Evolutionary conservation of zinc finger transcription factor binding sites in promoters of genes co-expressed with WT1 in prostate cancer

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Eisermann, Kurtis ^a   Tandon, Sunpreet ^a   Bazarov, Anton ^a   Brett, Adina ^a   Fraizer, Gail ^a   Piontkivska, Helen ^a  

^a KENT STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANDROGEN RECEPTOR; CELL PROTEIN; N MYC DOWNSTREAM REGULATED 1 PROTEIN; NEUROPEPTIDE Y; PROSTATE SPECIFIC ANTIGEN; SOMATOMEDIN BINDING PROTEIN 2; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR AP 2; TRANSCRIPTION FACTOR AP 2 GAMMA; TRANSCRIPTION FACTOR EGR 1; TRANSCRIPTION FACTOR GATA 1; TRANSCRIPTION FACTOR GATA 2; TRANSCRIPTION FACTOR SOX4; TRANSCRIPTION FACTOR SOX9; TRANSCRIPTION FACTOR SP1; TRANSCRIPTION FACTOR SP2; TRANSCRIPTOME; UVOMORULIN; VASCULOTROPIN; WILMS TUMOR 1 PROTEIN; ZINC FINGER PROTEIN; VASCULOTROPIN A; WT1 PROTEIN;

ANIMAL CELL; ARTICLE; BINDING SITE; CANCER INHIBITION; CHIMPANZEE; CHROMATIN IMMUNOPRECIPITATION; COMPUTER MODEL; CONTROLLED STUDY; COW; DOG; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE TARGETING; GENETIC CONSERVATION; HUMAN; HUMAN CELL; IN VIVO STUDY; MACACA; MALE; MOLECULAR EVOLUTION; MOUSE; NONHUMAN; OPOSSUM; PROMOTER REGION; PROSTATE CANCER; PROTEIN ANALYSIS; PROTEIN BINDING; RAT; REGULATORY SEQUENCE; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION; ANIMAL; EVOLUTION; GENE EXPRESSION REGULATION; GENETICS; GENOME; NUCLEOTIDE SEQUENCE; PROSTATE TUMOR; SEQUENCE ALIGNMENT;

EUTHERIA; MAMMALIA; METATHERIA; PRIMATES;

ANIMALS; BASE SEQUENCE; BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; CONSERVED SEQUENCE; EVOLUTION; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOME, HUMAN; HUMANS; MALE; PROMOTER REGIONS (GENETICS); PROSTATE-SPECIFIC ANTIGEN; PROSTATIC NEOPLASMS; RECEPTORS, ANDROGEN; SEQUENCE ALIGNMENT; TRANSCRIPTION FACTORS; VASCULAR ENDOTHELIAL GROWTH FACTOR A; WT1 PROTEINS; ZINC FINGERS;

EID: 49249123274     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-337     Document Type: Article

References (105)

1. Jemal A Siegel R Ward E Murray T Xu J Thun MJ Cancer statistics, 2007 CA Cancer J Clin 2007, 57:43-66. 17237035
2. Stamey TA Caldwell M McNeal JE Nolley R Hemenez M Downs J The prostate specific antigen era in the United States is over for prostate cancer: what happened in the last 20 years? J Urol 2004, 172:1297-1301. 15371827 10.1097/01.ju.0000139993.51181.5d
3. Luo JH Yu YP Cieply K Lin F Deflavia P Dhir R Finkelstein S Michalopoulos G Becich M Gene expression analysis of prostate cancers Mol Carcinog 2002, 33:25-35. 11807955 10.1002/mc.10018
4. Singh D Febbo PG Ross K Jackson DG Manola J Ladd C Tamayo P Renshaw AA D'Amico AV Richie JP Lander ES Loda M Kantoff PW Golub TR Sellers WR Gene expression correlates of clinical prostate cancer behavior Cancer Cell 2002, 1:203-209. 12086878 10.1016/S1535-6108(02)00030-2
5. Chandran UR Dhir R Ma C Michalopoulos G Becich M Gilbertson J Differences in gene expression in prostate cancer, normal appearing prostate tissue adjacent to cancer and prostate tissue from cancer free organ donors BMC Cancer 2005, 5:45. 15892885 10.1186/1471-2407-5-45 1173092
6. Brown K Differential Gene Expression Patterns in Prostate Cancer Epithelial and Interstitial Stromal Cells MS Thesis, Kent State University 2006.
