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Volumn 11, Issue 19, 2011, Pages 3845-3852

Identifying differentially expressed genes in cancer patients using a non-parameter Ising model

Author keywords

Bioinformatics; Differentially expressed genes; Ising model; Microarray; Protein interaction network

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; BREAST CANCER; CANCER PATIENT; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; HUMAN; MICROARRAY ANALYSIS; NON PARAMETER ISING MODEL; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SENSITIVITY AND SPECIFICITY; SIMULATION;

EID: 80053027482     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201100180     Document Type: Article
Times cited : (4)

References (42)
  • 1
    • 0034948896 scopus 로고    scopus 로고
    • A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes
    • Baldi, P., Long, A. D., A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 2001, 17, 509-519.
    • (2001) Bioinformatics , vol.17 , pp. 509-519
    • Baldi, P.1    Long, A.D.2
  • 2
    • 0037433040 scopus 로고    scopus 로고
    • Identifying differentially expressed genes using false discovery rate controlling procedures
    • Reiner, A., Yekutieli, D., Benjamini, Y., Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 2003, 19, 368-375.
    • (2003) Bioinformatics , vol.19 , pp. 368-375
    • Reiner, A.1    Yekutieli, D.2    Benjamini, Y.3
  • 3
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genome-wide studies
    • Storey, J. D., Tibshirani, R., Statistical significance for genome-wide studies. Proc. Natl. Acad. Sci. USA 2003, 100, 9440-9445.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 4
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S. et al., Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 2005, 102, 15545-15550.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 15545-15550
    • Subramanian, A.1    Tamayo, P.2    Mootha, V.K.3    Mukherjee, S.4
  • 5
  • 6
    • 34547844074 scopus 로고    scopus 로고
    • A Markov random field model for network-based analysis of genomic data
    • Wei, Z., Li, H., A Markov random field model for network-based analysis of genomic data. Bioinformatics 2007, 23, 1537-1544.
    • (2007) Bioinformatics , vol.23 , pp. 1537-1544
    • Wei, Z.1    Li, H.2
  • 7
    • 33947716431 scopus 로고
    • Beitrag zur Theorie des Ferromagnetismus
    • Ising, E., Beitrag zur Theorie des Ferromagnetismus. Z. Phys. A Hadrons Nucl. 1925, 31, 253-258.
    • (1925) Z. Phys. A Hadrons Nucl. , vol.31 , pp. 253-258
    • Ising, E.1
  • 8
    • 0034822166 scopus 로고    scopus 로고
    • The Ising model in physics and statistical genetics
    • Majewski, J., Li, H., Ott, J., The Ising model in physics and statistical genetics. Am. J. Hum. Genet. 2001, 69, 853-862.
    • (2001) Am. J. Hum. Genet. , vol.69 , pp. 853-862
    • Majewski, J.1    Li, H.2    Ott, J.3
  • 9
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa, M., Goto, S., KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28, 27-30.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 10
    • 0034923013 scopus 로고    scopus 로고
    • On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data
    • Newton, M. A., Kendziorski, C. M., Richmond, C. S., Blattner, F. R., Tsui, K. W., On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J. Comput. Biol. 2001, 8, 37-52.
    • (2001) J. Comput. Biol. , vol.8 , pp. 37-52
    • Newton, M.A.1    Kendziorski, C.M.2    Richmond, C.S.3    Blattner, F.R.4    Tsui, K.W.5
  • 11
  • 12
    • 13844310310 scopus 로고    scopus 로고
    • Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer
    • Wang, Y., Klijn, J. G., Zhang, Y., Sieuwerts, A. M. et al., Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 2005, 365, 671-679.
