human breast cancer cells transfected with tissue inhibitor of metalloproteinase 4. Oncogene 14,

2767-2774.Wang, Q., Tan, Y.X., Ren, Y.B., Dong, L.W., Xie, Z.F., Tang, L., Cao, D., Zhang, W.P., Hu, H.P., and Wang, H.Y. (2011). Zinc finger protein ZBTB20 expression is increased in hepatocellular carcinoma and associated with poor

prognosis. BMC cancer 11, 271.Wang, S.M., Ooi, L.L., and Hui, K.M. (2007). Identification and validation of a novel gene signature associated with the recurrence of human hepatocellular carcinoma. Clin Cancer Res 13, 6275-6283.Wang, X., and Gotoh, O. (2009). Accurate molecular classification of cancer using simple rules. BMC medical genomics 2, 64.Wang, X.Q., Luk, J.M., Garcia-Barcelo, M., Miao, X., Leung, P.P., Ho, D.W., Cheung, S.T., Lam, B.Y., Cheung, C.K., Wong, A.S., et al. (2006). Liver intestine-cadherin (CDH17) haplotype is associated with increased risk of

hepatocellular carcinoma. Clin Cancer Res 12, 5248-5252.Watanabe, T., Kobunai, T., Toda, E., Kanazawa, T., Kazama, Y., Tanaka, J., Tanaka, T., Yamamoto, Y., Hata, K., Kojima, T., et al. (2007). Gene expression signature and the prediction of ulcerative colitis-associated colorectal

cancer by DNA microarray. Clin Cancer Res 13, 415-420.Watanabe, Y., Kim, H.S., Castoro, R.J., Chung, W., Estecio, M.R., Kondo, K., Guo, Y., Ahmed, S.S., Toyota, M., Itoh, F., et al. (2009). Sensitive and specific detection of early gastric cancer with DNA methylation analysis of gastric

washes. Gastroenterology 136, 2149-2158.Weng, Y.C., Chuang, S.T., Lin, Y.C., Chuang, C.F., Chi, T.C., Chiu, H.L., Kuo, Y.H., and Su, M.J. (2012). Caffeic Acid Phenylethyl Amide Protects against the Metabolic Consequences in Diabetes Mellitus Induced by Diet and

Streptozocin. Evidence-based complementary and alternative medicine : eCAM 2012, 984780.

Wong, Y.F., Cheung, T.H., Tsao, G.S., Lo, K.W., Yim, S.F., Wang, V.W., Heung, M.M., Chan, S.C., Chan, L.K., Ho, T.W., et al. (2006). Genome-wide gene expression profiling of cervical cancer in Hong Kong women by oligonucleotide microarray. International journal of cancer Journal international du cancer 118, 2461-2469.

Wonsey, D.R., Zeller, K.I., and Dang, C.V. (2002). The c-Myc target gene PRDX3 is required for mitochondrial homeostasis and neoplastic transformation. Proceedings of the National Academy of Sciences of the United States of America 99, 6649-6654.

Xia, W., Unger, P., Miller, L., Nelson, J., and Gelman, I.H. (2001). The Src-suppressed C kinase substrate, SSeCKS, is a potential metastasis inhibitor in prostate cancer. Cancer Res 61, 5644-5651.Xu, Z.P., Zhu, J.S., Zhang, Q., and Wang, X.Y. (2011). A breakdown of the Hippo pathway in gastric cancer. Hepato-gastroenterology 58, 1611-1617.Yabuki, N., Sakata, K., Yamasaki, T., Terashima, H., Mio, T., Miyazaki, Y., Fujii, T., and Kitada, K. (2007). Gene amplification and expression in lung cancer cells with acquired paclitaxel resistance. Cancer genetics and cytogenetics

173, 1-9.Yang, J., Bielenberg, D.R., Rodig, S.J., Doiron, R., Clifton, M.C., Kung, A.L., Strong, R.K., Zurakowski, D., and Moses, M.A. (2009). Lipocalin 2 promotes breast cancer progression. Proceedings of the National Academy of Sciences

of the United States of America 106, 3913-3918.Yang, Y., Li, X., Yang, Q., Wang, X., Zhou, Y., Jiang, T., Ma, Q., and Wang, Y.J. (2010). The role of microRNA in human lung squamous cell carcinoma. Cancer genetics and cytogenetics 200, 127-133.Yook, J.I., Li, X.Y., Ota, I., Hu, C., Kim, H.S., Kim, N.H., Cha, S.Y., Ryu, J.K., Choi, Y.J., Kim, J., et al. (2006). A Wnt-Axin2-GSK3beta cascade regulates Snail1 activity in breast cancer cells. Nature cell biology 8, 1398-1406.Yousef, G.M., Scorilas, A., Kyriakopoulou, L.G., Rendl, L., Diamandis, M., Ponzone, R., Biglia, N., Giai, M., Roagna, R., Sismondi, P., et al. (2002). Human kallikrein gene 5 (KLK5) expression by quantitative PCR: an independent

indicator of poor prognosis in breast cancer. Clinical chemistry 48, 1241-1250.Yu, K.H., Barry, C.G., Austin, D., Busch, C.M., Sangar, V., Rustgi, A.K., and Blair, I.A. (2009). Stable isotope dilution multidimensional liquid chromatography-tandem mass spectrometry for pancreatic cancer serum biomarker

discovery. Journal of proteome research 8, 1565-1576.Zhang, H., Dong, Y., Zhao, H., Brooks, J.D., Hawthorn, L., Nowak, N., Marshall, J.R., Gao, A.C., and Ip, C. (2005). Microarray Data Mining for Potential Selenium Targets in Chemoprevention of Prostate Cancer. Cancer genomics &

proteomics 2, 97-114.Zhang, Z.H., Chen, Y., Zhao, H.J., Xie, C.Y., Ding, J., and Hou, Y.T. (2007). Silencing of heparanase by siRNA inhibits tumor metastasis and angiogenesis of human breast cancer in vitro and in vivo. Cancer biology & therapy 6,

587-595.Zhou, X., Chen, X., Hu, L., Han, S., Qiang, F., Wu, Y., Pan, L., Shen, H., Li, Y., and Hu, Z. (2010). Polymorphisms involved in the miR-218-LAMB3 pathway and susceptibility of cervical cancer, a case-control study in Chinese

women. Gynecologic oncology 117, 287-290.

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