메뉴 건너뛰기




Volumn 5, Issue , 2015, Pages

Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: Prostate cancer as a case

Author keywords

[No Author keywords available]

Indexed keywords

TUMOR MARKER;

EID: 84939795842     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep13192     Document Type: Article
Times cited : (28)

References (55)
  • 1
    • 84934441807 scopus 로고    scopus 로고
    • Microarrays for cancer diagnosis and classification
    • Perez-Diez, A., Morgun, A., Shulzhenko, N. Microarrays for cancer diagnosis and classification. Adv Exp Med Biol 593, 74-85 (2007).
    • (2007) Adv Exp Med Biol , vol.593 , pp. 74-85
    • Perez-Diez, A.1    Morgun, A.2    Shulzhenko, N.3
  • 2
    • 33645825183 scopus 로고    scopus 로고
    • Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer
    • Ein-Dor, L., Zuk, O., Domany, E. Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci USA 103, 5923-5928 (2006).
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 5923-5928
    • Ein-Dor, L.1    Zuk, O.2    Domany, E.3
  • 4
    • 28544446695 scopus 로고    scopus 로고
    • Biomarkers in cancer staging, prognosis and treatment selection
    • Ludwig, J. A., Weinstein, J. N. Biomarkers in cancer staging, prognosis and treatment selection. Nat Rev Cancer 5, 845-856 (2005).
    • (2005) Nat Rev Cancer , vol.5 , pp. 845-856
    • Ludwig, J.A.1    Weinstein, J.N.2
  • 5
    • 60149091657 scopus 로고    scopus 로고
    • Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression
    • Sreekumar, A. et al. Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature 457, 910-914 (2009).
    • (2009) Nature , vol.457 , pp. 910-914
    • Sreekumar, A.1
  • 6
    • 18244409687 scopus 로고    scopus 로고
    • Gene expression profiling predicts clinical outcome of breast cancer
    • Van 't Veer, L. J.et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 415, 530-536 (2002).
    • (2002) Nature , vol.415 , pp. 530-536
    • Van 't Veer, L.J.1
  • 7
    • 33846978784 scopus 로고    scopus 로고
    • Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting
    • Dupuy, A., Simon, R. M. Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. J Natl Cancer Inst 99, 147-157 (2007).
    • (2007) J Natl Cancer Inst , vol.99 , pp. 147-157
    • Dupuy, A.1    Simon, R.M.2
  • 8
    • 13444249852 scopus 로고    scopus 로고
    • Prediction of cancer outcome with microarrays: A multiple random validation strategy
    • Michiels, S., Koscielny, S., Hill, C. Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet 365, 488-492 (2005).
    • (2005) Lancet , vol.365 , pp. 488-492
    • Michiels, S.1    Koscielny, S.2    Hill, C.3
  • 9
    • 63249117669 scopus 로고    scopus 로고
    • Screening for prostate cancer-the controversy that refuses to die
    • Barry, M. J. Screening for prostate cancer-the controversy that refuses to die. N Engl J Med 360, 1351-1354 (2009).
    • (2009) N Engl J Med , vol.360 , pp. 1351-1354
    • Barry, M.J.1
  • 10
    • 77953797905 scopus 로고    scopus 로고
    • Exploiting the determinants of stochastic gene expression in Saccharomyces cerevisiae for genome-wide prediction of expression noise
    • Li, J. et al. Exploiting the determinants of stochastic gene expression in Saccharomyces cerevisiae for genome-wide prediction of expression noise. Proc Natl Acad Sci USA 107, 10472-10477 (2010).
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 10472-10477
    • Li, J.1
  • 11
    • 84878997106 scopus 로고    scopus 로고
    • Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
    • Shalek, A. K. et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 498, 236-240 (2013).
    • (2013) Nature , vol.498 , pp. 236-240
    • Shalek, A.K.1
  • 13
    • 25444456388 scopus 로고    scopus 로고
    • Towards precise classification of cancers based on robust gene functional expression profiles
    • Guo, Z. et al. Towards precise classification of cancers based on robust gene functional expression profiles. BMC Bioinformatics 6, 58 (2005).
    • (2005) BMC Bioinformatics , vol.6 , pp. 58
    • Guo, Z.1
  • 14
    • 57149092133 scopus 로고    scopus 로고
    • Inferring pathway activity toward precise disease classification
    • Lee, E., Chuang, H. Y., Kim, J. W., Ideker, T., Lee, D. Inferring pathway activity toward precise disease classification. PLoS Comput Biol 4, e1000217 (2008).
