MicroRNA expression analysis reveals significant biological pathways in human prostate cancer

2011 IEEE International Conference on Systems Biology, ISB 2011

Volumn , Issue , 2011, Pages 203-210

  Tang, Yifei ^a   Chen, Jiajia ^a   Luo, Cheng ^b   Kaipia, Antti ^c   Shen, Bairong ^a  

^a SOOCHOW UNIVERSITY   (China)

^b SHANGHAI INSTITUTE OF MATERIA MEDICA   (China)

^c TAMPERE UNIVERSITY HOSPITAL   (Finland)

Author keywords

GeneGO's database; Meta analysis; microRNA expression; pathway enrichment

Indexed keywords

BIOLOGICAL PATHWAYS; CANCER RESEARCH; DATA SETS; EXPRESSION PROFILE; GENE LEVELS; GENE ONTOLOGY; GENEGO'S DATABASE; HUMAN PROSTATE CANCER; META-ANALYSIS; MICROARRAY EXPERIMENTS; MICROARRAY EXPRESSIONS; MICROARRAY TECHNOLOGIES; MICRORNA EXPRESSION; MICRORNAS; OUTLIER DETECTION; PATHWAY ENRICHMENT; PROSTATE CANCERS;

BIOINFORMATICS; DATABASE SYSTEMS; GENE EXPRESSION; ONCOGENIC VIRUSES; ONTOLOGY; STATISTICS;

DISEASES;

EID: 80054863692     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ISB.2011.6033156     Document Type: Conference Paper

References (39)