7. Liu C Calogero A Ragona G Adamson E Mercola D EGR-1, the reluctant suppression factor: EGR-1 is known to function in the regulation of growth, differentiation, and also has significant tumor suppressor activity and a mechanism involving the induction of TGF-beta1 is postulated to account for this suppressor activity Crit Rev Oncog 1996, 7(1-2):101-125. 9109500
8. Madden SL Cook DM Morris JF Gashler A Sukhatme VP Rauscher FJ III Transcriptional repression mediated by the WT1 Wilms tumor gene product Science 1991, 253:1550-1553. 1654597 10.1126/science.1654597
9. Dey BR Sukhatme VP Roberts AB Sporn MB Rauscher FJ 3rd Kim SJ Repression of the transforming growth factor-beta 1 gene by the Wilms' tumor suppressor WT1 gene product Mol Endocrinol 1994, 8:595-602. 8058069 10.1210/me.8.5.595
10. Devilard E Bladou F Ramuz O Karsenty G Dales JP Gravis G Nguyen C Bertucci F Xerri L Birnbaum D FGFR1 and WT1 are markers of human prostate cancer progression BMC Cancer 2006 6 272 17137506 10.1186/ 1471-2407-6-272 1698935
11. Ogishima T Shiina H Breault JE Tabatabai L Bassett WW Enokida H Li LC Kawakami T Urakami S Ribeiro-Filho LA Terashima M Fujime M Igawa M Dahiya R Increased heparanase expression is caused by promoter hypomethylation and up-regulation of transcriptional factor early growth response-1 in human prostate cancer Clin Cancer Res 2005, 11(3):1028-1036. 15709168
12. Eid MA Kumar MV Iczkowski KA Bostwick DG Tindall DJ Expression of early growth response genes in human prostate cancer Cancer Res 1998, 58:2461-2468. 9622090
13. Rivera MN Haber DA Wilms' tumour: Connecting tumorigenesis and organ development in the kidney Nat Rev Cancer 2005, 5:699-712. 16110318 10.1038/nrc1696
14. Shimamura R Fraizer GC Trapman J Lau Y Saunders GF The Wilms' tumor gene WT1 can regulate genes involved in sex determination and differentiation: SRY, Mullerian-inhibiting substance, and the androgen receptor Clin Cancer Res 1997, 3(12 Pt 2):2571-2580. 9815658
15. Hanson J Gorman J Reese J Fraizer G Regulation of vascular endothelial growth factor, VEGF, gene promoter by the tumor suppressor, WT1 Front Biosci 2007, 12:2279-2290. 17127464 10.2741/2230
16. Thomas JW Touchman JW Vertebrate genome sequencing: Building a backbone for comparative genomics Trends in Genetics 2002, 18:104-108. 11818143 10.1016/S0168-9525(02)02599-4
17. Dubchak I Brudno M Loots GG Pachter L Mayor C Rubin EM Frazer KA Active conservation of noncoding sequences revealed by three-way species comparisons Genome Res 2000, 10:1304-1306. 10.1101/gr.142200 10984448 310906
18. Stojanovic N Florea L Riemer C Gumucio D Slightom J Goodman M Miller W Hardison R Journals O Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions Nucleic Acids Res 1999, 27:3899-3910. 10481030 10.1093/nar/27.19.3899 148654
19. Wang H Zhang Y Cheng Y Zhou Y King DC Taylor J Chiaromonte F Kasturi J Petrykowska H Gibb B Dorman C Miller W Dore LC Welch J Weiss MJ Hardison RC Experimental validation of predicted mammalian erythroid cis-regulatory modules Genome Res 2006, 16:1480-1492. 17038566 10.1101/ gr.5353806 1665632
20. Johnson DS Davidson B Brown CD Smith WC Sidow A Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance Genome Res 2004, 14:2448-2456. 15545496 10.1101/gr.2964504 534669