    • (2008) PLoS Comput Biol , vol.4 , pp. e1000217
    • Lee, E.1    Chuang, H.Y.2    Kim, J.W.3    Ideker, T.4    Lee, D.5
  • 15
    • 77949524863 scopus 로고    scopus 로고
    • Accurate and reliable cancer classification based on probabilistic inference of pathway activity
    • Su, J., Yoon, B. J., Dougherty, E. R. Accurate and reliable cancer classification based on probabilistic inference of pathway activity. PLoS One 4, e8161 (2009).
    • (2009) PLoS One , vol.4 , pp. e8161
    • Su, J.1    Yoon, B.J.2    Dougherty, E.R.3
  • 16
    • 84863193521 scopus 로고    scopus 로고
    • Pathway-based classification of cancer subtypes
    • Kim, S., Kon, M., DeLisi, C. Pathway-based classification of cancer subtypes. Biol Direct 7, 21 (2012).
    • (2012) Biol Direct , vol.7 , pp. 21
    • Kim, S.1    Kon, M.2    DeLisi, C.3
  • 17
    • 5044245707 scopus 로고    scopus 로고
    • Gene co-expression network topology provides a framework for molecular characterization of cellular state
    • Carter, S. L., Brechbuhler, C. M., Griffin, M., Bond, A. T. Gene co-expression network topology provides a framework for molecular characterization of cellular state. Bioinformatics 20, 2242-2250 (2004).
    • (2004) Bioinformatics , vol.20 , pp. 2242-2250
    • Carter, S.L.1    Brechbuhler, C.M.2    Griffin, M.3    Bond, A.T.4
  • 18
    • 34247217200 scopus 로고    scopus 로고
    • Hubs in biological interaction networks exhibit low changes in expression in experimental asthma
    • Lu, X., Jain, V. V., Finn, P. W., Perkins, D. L. Hubs in biological interaction networks exhibit low changes in expression in experimental asthma. Mol Syst Biol 3, 98 (2007).
    • (2007) Mol Syst Biol , vol.3 , pp. 98
    • Lu, X.1    Jain, V.V.2    Finn, P.W.3    Perkins, D.L.4
  • 19
    • 53549123008 scopus 로고    scopus 로고
    • Nature nurture, or chance: Stochastic gene expression and its consequences
    • Raj, A., van Oudenaarden, A. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135, 216-226 (2008).
    • (2008) Cell , vol.135 , pp. 216-226
    • Raj, A.1    Van Oudenaarden, A.2
  • 20
    • 78049444975 scopus 로고    scopus 로고
    • Gene expression variability within and between human populations and implications toward disease susceptibility
    • Li, J., Liu, Y., Kim, T., Min, R., Zhang, Z. Gene expression variability within and between human populations and implications toward disease susceptibility. PLoS Comput Biol 6 (2010).
    • (2010) PLoS Comput Biol , vol.6
    • Li, J.1    Liu, Y.2    Kim, T.3    Min, R.4    Zhang, Z.5
  • 21
    • 84882589554 scopus 로고    scopus 로고
    • Topologically inferring risk-active pathways toward precise cancer classification by directed random walk
    • Liu, W. et al. Topologically inferring risk-active pathways toward precise cancer classification by directed random walk. Bioinformatics 29, 2169-2177 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 2169-2177
    • Liu, W.1
  • 22
    • 77954195272 scopus 로고    scopus 로고
    • Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
    • Vaske, C. J. et al. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics 26, i237-245 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 1237-1245
    • Vaske, C.J.1
  • 23
    • 84904993615 scopus 로고    scopus 로고
    • Identification of coregulators influenced by estrogen receptor subtype specific binding of the ER antagonists 4-hydroxytamoxifen and fulvestrant
    • Evers, N. M. et al. Identification of coregulators influenced by estrogen receptor subtype specific binding of the ER antagonists 4-hydroxytamoxifen and fulvestrant. Chem Biol Interact 220, 222-230 (2014).
    • (2014) Chem Biol Interact , vol.220 , pp. 222-230
    • Evers, N.M.1
  • 24
    • 26444546442 scopus 로고    scopus 로고
    • An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival
    • Miller, L. D. et al. An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci USA 102, 13550-13555 (2005).
