Detecting cancer outlier genes with potential rearrangement using gene expression data and biological networks

Advances in Bioinformatics

Volumn 2012, Issue , 2012, Pages

  Alshalalfa, Mohammed ^a   Bismar, Tarek A ^b   Alhajj, Reda ^a  

^a UNIVERSITY OF CALGARY   (Canada)

^b UNIVERSITY OF CALGARY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84864914160     PISSN: 16878027     EISSN: 16878035     Source Type: Journal    
DOI: 10.1155/2012/373506     Document Type: Article

References (26)

1. de Klein A., van Kessel A. G., Grosveld G., A celllular oncogene is translocated to the Philadelphia chromosome in chronic myelocytic leukaemia Nature 1982 300 5894 765 767 (Pubitemid 13224358)
2. Soda M., Choi Y. L., Enomoto M., Takada S., Yamashita Y., Ishikawa S., Fujiwara S. I., Watanabe H., Kurashina K., Hatanaka H., Bando M., Ohno S., Ishikawa Y., Aburatani H., Niki T., Sohara Y., Sugiyama Y., Mano H., Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer Nature 2007 448 7153 561 566 (Pubitemid 47206930)
3. Kumar-Sinha C., Tomlins S. A., Chinnaiyan A. M., Recurrent gene fusions in prostate cancer Nature Reviews Cancer 2008 8 7 497 511
4. Squire J. A., TMPRSS2-ERG and PTEN loss in prostate cancer Nature Genetics 2009 41 5 509 510
5. Berger M. F., Lawrence M. S., Demichelis F., The genome complexity of primary human prostate cancer Nature 2011 470 214 220
6. Skotheim R. I., Thomassen G. O. S., Eken M., Lind G. E., Micci F., Ribeiro F. R., Cerveira N., Teixeira M. R., Heim S., Rognes T., Lothe R. A., A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis Molecular Cancer 2009 8 1 2
7. Edgren H., Murumagi A., Kangaspeska S., Nicorici D., Hongisto V., Kleivi K., Rye I. H., Nyberg S., Wolf M., Borresen-Dale A. L., Kallioniemi O., Identification of fusion genes in breast cancer by paired-end RNA-sequencing Genome Biology 2011 12 1, article R6
8. Hu Y., Wang K., He X., Chiang D. Y., Prins J. F., Liu J., A probabilistic framework for aligning paired-end RNA-seq data Bioinformatics 2010 26 16 1950 1957
9. Wang K., Singh D., Zeng Z., Coleman S. J., Huang Y., Savich G. L., He X., Mieczkowski P., Grimm S. A., Perou C. M., MacLeod J. N., Chiang D. Y., Prins J. F., Liu J., MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery Nucleic Acids Research 2010 38 18, article e178
10. McPherson A., Hormozdiari F., Zayed A., Giuliany R., Ha G., Sun M. G. F., Griffith M., Moussavi A., Senz J., Melnyk N., Pacheco M., Marra M. A., Hirst M., Nielsen T. O., Sahinalp S. C., Huntsman D., Shah S. P., Defuse: An algorithm for gene fusion discovery in tumor rna-seq data PLoS Computational Biology 2011 7 5
11. Rubin M. A., Chinnaiyan A. M., Bioinformatics approach leads to the discovery of the TMPRSS2:ETS gene fusion in prostate cancer Laboratory Investigation 2006 86 11 1099 1102 (Pubitemid 44624146)
12. Baolin W. U., Cancer outlier differential gene expression detection Biostatistics 2007 8 3 566 575
13. Li L., Chaudhuri A., Chant J., Tang Z., PADGE: Analysis of heterogeneous patterns of differential gene expression Physiological Genomics 2007 32 1 154 159
14. Tomlins S. A., Rhodes D. R., Perner S., Dhanasekaran S. M., Mehra R., Sun X. W., Varambally S., Cao X., Tchinda J., Kuefer R., Lee C., Montie J. E., Shah R. B., Pienta K. J., Rubin M. A., Chinnaiyan A. M., Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer Science 2005 310 5748 644 648 (Pubitemid 41528150)