21. Hedges S Kumar S Genomic clocks and evolutionary timescales Trends in Genetics 2003, 19:200-206. 12683973 10.1016/S0168-9525(03)00053-2
22. Fraizer G Leahy R Priyadarshini S Graham K Delacerda J Diaz M Suppression of prostate tumor cell growth in vivo by WT1, the Wilms' tumor suppressor gene Int J Oncol 2004, 24:461-471. 14767530
23. Kohler B Delezoide AL Boizet-Bonhoure B McPhaul MJ Sultan C Lumbroso S Coexpression of Wilms' tumor suppressor 1 (WT1) and androgen receptor (AR) in the genital tract of human male embryos and regulation of AR promoter activity by WT1 J Mol Endocrinol 2007, 38:547-554. 17496156 10.1677/JME-06-0020
24. Husbeck B Bhattacharyya RS Feldman D Knox SJ Inhibition of androgen receptor signaling by selenite and methylseleninic acid in prostate cancer cells: Two distinct mechanisms of action Mol Cancer Ther 2006, 5:2078-2085. 16928829 10.1158/1535-7163.MCT-06-0056
25. Pore N Gupta AK Cerniglia GJ Jiang Z Bernhard EJ Evans SM Koch CJ Hahn SM Maity A Nelfinavir down-regulates hypoxia-inducible factor 1alpha and VEGF expression and increases tumor oxygenation: Implications for radiotherapy Cancer Res 2006, 66:9252-9259. 16982770 10.1158/ 0008-5472.CAN-06-1239
26. Englert C Hou X Maheswaran S Bennett P Ngwu C Re GG Garvin AJ Rosner MR Haber DA WT1 suppresses synthesis of the epidermal growth factor receptor and induces apoptosis EMBO J 1995, 14(19):4662-4675. 394563 7588596
27. Tagle DA Koop BF Goodman M Slightom JL Hess DL Jones RT Embryonic and globin genes of a prosimian primate (Galago crassicaudatus): Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints J Mol Biol 1988, 203:439-455. 3199442 10.1016/ 0022-2836(88)90011-3
28. Elnitski L Miller W Hardison R Conserved E boxes function as part of the enhancer in hypersensitive site 2 of the beta-globin locus control region. Role of basic helix-loop-helix proteins J Biol Chem 1997, 272:369-378. 8995271 10.1074/jbc.272.1.369
29. Hardison RC Oeltjen J Miller W Long human-mouse sequence alignments reveal novel regulatory elements: A reason to sequence the mouse genome Genome Res 1997, 7(10):959-966. 9331366
30. Vuillaumier S Dixmeras I Messai H Lapoumeroulie C Lallemand D Gekas J Chehab FF Perret C Elion J Denamur E Cross-species characterization of the promoter region of the cystic fibrosis transmembrane conductance regulator gene reveals multiple levels of regulation Biochem J 1997, 327(Pt 3):651-662. 1218840 9581539
31. Loots GG Locksley RM Blankespoor CM Wang ZE Miller W Rubin EM Frazer KA Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons Science 2000, 288:136-140. 10.1126/ science.288.5463.136 10753117
32. Cliften P Sudarsanam P Desikan A Fulton L Fulton B Majors J Waterston R Cohen BA Johnston M Finding functional features in saccharomyces genomes by phylogenetic footprinting Science 2003, 301:71-76. 10.1126/ science.1084337 12775844
33. Kellis M Patterson N Endrizzi M Birren B Lander ES Sequencing and comparison of yeast species to identify genes and regulatory elements Nature 2003, 423:241-254. 12748633 10.1038/nature01644
34. Xie X Lu J Kulbokas EJ Golub TR Mootha V Lindblad-Toh K Lander ES Kellis M Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals Nature 2005, 434:338-345. 15735639 10.1038/nature03441