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 13550-13555
    • Miller, L.D.1
  • 25
    • 85027951375 scopus 로고    scopus 로고
    • Association of CYP1A1 polymorphisms with prostate cancer risk: An updated meta-analysis
    • Li, H., Xiao, D., Hu, L., He, T. Association of CYP1A1 polymorphisms with prostate cancer risk: an updated meta-analysis. Mol Biol Rep 39, 10273-10284 (2012).
    • (2012) Mol Biol Rep , vol.39 , pp. 10273-10284
    • Li, H.1    Xiao, D.2    Hu, L.3    He, T.4
  • 26
    • 66549097871 scopus 로고    scopus 로고
    • CYP1A1 polymorphisms and risk of prostate cancer: A meta-analysis
    • Shaik, A. P., Jamil, K., Das, P. CYP1A1 polymorphisms and risk of prostate cancer: a meta-analysis. Urol J 6, 78-86 (2009).
    • (2009) Urol J , vol.6 , pp. 78-86
    • Shaik, A.P.1    Jamil, K.2    Das, P.3
  • 27
    • 32644470054 scopus 로고    scopus 로고
    • Polymorphisms of CYP1A1, GSTM1, GSTT1, and prostate cancer risk in Turkish population
    • Silig, Y. et al. Polymorphisms of CYP1A1, GSTM1, GSTT1, and prostate cancer risk in Turkish population. Cancer Invest 24, 41-45 (2006).
    • (2006) Cancer Invest , vol.24 , pp. 41-45
    • Silig, Y.1
  • 28
    • 0037491685 scopus 로고    scopus 로고
    • Polymorphisms in the CYP1A1 gene are associated with prostate cancer risk
    • Chang, B. L. et al. Polymorphisms in the CYP1A1 gene are associated with prostate cancer risk. Int J Cancer 106, 375-378 (2003).
    • (2003) Int J Cancer , vol.106 , pp. 375-378
    • Chang, B.L.1
  • 29
    • 84856454111 scopus 로고    scopus 로고
    • Tumour suppressors MIR-1 and MIR-133a target the oncogenic function of purine nucleoside phosphorylase (PNP) in prostate cancer
    • Kojima, S. et al. Tumour suppressors miR-1 and miR-133a target the oncogenic function of purine nucleoside phosphorylase (PNP) in prostate cancer. Br J Cancer 106, 405-413 (2012).
    • (2012) Br J Cancer , vol.106 , pp. 405-413
    • Kojima, S.1
  • 30
    • 0036935082 scopus 로고    scopus 로고
    • Polyamine levels of human colorectal adenocarcinomas are correlated with tumor stage and grade
    • Weiss, T. S. et al. Polyamine levels of human colorectal adenocarcinomas are correlated with tumor stage and grade. Int J Colorectal Dis 17, 381-387 (2002).
    • (2002) Int J Colorectal Dis , vol.17 , pp. 381-387
    • Weiss, T.S.1
  • 31
    • 0036339820 scopus 로고    scopus 로고
    • Prognostic value of tissue polyamine levels in human colorectal carcinoma
    • Linsalata, M. et al. Prognostic value of tissue polyamine levels in human colorectal carcinoma. Anticancer Res 22, 2465-2469 (2002).
    • (2002) Anticancer Res , vol.22 , pp. 2465-2469
    • Linsalata, M.1
  • 32
    • 80053643585 scopus 로고    scopus 로고
    • The mechanisms by which polyamines accelerate tumor spread
    • Soda, K. The mechanisms by which polyamines accelerate tumor spread. J Exp Clin Cancer Res 30, 95 (2011).
    • (2011) J Exp Clin Cancer Res , vol.30 , pp. 95
    • Soda, K.1
  • 33
    • 33644820339 scopus 로고    scopus 로고
    • Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis
    • Phillips, H. S. et al. Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. Cancer Cell 9, 157-173 (2006).
    • (2006) Cancer Cell , vol.9 , pp. 157-173
    • Phillips, H.S.1
  • 34
    • 8444231965 scopus 로고    scopus 로고
    • The influence of androgen deprivation therapy on dihydrotestosterone levels in the prostatic tissue of patients with prostate cancer
    • Nishiyama, T., Hashimoto, Y., Takahashi, K. The influence of androgen deprivation therapy on dihydrotestosterone levels in the prostatic tissue of patients with prostate cancer. Clin Cancer Res 10, 7121-7126 (2004).