    • (2005) Lancet , vol.365 , pp. 671-679
    • Wang, Y.1    Klijn, J.G.2    Zhang, Y.3    Sieuwerts, A.M.4
  • 13
    • 42249100669 scopus 로고    scopus 로고
    • Disrupted expression of CXCL5 in colorectal cancer is associated with rapid tumor formation in rats and poor prognosis in patients
    • Speetjens, F. M., Kuppen, P. J., Sandel, M. H., Menon, A. G. et al., Disrupted expression of CXCL5 in colorectal cancer is associated with rapid tumor formation in rats and poor prognosis in patients. Clin. Cancer Res. 2008, 14, 2276-2284.
    • (2008) Clin. Cancer Res. , vol.14 , pp. 2276-2284
    • Speetjens, F.M.1    Kuppen, P.J.2    Sandel, M.H.3    Menon, A.G.4
  • 14
    • 0034618408 scopus 로고    scopus 로고
    • Human breast carcinoma desmoplasia is PDGF initiated
    • Shao, Z. M., Nguyen, M., Barsky, S. H., Human breast carcinoma desmoplasia is PDGF initiated. Oncogene 2000, 19, 4337-4345.
    • (2000) Oncogene , vol.19 , pp. 4337-4345
    • Shao, Z.M.1    Nguyen, M.2    Barsky, S.H.3
  • 15
    • 0346122895 scopus 로고    scopus 로고
    • Targeted expression of HGF/SF in mouse mammary epithelium leads to metastatic adenosquamous carcinomas through the activation of multiple signal transduction pathways
    • Gallego, M. I., Bierie, B., Hennighausen, L., Targeted expression of HGF/SF in mouse mammary epithelium leads to metastatic adenosquamous carcinomas through the activation of multiple signal transduction pathways. Oncogene 2005, 22, 8498-8508.
    • (2005) Oncogene , vol.22 , pp. 8498-8508
    • Gallego, M.I.1    Bierie, B.2    Hennighausen, L.3
  • 17
    • 17744412020 scopus 로고    scopus 로고
    • The expression and localization of fibroblast growth factor-1 (FGF-1) and FGF receptor-1 (FGFR-1) in human breast cancer
    • Yoshimura, N., Sano, H., Hashiramoto, A., Yamada, R. et al., The expression and localization of fibroblast growth factor-1 (FGF-1) and FGF receptor-1 (FGFR-1) in human breast cancer. Clin. Immunol. Immunopathol. 1998, 89, 28-34.
    • (1998) Clin. Immunol. Immunopathol. , vol.89 , pp. 28-34
    • Yoshimura, N.1    Sano, H.2    Hashiramoto, A.3    Yamada, R.4
  • 18
    • 0034469902 scopus 로고    scopus 로고
    • Characterization of fibroblast growth factor receptor 2 overexpression in the human breast cancer cell line SUM-52PE
    • Tannheimer, S. L., Rehemtulla, A., Ethier, S. P., Characterization of fibroblast growth factor receptor 2 overexpression in the human breast cancer cell line SUM-52PE. Breast Cancer Res. 2000, 2, 311-320.
    • (2000) Breast Cancer Res. , vol.2 , pp. 311-320
    • Tannheimer, S.L.1    Rehemtulla, A.2    Ethier, S.P.3
  • 19
  • 20
    • 58149177394 scopus 로고    scopus 로고
    • Differential effects of serine proteases on the migration of normal and tumor cells: implications for tumor microenvironment
    • Elzer, K. L., Heitzman, D. A., Chernin, M. I., Novak, J. F., Differential effects of serine proteases on the migration of normal and tumor cells: implications for tumor microenvironment. Integr. Cancer Ther. 2008, 7, 282-294.
    • (2008) Integr. Cancer Ther. , vol.7 , pp. 282-294
    • Elzer, K.L.1    Heitzman, D.A.2    Chernin, M.I.3    Novak, J.F.4
  • 21
    • 0037180757 scopus 로고    scopus 로고
    • Inflammation and cancer
    • Coussens, L. M., Werb, Z., Inflammation and cancer. Nature 2002, 420, 860-867.
    • (2002) Nature , vol.420 , pp. 860-867
    • Coussens, L.M.1    Werb, Z.2
  • 22
    • 30944439492 scopus 로고    scopus 로고
    • Differential expression of MHC class II molecules in highly metastatic breast cancer cells is mediated by the regulation of the CIITA transcription: implication of CIITA in tumor and metastasis development