35. Hughes JR Cheng JF Ventress N Prabhakar S Clark K Anguita E De Gobbi M de Jong P Rubin E Higgs DR Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences Proc Natl Acad Sci USA 2005, 102:9830. 15998734 10.1073/pnas.0503401102 1174996
36. King DC Taylor J Elnitski L Chiaromonte F Miller W Hardison RC Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences Genome Res 2005, 15:1051-1060. 16024817 10.1101/gr.3642605 1182217
37. Frith MC Ponjavic J Fredman D Kai C Kawai J Carninci P Hayshizaki Y Sandelin A Evolutionary turnover of mammalian transcription start sites Genome Res 2006, 16:713-722. 16687732 10.1101/gr.5031006 1473182
38. Loots GG Ovcharenko I rVISTA 2.0: Evolutionary analysis of transcription factor binding sites Nucleic Acids Res 2004, 32:W217-221. 15215384 10.1093/nar/gkh383 441521
39. Ovcharenko I Loots GG Giardine BM Hou M Ma J Hardison RC Stubbs L Miller W Mulan: Multiple-sequence local alignment and visualization for studying function and evolution Genome Res 2005, 15:184-194. 15590941 10.1101/gr.3007205 540288
40. Dermitzakis ET Clark AG Evolution of transcription factor binding sites in mammalian gene regulatory regions: Conservation and turnover Mol Biol Evol 2002, 19:1114-1121. 12082130
41. Hewitt SM Hamada S McDonnell TJ Rauscher FJ 3rd Saunders GF Regulation of the proto-oncogenes bcl-2 and c-myc by the Wilms' tumor suppressor gene WT1 Cancer Res 1995, 55(22):5386-5389. 7585606
42. Mayo MW Wang CY Drouin SS Madrid LV Marshall AF Reed JC Weissman BE Baldwin AS WT1 modulates apoptosis by transcriptionally upregulating the bcl-2 proto-oncogene EMBO J 1999, 18:3990-4003. 10406804 10.1093/emboj/ 18.14.3990 1171475
43. Werner H Rauscher FJ 3rd Sukhatme VP Drummond IA Roberts CT Jr LeRoith D Transcriptional repression of the insulin-like growth factor I receptor (IGF-I-R) gene by the tumor suppressor WT1 involves binding to sequences both upstream and downstream of the IGF-I-R gene transcription start site J Biol Chem 1994, 269(17):12577-12582. 8175666
44. Werner H Re GG Drummond IA Sukhatme VP Rauscher FJ 3rd Sens DA Garvin AJ LeRoith D Roberts CT Jr Increased expression of the insulin-like growth factor I receptor gene, IGF1R, in Wilms tumor is correlated with modulation of IGF1R promoter activity by the WT1 Wilms tumor gene product Proc Natl Acad Sci U S A 1993, 90:5828-5832. 8390684 10.1073/ pnas.90.12.5828 46816
45. Drummond IA Madden SL Rohwer-Nutter P Bell GI Sukhatme VP Rauscher FJ Repression of the insulin-like growth factor II gene by the Wilms tumor suppressor WT1 Science 1992, 257:674-678. 1323141 10.1126/science.1323141
46. Hosono S Gross I English MA Hajra KM Fearon ER Licht JD E-cadherin is a WT1 target gene J Biol Chem 2000, 275:10943-10953. 10753894 10.1074/ jbc.275.15.10943
47. Hewitt SM Fraizer GC Wu YJ Rauscher FJ 3rd Saunders GF Differential function of Wilms' tumor gene WT1 splice isoforms in transcriptional regulation J Biol Chem 1996, 271:8588-8592. 8621487 10.1074/ jbc.271.15.8588
48. Yin H Radomska HS Tenen DG Glass J Down regulation of PSA by C/EBPalpha is associated with loss of AR expression and inhibition of PSA promoter activity in the LNCaP cell line BMC Cancer 2006, 6:158. 16774685 10.1186/ 1471-2407-6-158 1544346
49. Borgono CA Diamandis EP The emerging roles of human tissue kallikreins in cancer Nat Rev Cancer 2004, 4:876-890. 15516960 10.1038/nrc1474