1. D. P. Bartel, "MicroRNAs: target recognition and regulatory functions", Cell, vol. 136, (no. 2), pp. 215-33, Jan 23 2009.
2. A. Kozomara and S. Griffiths-Jones, "miRBase: integrating microRNA annotation and deep-sequencing data", Nucleic Acids Res, vol. 39, (no. Database issue), pp. D152-7, Jan 2010.
3. S. L. Lin, D. C. Chang, S. Y. Ying, D. Leu, and D. T. Wu, "MicroRNA miR-302 inhibits the tumorigenecity of human pluripotent stem cells by coordinate suppression of the CDK2 and CDK4/6 cell cycle pathways", Cancer Res, vol. 70, (no. 22), pp. 9473-82, Nov. 15 2010.
4. C. Liu, K. Kelnar, B. Liu, X. Chen, T. Calhoun-Davis, H. Li, L. Patrawala, H. Yan, C. Jeter, S. Honorio, J. F. Wiggins, A. G. Bader, R. Fagin, D. Brown, and D. G. Tang, "The microRNA miR-34a inhibits prostate cancer stem cells and metastasis by directly repressing CD44", Nat Med, vol. 17, (no. 2), pp. 211-5, Feb. 2011.
5. B. Mallick, J. Chakrabarti, and Z. Ghosh, "MicroRNA reins in embryonic and cancer stem cells", RNA Biol, vol. 8, (no. 3), May 1 2011.
6. D. R. Rhodes, T. R. Barrette, M. A. Rubin, D. Ghosh, and A. M. Chinnaiyan, "Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer", Cancer Res, vol. 62, (no. 15), pp. 4427-33, Aug. 1 2002.
7. P. Cahan, F. Rovegno, D. Mooney, J. C. Newman, G. St Laurent, 3rd, and T. A. McCaffrey, "Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization", Gene, vol. 401, (no. 1-2), pp. 12-8, Oct. 15 2007.
8. L. Ein-Dor, I. Kela, G. Getz, D. Givol, and E. Domany, "Outcome signature genes in breast cancer: is there a unique set", Bioinformatics, vol. 21, (no. 2), pp. 171-8, Jan 15 2005.
9. S. Michiels, S. Koscielny, and C. Hill, "Prediction of cancer outcome with microarrays: a multiple random validation strategy", Lancet, vol. 365, (no. 9458), pp. 488-92, Feb. 5-11 2005.
10. J. E. Korkola, E. Blaveri, S. DeVries, D. H. Moore, 2nd, E. S. Hwang, Y. Y. Chen, A. L. Estep, K. L. Chew, R. H. Jensen, and F. M. Waldman, "Identification of a robust gene signature that predicts breast cancer outcome in independent data sets", BMC Cancer, vol. 7, pp. 61, 2007.
11. Y. Wang, J. Chen, Q. Li, H. Wang, G. Liu, Q. Jing, and B. Shen, "Identifying novel prostate cancer associated pathways based on integrative microarray data analysis", Computational Biology and Chemistry, vol. In Press, Accepted Manuscript, 2011.
12. H. Lian, "MOST: detecting cancer differential gene expression", Biostatistics, vol. 9, (no. 3), pp. 411-8, Jul. 2008.
13. S. A. Tomlins, D. R. Rhodes, S. Perner, S. M. Dhanasekaran, R. Mehra, X. W. Sun, S. Varambally, X. Cao, J. Tchinda, R. Kuefer, C. Lee, J. E. Montie, R. B. Shah, K. J. Pienta, M. A. Rubin, and A. M. Chinnaiyan, "Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer", Science, vol. 310, (no. 5748), pp. 644-8, Oct. 28 2005.
14. Y. Wang and R. Rekaya, "LSOSS: Detection of Cancer Outlier Differential Gene Expression", Biomark Insights, vol. 5, pp. 69-78, 2010.
15. J. W. MacDonald and D. Ghosh, "COPA-cancer outlier profile analysis", Bioinformatics, vol. 22, (no. 23), pp. 2950-1, Dec. 1 2006.
16. B. Wu, "Cancer outlier differential gene expression detection", Biostatistics, vol. 8, (no. 3), pp. 566-75, Jul. 2007.
17. R. Tibshirani and T. Hastie, "Outlier sums for differential gene expression analysis", Biostatistics, vol. 8, (no. 1), pp. 2-8, Jan 2007.
18. M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler, J. M. Cherry, A. P. Davis, K. Dolinski, S. S. Dwight, J. T. Eppig, M. A. Harris, D. P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J. C. Matese, J. E. Richardson, M. Ringwald, G. M. Rubin, and G. Sherlock, "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium", Nat Genet, vol. 25, (no. 1), pp. 25-9, May 2000.
19. M. Kanehisa, M. Araki, S. Goto, M. Hattori, M. Hirakawa, M. Itoh, T. Katayama, S. Kawashima, S. Okuda, T. Tokimatsu, and Y. Yamanishi, "KEGG for linking genomes to life and the environment", Nucleic Acids Res, vol. 36, (no. Database issue), pp. D480-4, Jan 2008.
20. M. Kanehisa, S. Goto, M. Furumichi, M. Tanabe, and M. Hirakawa, "KEGG for representation and analysis of molecular networks involving diseases and drugs", Nucleic Acids Res, vol. 38, (no. Database issue), pp. D355-60, Jan 2010.
21. G. Kharaishvili, D. Simkova, E. Makharoblidze, K. Trtkova, Z. Kolar, and J. Bouchal, "Wnt signaling in prostate development and carcinogenesis" , Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub, vol. 155, (no. 1), pp. 11-8, Mar. 2011.