    • Shi, B., Vinyals, A., Alia, P., Broceño, C. et al., Differential expression of MHC class II molecules in highly metastatic breast cancer cells is mediated by the regulation of the CIITA transcription: implication of CIITA in tumor and metastasis development. Int. J. Biochem. Cell Biol. 2006, 38, 544-562.
    • (2006) Int. J. Biochem. Cell Biol. , vol.38 , pp. 544-562
    • Shi, B.1    Vinyals, A.2    Alia, P.3    Broceño, C.4
  • 23
    • 0028859774 scopus 로고
    • CD4+ T lymphocytes infiltrating human breast cancer recognise autologous tumor in an MHC-class-II restricted fashion
    • Dadmarz, R., Sgagias, M. K., Rosenberg, S. A., Schwartzentruber, D. J., CD4+ T lymphocytes infiltrating human breast cancer recognise autologous tumor in an MHC-class-II restricted fashion. Cancer Immunol. Immunother. 1995, 40, 1-9.
    • (1995) Cancer Immunol. Immunother. , vol.40 , pp. 1-9
    • Dadmarz, R.1    Sgagias, M.K.2    Rosenberg, S.A.3    Schwartzentruber, D.J.4
  • 24
    • 0028820949 scopus 로고
    • Expression of MHC class I and class II antigens in primary breast carcinomas and synchronous nodal metastases
    • Maiorana, A., Cesinaro, A. M., Fano, R. A., Collina, G., Expression of MHC class I and class II antigens in primary breast carcinomas and synchronous nodal metastases. Clin. Exp. Metastasis 1995, 13, 43-48.
    • (1995) Clin. Exp. Metastasis , vol.13 , pp. 43-48
    • Maiorana, A.1    Cesinaro, A.M.2    Fano, R.A.3    Collina, G.4
  • 26
    • 79952423076 scopus 로고    scopus 로고
    • Molecular characterization of E2F1 and PSMB9 expression in breast cancer and correlation with poor prognosis and disease recurrence
    • King, L. M., Nelson, R. R., Hudson, R., Gore, M. et al., Molecular characterization of E2F1 and PSMB9 expression in breast cancer and correlation with poor prognosis and disease recurrence. Breast 2007, 16, S26-S26.
    • (2007) Breast , vol.16
    • King, L.M.1    Nelson, R.R.2    Hudson, R.3    Gore, M.4
  • 27
    • 0021332973 scopus 로고
    • Retinoblastoma: clues to human oncogenesis
    • Murphree, A. L., Benedict, W. F., Retinoblastoma: clues to human oncogenesis. Science 1984, 223, 1028-1033.
    • (1984) Science , vol.223 , pp. 1028-1033
    • Murphree, A.L.1    Benedict, W.F.2
  • 28
    • 29144441108 scopus 로고    scopus 로고
    • Extra-hepatic transcription of the human mannose-binding lectin gene (mbl2) and the MBL-associated serine protease 1-3 genes
    • Seyfarth, J., Garred, P., Madsen, H. O., Extra-hepatic transcription of the human mannose-binding lectin gene (mbl2) and the MBL-associated serine protease 1-3 genes. Mol. Immunol. 2006, 43, 962-971.
    • (2006) Mol. Immunol. , vol.43 , pp. 962-971
    • Seyfarth, J.1    Garred, P.2    Madsen, H.O.3
  • 29
    • 34047120777 scopus 로고    scopus 로고
    • The mannose-binding lectin (MBL2) haplotype and breast cancer: an association study in African-American and Caucasian women
    • Bernig, T., Boersma, B. J., Howe, T. M., Welch, R. et al., The mannose-binding lectin (MBL2) haplotype and breast cancer: an association study in African-American and Caucasian women. Carcinogenesis 2007, 28, 828-836.
    • (2007) Carcinogenesis , vol.28 , pp. 828-836
    • Bernig, T.1    Boersma, B.J.2    Howe, T.M.3    Welch, R.4
  • 30
    • 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., Bjohle, J., Amler, L., Borg, A. L. et al., Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res. 2005, 7, R953-R964.
    • (2005) Breast Cancer Res. , vol.7
    • Pawitan, Y.1    Bjohle, J.2    Amler, L.3    Borg, A.L.4
  • 31
    • 33751530490 scopus 로고    scopus 로고
    • Mining the Wnt pathway for cancer therapeutics
    • Barker, N., Clevers, H., Mining the Wnt pathway for cancer therapeutics. Nat. Rev. Drug Discov. 2006, 5, 997-1014.