50. Merika M Orkin SH DNA-binding specificity of GATA family transcription factors Mol Cell Biol 1993, 13:3999-4010. 359949 8321207
51. Tremblay JJ Viger RS Novel roles for GATA transcription factors in the regulation of steroidogenesis J Steroid Biochem Mol Biol 2003, 85:291-298. 12943715 10.1016/S0960-0760(03)00211-5
52. Viger RS Guittot SM Anttonen M Wilson DB Heikinheimo M Role of the GATA family of transcription factors in endocrine development, function, and disease Mol Endocrinol 2008, 22:781-798. 18174356 10.1210/me.2007-0513 2276466
53. Fraizer GC Wu YJ Hewitt SM Maity T Ton CC Huff V Saunders GF Transcriptional regulation of the human Wilms' tumor gene (WT1). cell type-specific enhancer and promiscuous promoter J Biol Chem 1994, 269(12):8892-8900. 8132626
54. Wu Y Fraizer GC Saunders GF GATA-1 Transactivates the WT1 Hematopoietic Specific Enhancer J Biol Chem 1995, 270:5944-5949. 7890725 10.1074/ jbc.270.11.5944
55. Zhang X Xing G Fraizer GC Saunders GF Transactivation of an Intronic Hematopoietic-specific Enhancer of the Human Wilms' Tumor 1 Gene by GATA-1 and c-Myb J Biol Chem 1997, 272:29272-29280. 9361007 10.1074/ jbc.272.46.29272
56. Perez-Stable CM Pozas A Roos BA A role for GATA transcription factors in the androgen regulation of the prostate-specific antigen gene enhancer Mol Cell Endocrinol 2000, 167:43-53. 11000519 10.1016/ S0303-7207(00)00300-2
57. Miyamoto Y Silversides D Viger R GATA4 Enhances SRY Gene Transcription Through a Direct Interaction with Wilms Tumor 1 (WT1) Biology of Reproduction 2005, 97. http://abstracts.co.allenpress.com/pweb/ssr2005/ document/47755
58. Rauscher FJ Morris JF Tournay OE Cook DM Curran T Binding of the Wilms' tumor locus zinc finger protein to the EGR-1 consensus sequence Science 1990, 250:1259-1262. 2244209 10.1126/science.2244209
59. Larsson SH Charlieu JP Miyagawa K Engelkamp D Rassoulzadegan M Ross A Cuzin F van Heyningen V Hastie ND Subnuclear localization of WT1 in splicing or transcription factor domains is regulated by alternative splicing Cell 1995, 81:391-401. 7736591 10.1016/0092-8674(95)90392-5
60. Ladomery M Sommerville J Woolner S Slight J Hastie N Expression in Xenopus oocytes shows that WT1 binds transcripts in vivo, with a central role for zinc finger one J Cell Sci 2003, 116:1539-1549. 10.1242/ jcs.00324 12640038
61. Abdulkadir SA Qu Z Garabedian E Song SK Peters TJ Svaren J Carbone JM Naughton CK Catalona WJ Ackerman JJ Gordon JI Humphrey PA Milbrandt J Impaired prostate tumorigenesis in Egr1-deficient mice Nat Med 2001, 7:101-107. 11135623 10.1038/83231
62. Ellen T Ke Q Zhang P Costa M NDRG1, a Growth and Cancer Related Gene: Regulation of Gene Expression and Function in Normal and Disease States Carcinogenesis 2008, 29:2-8. 17916902 10.1093/carcin/bgm200
63. Caruso RP Levinson B Melamed J Wieczorek R Taneja S Polsky D Chang C Zeleniuch-Jacquotte A Salnikow K Yee H Costa M Osman I Altered N-myc downstream-regulated gene 1 protein expression in African-American compared with caucasian prostate cancer patients Clin Cancer Res 2004, 10:222-227. 14734473 10.1158/1078-0432.CCR-0604-3
64. Rong Y Hu F Huang R Mackman N Horowitz JM Jensen RL Durden DL Van Meir EG Brat DJ Early growth response gene-1 regulates hypoxia-induced expression of tissue factor in glioblastoma multiforme through hypoxia-inducible factor-1-independent mechanisms Cancer Res 2006, 66:7067-7074. 16849552 10.1158/0008-5472.CAN-06-0346