    • (2004) Clin Cancer Res , vol.10 , pp. 7121-7126
    • Nishiyama, T.1    Hashimoto, Y.2    Takahashi, K.3
  • 35
    • 34548383053 scopus 로고    scopus 로고
    • The change in the dihydrotestosterone level in the prostate before and after androgen deprivation therapy in connection with prostate cancer aggressiveness using the Gleason score
    • Discussion 1288-1289
    • Nishiyama, T., Ikarashi, T., Hashimoto, Y., Wako, K., Takahashi, K. The change in the dihydrotestosterone level in the prostate before and after androgen deprivation therapy in connection with prostate cancer aggressiveness using the Gleason score. J Urol 178, 1282-1288; discussion 1288-1289 (2007).
    • (2007) J Urol , vol.178 , pp. 1282-1288
    • Nishiyama, T.1    Ikarashi, T.2    Hashimoto, Y.3    Wako, K.4    Takahashi, K.5
  • 36
    • 4644313275 scopus 로고    scopus 로고
    • Gene expression profiling of gliomas strongly predicts survival
    • Freije, W. A. et al. Gene expression profiling of gliomas strongly predicts survival. Cancer Res 64, 6503-6510 (2004).
    • (2004) Cancer Res , vol.64 , pp. 6503-6510
    • Freije, W.A.1
  • 37
    • 34447632167 scopus 로고    scopus 로고
    • Gene expression profiling spares early breast cancer patients from adjuvant therapy: Derived and validated in two population-based cohorts
    • Pawitan, Y. et al. Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res 7, R953-964 (2005).
    • (2005) Breast Cancer Res , vol.7 , pp. R953-964
    • Pawitan, Y.1
  • 39
    • 84901199835 scopus 로고    scopus 로고
    • Steroid hormone synthetic pathways in prostate cancer
    • Mostaghel, E. A. Steroid hormone synthetic pathways in prostate cancer. Translational Andrology and Urology 2, 212-227 (2013).
    • (2013) Translational Andrology and Urology , vol.2 , pp. 212-227
    • Mostaghel, E.A.1
  • 40
    • 0035300409 scopus 로고    scopus 로고
    • Androgen receptor stabilization in recurrent prostate cancer is associated with hypersensitivity to low androgen
    • Gregory, C. W., Johnson, R. T., Jr., Mohler, J. L., French, F. S., Wilson, E. M. Androgen receptor stabilization in recurrent prostate cancer is associated with hypersensitivity to low androgen. Cancer Res 61, 2892-2898 (2001).
    • (2001) Cancer Res , vol.61 , pp. 2892-2898
    • Gregory, C.W.1    Johnson, R.T.2    Mohler, J.L.3    French, F.S.4    Wilson, E.M.5
  • 41
    • 0036604401 scopus 로고    scopus 로고
    • Identification of differentially expressed genes associated with androgen-independent growth of prostate cancer
    • Mohler, J. L. et al. Identification of differentially expressed genes associated with androgen-independent growth of prostate cancer. Prostate 51, 247-255 (2002).
    • (2002) Prostate , vol.51 , pp. 247-255
    • Mohler, J.L.1
  • 42
    • 77954909020 scopus 로고    scopus 로고
    • 3beta-hydroxysteroid dehydrogenase is a possible pharmacological target in the treatment of castration-resistant prostate cancer
    • Evaul, K., Li, R., Papari-Zareei, M., Auchus, R. J., Sharifi, N. 3beta-hydroxysteroid dehydrogenase is a possible pharmacological target in the treatment of castration-resistant prostate cancer. Endocrinology 151, 3514-3520 (2010).
    • (2010) Endocrinology , vol.151 , pp. 3514-3520
    • Evaul, K.1    Li, R.2    Papari-Zareei, M.3    Auchus, R.J.4    Sharifi, N.5
  • 43
    • 41549139527 scopus 로고    scopus 로고
    • Walking the interactome for prioritization of candidate disease genes
    • Kohler, S., Bauer, S., Horn, D., Robinson, P. N. Walking the interactome for prioritization of candidate disease genes. Am J Hum Genet 82, 949-958 (2008).
    • (2008) Am J Hum Genet , vol.82 , pp. 949-958
    • Kohler, S.1    Bauer, S.2    Horn, D.3    Robinson, P.N.4
  • 44
    • 75149162979 scopus 로고    scopus 로고
    • Integration of multiple data sources to prioritize candidate genes using discounted rating system
    • Li, Y., Patra, J. C. Integration of multiple data sources to prioritize candidate genes using discounted rating system. BMC Bioinformatics 11 Suppl 1, S20 (2010).