    • (2006) Nat. Rev. Drug Discov. , vol.5 , pp. 997-1014
    • Barker, N.1    Clevers, H.2
  • 34
    • 33645316142 scopus 로고    scopus 로고
    • Targeting polo-like kinase 1 for cancer therapy
    • Strebhardt, K., Ullrich, A., Targeting polo-like kinase 1 for cancer therapy. Nat. Rev. Cancer 2006, 6, 321-330.
    • (2006) Nat. Rev. Cancer , vol.6 , pp. 321-330
    • Strebhardt, K.1    Ullrich, A.2
  • 35
    • 0345059753 scopus 로고    scopus 로고
    • The 14-3-3 cancer connection
    • Hermeking, H., The 14-3-3 cancer connection. Nat. Rev. Cancer 2003, 3, 931-943.
    • (2003) Nat. Rev. Cancer , vol.3 , pp. 931-943
    • Hermeking, H.1
  • 36
    • 65949124697 scopus 로고    scopus 로고
    • 14-3-3{zeta} overexpression defines high risk for breast cancer recurrence and promotes cancer cell survival
    • Neal, C. L., Yao, J., Yang, W., Zhou, X. et al., 14-3-3{zeta} overexpression defines high risk for breast cancer recurrence and promotes cancer cell survival. Cancer Res. 2009, 69, 3425-3432.
    • (2009) Cancer Res. , vol.69 , pp. 3425-3432
    • Neal, C.L.1    Yao, J.2    Yang, W.3    Zhou, X.4
  • 37
    • 63949088181 scopus 로고    scopus 로고
    • High cyclin B1 expression is associated with poor survival in breast cancer
    • Aaltonen, K., Amini, R. M., Heikkila, P., Aittomaki, K. et al., High cyclin B1 expression is associated with poor survival in breast cancer. Br. J. Cancer 2009, 100, 1055-1060.
    • (2009) Br. J. Cancer , vol.100 , pp. 1055-1060
    • Aaltonen, K.1    Amini, R.M.2    Heikkila, P.3    Aittomaki, K.4
  • 38
    • 34547930725 scopus 로고    scopus 로고
    • Claudin-1 and claudin-5 expression patterns differentiate lung squamous cell carcinomas from adenocarcinomas
    • Paschoud, S., Bongiovanni, M., Pache, J.-C., Citi, S., Claudin-1 and claudin-5 expression patterns differentiate lung squamous cell carcinomas from adenocarcinomas. Mod. Pathol. 2007, 20, 947-954.
    • (2007) Mod. Pathol. , vol.20 , pp. 947-954
    • Paschoud, S.1    Bongiovanni, M.2    Pache, J.-C.3    Citi, S.4
  • 39
    • 27544448588 scopus 로고    scopus 로고
    • Claudin proteins in human cancer: promising new targets for diagnosis and therapy
    • Morin, P. J., Claudin proteins in human cancer: promising new targets for diagnosis and therapy. Cancer Res. 2005, 65, 9603-9606.
    • (2005) Cancer Res. , vol.65 , pp. 9603-9606
    • Morin, P.J.1
  • 40
    • 1942501592 scopus 로고    scopus 로고
    • Clostridium perfringens enterotoxin elicits rapid and specific cytolysis of breast carcinoma cells mediated through tight junction proteins claudin 3 and 4
    • Kominsky, S. L., Vali, M., Korz, D., Gabig, T. G. et al., Clostridium perfringens enterotoxin elicits rapid and specific cytolysis of breast carcinoma cells mediated through tight junction proteins claudin 3 and 4. Am. J. Pathol. 2004, 164, 1627-1633.
    • (2004) Am. J. Pathol. , vol.164 , pp. 1627-1633
    • Kominsky, S.L.1    Vali, M.2    Korz, D.3    Gabig, T.G.4
  • 41
    • 79952399416 scopus 로고    scopus 로고
    • The role of claudin- 5 and the paracellular barrier function in endothelial cells during invasion of breast cancer cells
    • Escudero-Esparza, A., Martin, T., Jiang, W., The role of claudin- 5 and the paracellular barrier function in endothelial cells during invasion of breast cancer cells. Cancer Res. 2009, 69, 6170.
    • (2009) Cancer Res. , vol.69 , pp. 6170
    • Escudero-Esparza, A.1    Martin, T.2    Jiang, W.3
  • 42
    • 33646023117 scopus 로고    scopus 로고
    • An introduction to ROC analysis
    • Fawcett, T., An introduction to ROC analysis. Pattern Recogn. Lett. 2006, 27, 861-874.
    • (2006) Pattern Recogn. Lett. , vol.27 , pp. 861-874
    • Fawcett, T.1


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