65. Zhang P Tchou-Wong KM Costa M Egr-1 Mediates Hypoxia-Inducible Transcription of the NDRG1 Gene through an Overlapping Egr-1/Sp1 Binding Site in the Promoter Cancer Res 2007, 67:9125. 17909017 10.1158/ 0008-5472.CAN-07-1525
66. Minc E de Coppet P Masson P Thiery L Dutertre S Amor-Gueret M Jaulin C The human copper-zinc superoxide dismutase gene (SOD1) proximal promoter is regulated by Sp1, Egr-1, and WT1 via non-canonical binding sites J Biol Chem 1999, 274:503-509. 9867871 10.1074/jbc.274.1.503
67. Harrington MA Konicek B Song A Xia XL Fredericks WJ Rauscher FJ 3rd Inhibition of colony-stimulating factor-1 promoter activity by the product of the Wilms' tumor locus J Biol Chem 1993, 268(28):21271-21275. 8407965
68. Wang ZY Madden SL Deuel TF Rauscher FJ The Wilms' tumor gene product, WT1, represses transcription of the platelet-derived growth factor A-chain gene J Biol Chem 1992, 267:21999-22002. 1429549
69. Stoner M Wormke M Saville B Samudio I Qin C Abdelrahim M Safe S Estrogen regulation of vascular endothelial growth factor gene expression in ZR-75 breast cancer cells through interaction of estrogen receptor alpha and SP proteins Oncogene 2004, 23:1052-1063. 14647449 10.1038/ sj.onc.1207201
70. Reizner N Maor S Sarfstein R Abramovitch S Welshons WV Curran EM Lee AV Werner H The WT1 Wilms' tumor suppressor gene product interacts with estrogen receptor-alpha and regulates IGF-I receptor gene transcription in breast cancer cells J Mol Endocrinol 2005, 35:135-144. 16087727 10.1677/jme.1.01761
71. Ensembl Genome Browser http://www.ensembl.org/
72. Hubbard TJ Aken BL Beal K Ballester B Caccamo M Chen Y Clarke L Coates G Cunningham F Cutts T Down T Dyer SC Fitzgerald S Fernandez-Banet J Graf S Haider S Hammond M Herrero J Holland R Howe K Howe K Johnson N Kahari A Keefe D Kokocinski F Kulesha E Lawson D Longden I Melsopp C Megy K Meidl P Ouverdin B Parker A Prlic A Rice S Rios D Schuster M Sealy I Severin J Slater G Smedley D Spudich G Trevanion S Vilella A Vogel J White S Wood M Cox T Curwen V Durbin R Fernandez-Suarez XM Flicek P Kasprzyk A Proctor G Searle S Smith J Ureta-Vidal A Birney E Ensembl 2007 Nucleic Acids Res 2007, 35:D610-7. 17148474 10.1093/nar/gkl996 1761443
73. Dieterich C Cusack B Wang H Rateitschak K Krause A Vingron M Annotating regulatory DNA based on man-mouse genomic comparison Bioinformatics 2002, 18(Suppl 2):S84-90. 12385988
74. Rutherford K Parkhill J Crook J Horsnell T Rice P Rajandream MA Barrell B Artemis: Sequence visualization and annotation Bioinformatics 2000 16 944 945 11120685 10.1093/bioinformatics/16.10.944
75. Cartharius K Frech K Grote K Klocke B Haltmeier M Klingenhoff A Frisch M Bayerlein M Werner T MatInspector and beyond: Promoter analysis based on transcription factor binding sites Bioinformatics 2005, 21:2933-2942. 15860560 10.1093/bioinformatics/bti473
76. Wingender E Chen X Hehl R Karas H Liebich I Matys V Meinhardt T Prüß M Reuter I Schacherer F TRANSFAC: An integrated system for gene expression regulation Nucleic Acids Res 2000, 28:316-319. 10592259 10.1093/nar/28.1.316 102445
77. Werner T Computer-assisted analysis of transcription control regions Methods Mol Biol 2000, 132:337-349. 10547845
78. Genomatix-understanding gene regulation http://www.genomatix.de