15. Tibshirani R., Hastie T., Outlier sums for differential gene expression analysis Biostatistics 2007 8 1 2 8 (Pubitemid 44906100)
16. Mpindi J. P., Sara H., Haapa-Paananen S., Kilpinen S., Pisto T., Bucher E., Ojala K., Iljin K., Vainio P., Bjrkman M., Gupta S., Kohonen P., Nees M., Kallioniemi O., Gti: A novel algorithm for identifying outlier gene expression profiles from integrated microarray datasets PLoS ONE 2011 6 2
17. Wu G., Feng X., Stein L., A human functional protein interaction network and its application to cancer data analysis Genome Biology 2010 11 5, article R53
18. Singh D., Febbo P. G., Ross K., Jackson D. G., Manola J., Ladd C., Tamayo P., Renshaw A. A., D'Amico A. V., Richie J. P., Lander E. S., Loda M., Kantoff P. W., Golub T. R., Sellers W. R., Gene expression correlates of clinical prostate cancer behavior Cancer Cell 2002 1 2 203 209 (Pubitemid 41039166)
19. Tylor B., Schultz N., Hieronyymus H., Gerald W., Integrative genomic profiling of human prostate cancer Cancer Cell 2010 18 1 12
20. Darnel A. D., LaFargue C. J., Vollmer R. T., Corcos J., Bismar T. A., TMPRSS2-ERG fusion is frequently observed in gleason pattern 3 prostate cancer in a canadian cohort Cancer Biology and Therapy 2009 8 2 125 130
21. Tomlins S. A., Rhodes D. R., Yu J., Varambally S., Mehra R., Perner S., Demichelis F., Helgeson B. E., Laxman B., Morris D. S., Cao Q., Cao X., Andrén O., Fall K., Johnson L., Wei J. T., Shah R. B., Al-Ahmadie H., Eastham J. A., Eggener S. E., Fine S. W., Hotakainen K., Stenman U. H., Tsodikov A., Gerald W. L., Lilja H., Reuter V. E., Kantoff P. W., Scardino P. T., Rubin M. A., Bjartell A. S., Chinnaiyan A. M., The role of SPINK1 in ETS rearrangement-negative prostate cancers Cancer Cell 2008 13 6 519 528 (Pubitemid 351763901)
22. Setlur S. R., Mertz K. D., Hoshida Y., Demichelis F., Lupien M., Perner S., Sboner A., Pawitan Y., Andrén O., Johnson L. A., Tang J., Adami H. O., Calza S., Chinnaiyan A. M., Rhodes D., Tomlins S., Fall K., Mucci L. A., Kantoff P. W., Stampfer M. J., Andersson S. O., Varenhorst E., Johansson J. E., Brown M., Golub T. R., Rubin M. A., Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer Journal of the National Cancer Institute 2008 100 11 815 825 (Pubitemid 351809667)
23. Momand J., Wu H. H., Dasgupta G., MDM2master regulator of the p53 tumor suppressor protein Gene 2000 242 1-2 15 29 (Pubitemid 30064488)
24. Myatt S. S., Lam E. W. F., The emerging roles of forkhead box (Fox) proteins in cancer Nature Reviews Cancer 2007 7 11 847 859 (Pubitemid 350006253)
25. Maeda H., Nagata S., Wolfgang C. D., Bratthauer G. L., Bera T. K., Pastan I., The T cell receptor chain alternate reading frame protein (TARP), a prostate-specific protein localized in mitochondria Journal of Biological Chemistry 2004 279 23 24561 24568 (Pubitemid 38725322)
26. Morgan E. A., Forootan S. S., Adamson J., Foster C. S., Fujii H., Igarashi M., Beesley C., Smith P. H., Ke Y., Expression of cutaneous fatty acid-binding protein (C-FABP) in prostate cancer: potential prognostic marker and target for tumourigenicity-suppression International Journal of Oncology 2008 32 4 767 775 (Pubitemid 351780587)