22. E. C. Chu and A. S. Tarnawski, "PTEN regulatory functions in tumor suppression and cell biology", Med Sci Monit, vol. 10, (no. 10), pp. RA235-41, Oct. 2004.
23. C. Gennigens, C. Menetrier-Caux, and J. P. Droz, "Insulin-Like Growth Factor (IGF) family and prostate cancer", Crit Rev Oncol Hematol, vol. 58, (no. 2), pp. 124-45, May 2006.
24. I. C. Sroka, K. McDaniel, R. B. Nagle, and G. T. Bowden, "Differential localization of MT1-MMP in human prostate cancer tissue: role of IGF-1R in MT1-MMP expression", Prostate, vol. 68, (no. 5), pp. 463-76, Apr. 1 2008.
25. J. Mathieu, Z. Zhang, W. Zhou, A. J. Wang, J. M. Heddleston, C. M. Pinna, A. Hubaud, B. Stadler, M. Choi, M. Bar, M. Tewari, A. Liu, R. Vessella, R. Rostomily, D. Born, M. Horwitz, C. Ware, C. A. Blau, M. A. Cleary, J. N. Rich, and H. Ruohola-Baker, "HIF Induces Human Embryonic Stem Cell Markers in Cancer Cells", Cancer Res, vol. 71, (no. 13), pp. 4640-52, Jul. 1 2011.
26. J. Shin, H. J. Lee, D. B. Jung, J. H. Jung, E. O. Lee, S. G. Lee, B. S. Shim, S. H. Choi, S. G. Ko, K. S. Ahn, S. J. Jeong, and S. H. Kim, "Suppression of STAT3 and HIF-1 Alpha Mediates Anti-Angiogenic Activity of Betulinic Acid in Hypoxic PC-3 Prostate Cancer Cells", PLoS One, vol. 6, (no. 6), pp. e21492, 2011.
27. M. Wartenberg, M. Schallenberg, J. Hescheler, and H. Sauer, "Reactive oxygen species-mediated regulation of eNOS and iNOS expression in multicellular prostate tumor spheroids", Int J Cancer, vol. 104, (no. 3), pp. 274-82, Apr. 10 2003.
28. B. Cancilla, R. A. Jarred, H. Wang, S. L. Mellor, G. R. Cunha, and G. P. Risbridger, "Regulation of prostate branching morphogenesis by activin A and follistatin", Dev Biol, vol. 237, (no. 1), pp. 145-58, Sep. 1 2001.
29. H. Y. Kang, H. Y. Huang, C. Y. Hsieh, C. F. Li, C. R. Shyr, M. Y. Tsai, C. Chang, Y. C. Chuang, and K. E. Huang, "Activin A enhances prostate cancer cell migration through activation of androgen receptor and is overexpressed in metastatic prostate cancer", J Bone Miner Res, vol. 24, (no. 7), pp. 1180-93, Jul. 2009.
30. L. Wang, X. Zou, A. D. Berger, C. Twiss, Y. Peng, Y. Li, J. Chiu, H. Guo, J. Satagopan, A. Wilton, W. Gerald, R. Basch, Z. Wang, I. Osman, and P. Lee, "Increased expression of histone deacetylaces (HDACs) and inhibition of prostate cancer growth and invasion by HDAC inhibitor SAHA", Am J Transl Res, vol. 1, (no. 1), pp. 62-71, 2009.
31. C. Camacho, G. Coulouris, V. Avagyan, N. Ma, J. Papadopoulos, K. Bealer, and T. L. Madden, "BLAST+: architecture and applications", BMC Bioinformatics, vol. 10, pp. 421, 2009.
32. B. John, A. J. Enright, A. Aravin, T. Tuschl, C. Sander, and D. S. Marks, "Human MicroRNA targets", PLoS Biol, vol. 2, (no. 11), pp. e363, Nov. 2004.
33. M. Rehmsmeier, P. Steffen, M. Hochsmann, and R. Giegerich, "Fast and effective prediction of microRNA/target duplexes", RNA, vol. 10, (no. 10), pp. 1507-17, Oct. 2004.
34. M. Sturm, M. Hackenberg, D. Langenberger, and D. Frishman, "TargetSpy: a supervised machine learning approach for microRNA target prediction", BMC Bioinformatics, vol. 11, pp. 292, 2010.
35. J. M. Brockman, P. Singh, D. Liu, S. Quinlan, J. Salisbury, and J. H. Graber, "PACdb: PolyA Cleavage Site and 3'-UTR Database", Bioinformatics, vol. 21, (no. 18), pp. 3691-3, Sep. 15 2005.
36. S. Ambs, R. L. Prueitt, M. Yi, R. S. Hudson, T. M. Howe, F. Petrocca, T. A. Wallace, C. G. Liu, S. Volinia, G. A. Calin, H. G. Yfantis, R. M. Stephens, and C. M. Croce, "Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer", Cancer Res, vol. 68, (no. 15), pp. 6162-70, Aug. 1 2008.
37. A. Schaefer, M. Jung, H. J. Mollenkopf, I. Wagner, C. Stephan, F. Jentzmik, K. Miller, M. Lein, G. Kristiansen, and K. Jung, "Diagnostic and prognostic implications of microRNA profiling in prostate carcinoma", Int J Cancer, vol. 126, (no. 5), pp. 1166-76, Mar. 1 2010.
38. B. S. Taylor, N. Schultz, H. Hieronymus, A. Gopalan, Y. Xiao, B. S. Carver, V. K. Arora, P. Kaushik, E. Cerami, B. Reva, Y. Antipin, N. Mitsiades, T. Landers, I. Dolgalev, J. E. Major, M. Wilson, N. D. Socci, A. E. Lash, A. Heguy, J. A. Eastham, H. I. Scher, V. E. Reuter, P. T. Scardino, C. Sander, C. L. Sawyers, and W. L. Gerald, "Integrative genomic profiling of human prostate cancer", Cancer Cell, vol. 18, (no. 1), pp. 11-22, Jul. 13 2010.
39. S. Wach, E. Nolte, J. Szczyrba, R. Stohr, A. Hartmann, T. Orntoft, L. Dyrskjot, E. Eltze, W. Wieland, B. Keck, A. B. Ekici, F. Grasser, and B. Wullich, "MiRNA profiles of prostate carcinoma detected by multi-platform miRNA screening", Int J Cancer, Mar. 11 2011.