79. Schwartz S Elnitski L Li M Weirauch M Riemer C Smit A NISC Comparative Sequencing Program Green ED Hardison RC Miller W MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences Nucleic Acids Res 2003, 31:3518-3524. 12824357 10.1093/nar/ gkg579 168985
80. Frazer KA Tao H Osoegawa K de Jong PJ Chen X Doherty MF Cox DR Noncoding Sequences Conserved in a Limited Number of Mammals in the SIM2 Interval are Frequently Functional Genome Res 2004, 14:367-372. 14962988 10.1101/ gr.1961204 353216
81. Berquin IM Min Y Wu R Wu H Chen YQ Expression signature of the mouse prostate J Biol Chem 2005, 280:36442-36451. 16055444 10.1074/ jbc.M504945200
82. Dutton JR Lahiri D Ward A Different isoforms of the Wilms' tumour protein WT1 have distinct patterns of distribution and trafficking within the nucleus Cell Prolif 2006, 39:519-535. 17109636 10.1111/ j.1365-2184.2006.00409.x
83. Weinmann AS Farnham PJ Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation Methods 2002, 26:37-47. 12054903 10.1016/S1046-2023(02)00006-3
84. Hanson J Brown K Reese J Gorman J Cash J Graham K Fraizer GC Wilms' tumor suppressor gene, WT1, modulates VEGF expression and is differentially expressed in prostate tumor cells Proc Amer Assoc Cancer Res 2006, 47:2492. http://www.aacrmeetingabstracts.org/cgi/content/ abstract/2006/1/590
85. Sroka IC Nagle RB Bowden GT Membrane-type 1 matrix metalloproteinase is regulated by sp1 through the differential activation of AKT, JNK, and ERK pathways in human prostate tumor cells Neoplasia 2007, 9:406-417. 17534446 10.1593/neo.07193 1877982
86. Phan D Cheng CJ Galfione M Vakar-Lopez F Tunstead J Thompson NE Burgess RR Najjar SM Yu-Lee LY Lin SH Identification of Sp2 as a Transcriptional Repressor of Carcinoembryonic Antigen-Related Cell Adhesion Molecule 1 in Tumorigenesis Cancer Res 2004, 64:3072-3078. 15126343 10.1158/ 0008-5472.CAN-03-3730
87. Ho SM Leung YK Chung I Estrogens and antiestrogens as etiological factors and therapeutics for prostate cancer Ann N Y Acad Sci 2006 1089, 177-193. 17261766 10.1196/annals.1386.005
88. Ruiz M Pettaway C Song R Stoeltzing O Ellis L Bar-Eli M Activator protein 2alpha inhibits tumorigenicity and represses vascular endothelial growth factor transcription in prostate cancer cells Cancer Res 2004, 64:631-638. 14744778 10.1158/0008-5472.CAN-03-2751
89. Zhang X Leung YK Ho SM AP-2 regulates the transcription of estrogen receptor (ER)-beta by acting through a methylation hotspot of the oN promoter in prostate cancer cells Oncogene 2007, 26:7346-7354. 17525739 10.1038/sj.onc.1210537
90. Rhodes DR Sanda MG Otte AP Chinnaiyan AM Rubin MA Multiplex biomarker approach for determining risk of prostate-specific antigen-defined recurrence of prostate cancer J Natl Cancer Inst 2003, 95:661-668. 12734317
91. Mehrian-Shai R Chen CD Shi T Horvath S Nelson SF Reichardt JK Sawyers CL Insulin growth factor-binding protein 2 is a candidate biomarker for PTEN status and PI3K/Akt pathway activation in glioblastoma and prostate cancer Proc Natl Acad Sci USA 2007, 104:5563-5568. 17372210 10.1073/ pnas.0609139104 1838515
92. Chatterjee S Park ES Soloff MS Proliferation of DU145 prostate cancer cells is inhibited by suppressing insulin-like growth factor binding protein-2 Int J Urol 2004, 11:876-884. 15479293 10.1111/ j.1442-2042.2004.00898.x