    • (2010) BMC Bioinformatics , vol.11 , pp. S20
    • Li, Y.1    Patra, J.C.2
  • 45
    • 34548400259 scopus 로고    scopus 로고
    • A systems biology approach for pathway level analysis
    • Draghici, S. et al. A systems biology approach for pathway level analysis. Genome Res 17, 1537-1545 (2007).
    • (2007) Genome Res , vol.17 , pp. 1537-1545
    • Draghici, S.1
  • 46
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher, V. G., Tibshirani, R., Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98, 5116-5121 (2001).
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 47
    • 35348891430 scopus 로고    scopus 로고
    • Network-based classification of breast cancer metastasis
    • Chuang, H. Y., Lee, E., Liu, Y. T., Lee, D., Ideker, T. Network-based classification of breast cancer metastasis. Mol Syst Biol 3, 140 (2007).
    • (2007) Mol Syst Biol , vol.3 , pp. 140
    • Chuang, H.Y.1    Lee, E.2    Liu, Y.T.3    Lee, D.4    Ideker, T.5
  • 48
    • 84860696573 scopus 로고    scopus 로고
    • Pathway-directed weighted testing procedures for the integrative analysis of gene expression and metabolomic data
    • Poisson, L. M., Sreekumar, A., Chinnaiyan, A. M., Ghosh, D. Pathway-directed weighted testing procedures for the integrative analysis of gene expression and metabolomic data. Genomics 99, 265-274 (2012).
    • (2012) Genomics , vol.99 , pp. 265-274
    • Poisson, L.M.1    Sreekumar, A.2    Chinnaiyan, A.M.3    Ghosh, D.4
  • 49
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • Edgar, R., Domrachev, M., Lash, A. E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30, 207-210 (2002).
    • (2002) Nucleic Acids Res , vol.30 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 50
    • 27644506613 scopus 로고    scopus 로고
    • Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression
    • Varambally, S. et al. Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer Cell 8, 393-406 (2005).
    • (2005) Cancer Cell , vol.8 , pp. 393-406
    • Varambally, S.1
  • 51
    • 84863723010 scopus 로고    scopus 로고
    • The mutational landscape of lethal castration-resistant prostate cancer
    • Grasso, C. S. et al. The mutational landscape of lethal castration-resistant prostate cancer. Nature 487, 239-243 (2012).
    • (2012) Nature , vol.487 , pp. 239-243
    • Grasso, C.S.1
  • 52
    • 84874598190 scopus 로고    scopus 로고
    • ERG induces androgen receptor-mediated regulation of SOX9 in prostate cancer
    • Cai, C. et al. ERG induces androgen receptor-mediated regulation of SOX9 in prostate cancer. J Clin Invest 123, 1109-1122 (2013).
    • (2013) J Clin Invest , vol.123 , pp. 1109-1122
    • Cai, C.1
  • 53
    • 71049148804 scopus 로고    scopus 로고
    • SubpathwayMiner: A software package for flexible identification of pathways
    • Li, C. et al. SubpathwayMiner: a software package for flexible identification of pathways. Nucleic Acids Res 37, e131 (2009).
    • (2009) Nucleic Acids Res , vol.37 , pp. e131
    • Li, C.1
  • 54
    • 79959575935 scopus 로고    scopus 로고
    • Leaders in Social Networks, the Delicious Case
    • Lu L., Zhang, Y.-C., Yeung, C. H., Zhou, T. Leaders in Social Networks, the Delicious Case. PLoS One 6, e21202 (2011).
    • (2011) PLoS One , vol.6 , pp. e21202
    • Lu, L.1    Zhang, Y.-C.2    Yeung, C.H.3    Zhou, T.4
  • 55
    • 84855890503 scopus 로고    scopus 로고
    • 3rd Core module biomarker identification with network exploration for breast cancer metastasis
    • Yang, R., Daigle, B. J., Jr., Petzold, L. R., Doyle, F. J., 3rd. Core module biomarker identification with network exploration for breast cancer metastasis. BMC Bioinformatics 13, 12 (2012).
    • (2012) BMC Bioinformatics , vol.13 , pp. 12
    • Yang, R.1    Daigle, B.J.2    Petzold, L.R.3    Doyle, F.J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.