93. Le H Arnold JT McFann KK Blackman MR DHT and testosterone, but not DHEA or E2, differentially modulate IGF-I, IGFBP-2, and IGFBP-3 in human prostatic stromal cells Am J Physiol Endocrinol Metab 2006, 290:E952-E960. 16368782 10.1152/ajpendo.00451.2005
94. Nagpal ML Davis J Lin T Overexpression of CXCL10 in human prostate LNCaP cells activates its receptor (CXCR3) expression and inhibits cell proliferation Biochim Biophys Acta 2006, 1762:811-818. 16934957
95. Tu LC Yan X Hood L Lin B Proteomics analysis of the interactome of N-myc downstream regulated gene 1 and its interactions with the androgen response program in prostate cancer cells Mol Cell Proteomics 2007, 6:575-588. 17220478 10.1074/mcp.M600249-MCP200
96. Kim KH Dobi A Shaheduzzaman S Gao CL Masuda K Li H Drukier A Gu Y Srikantan V Rhim JS Srivastava S Characterization of the androgen receptor in a benign prostate tissue-derived human prostate epithelial cell line: RC-165N/human telomerase reverse transcriptase Prostate Cancer Prostatic Dis 2007, 10:30-38. 17075604 10.1038/sj.pcan.4500915
97. Ruscica M Dozio E Boghossian S Bovo G Martos Riano V Motta M Magni P Activation of the Y1 receptor by neuropeptide Y regulates the growth of prostate cancer cells Endocrinology 2006, 147:1466-1473. 16339211 10.1210/en.2005-0925
98. Rasiah KK Kench JG Gardiner-Garden M Biankin AV Golovsky D Brenner PC Kooner R O'neill GF Turner JJ Delprado W Lee CS Brown DA Breit SN Grygiel JJ Horvath LG Stricker PD Sutherland RL Henshall SM Aberrant neuropeptide Y and macrophage inhibitory cytokine-1 expression are early events in prostate cancer development and are associated with poor prognosis Cancer Epidemiol Biomarkers Prev 2006, 15:711-716. 16614113 10.1158/1055-9965.EPI-05-0752
99. Liu P Ramachandran S Ali Seyed M Scharer CD Laycock N Dalton WB Williams H Karanam S Datta MW Jaye DL Moreno CS Sex-determining region Y box 4 is a transforming oncogene in human prostate cancer cells Cancer Res 2006, 66:4011-4019. 16618720 10.1158/0008-5472.CAN-05-3055
100. Vanaja DK Ballman KV Morlan BW Cheville JC Neumann RM Lieber MM Tindall DJ Young CY PDLIM4 repression by hypermethylation as a potential biomarker for prostate cancer Clin Cancer Res 2006, 12:1128-1136. 16489065 10.1158/1078-0432.CCR-05-2072
101. Wang H McKnight NC Zhang T Lu ML Balk SP Yuan X SOX9 is expressed in normal prostate basal cells and regulates androgen receptor expression in prostate cancer cells Cancer Res 2007, 67:528-536. 17234760 10.1158/ 0008-5472.CAN-06-1672
102. Drivdahl R Haugk KH Sprenger CC Nelson PS Tennant MK Plymate SR Suppression of growth and tumorigenicity in the prostate tumor cell line M12 by overexpression of the transcription factor SOX9 Oncogene 2004, 23:4584-4593. 15077158 10.1038/sj.onc.1207603
103. ExPASy-UniProt Knowledgebase: Swiss-Prot and TrEMBL http://ca.expasy.org/ sprot/
104. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Harris MA Hill DP Issel-Tarver L Kasarskis A Lewis S Matese JC Richardson JE Ringwald M Rubin GM Sherlock G Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nat Genet 2000, 25:25-29. 10802651 10.1038/75556
105. Dennis G Jr Sherman BT Hosack DA Yang J Gao W Lane HC Lempicki RA DAVID: Database for Annotation, Visualization, and Integrated Discovery Genome Biol 2003, 4:P3. 12734009 10.1186/gb-2003-4-5-p3