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Volumn 9, Issue 2, 2014, Pages

Gene co-expression modules as clinically relevant hallmarks of breast cancer diversity

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR 2; ESTROGEN; HISTONE; TUMOR MARKER;

EID: 84895739525     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0088309     Document Type: Article
Times cited : (93)

References (54)
  • 2
    • 78049308800 scopus 로고    scopus 로고
    • Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer
    • Prat A, Parker JS, Karginova O, Fan C, Livasy C, et al. (2010) Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer. Breast Cancer Research 12.
    • (2010) Breast Cancer Research , pp. 12
    • Prat, A.1    Parker, J.S.2    Karginova, O.3    Fan, C.4    Livasy, C.5
  • 3
    • 84877028141 scopus 로고    scopus 로고
    • Comprehensive molecular portraits of human breast tumours
    • TCGA-network
    • TCGA-network (2012) Comprehensive molecular portraits of human breast tumours. Nature 490: 61-70.
    • (2012) Nature , vol.490 , pp. 61-70
  • 4
    • 84861527388 scopus 로고    scopus 로고
    • The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
    • Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, et al. (2012) The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486: 346-352.
    • (2012) Nature , vol.486 , pp. 346-352
    • Curtis, C.1    Shah, S.P.2    Chin, S.F.3    Turashvili, G.4    Rueda, O.M.5
  • 6
    • 0037676107 scopus 로고    scopus 로고
    • Motifs, modules and games in bacteria
    • DOI 10.1016/S1369-5274(03)00033-X
    • Wolf DM, Arkin AP (2003) Motifs, modules and games in bacteria. Curr Opin Microbiol 6: 125-134. (Pubitemid 36628655)
    • (2003) Current Opinion in Microbiology , vol.6 , Issue.2 , pp. 125-134
    • Wolf, D.M.1    Arkin, A.P.2
  • 7
    • 0034614637 scopus 로고    scopus 로고
    • The hallmarks of cancer
    • Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100: 57-70. (Pubitemid 30046295)
    • (2000) Cell , vol.100 , Issue.1 , pp. 57-70
    • Hanahan, D.1    Weinberg, R.A.2
  • 8
    • 79952284127 scopus 로고    scopus 로고
    • Hallmarks of cancer: The next generation
    • Hanahan D,Weinberg RA (2011) Hallmarks of cancer: the next generation. Cell 144: 646-674.
    • (2011) Cell , vol.144 , pp. 646-674
    • Hanahan, D.1    Weinberg, R.A.2
  • 9
    • 6944244084 scopus 로고    scopus 로고
    • A module map showing conditional activity of expression modules in cancer
    • DOI 10.1038/ng1434
    • Segal E, Friedman N, Koller D, Regev A (2004) A module map showing conditional activity of expression modules in cancer. Nat Genet 36: 1090-1098. (Pubitemid 41184471)
    • (2004) Nature Genetics , vol.36 , Issue.10 , pp. 1090-1098
    • Segal, E.1    Friedman, N.2    Koller, D.3    Regev, A.4
  • 10
    • 84860343391 scopus 로고    scopus 로고
    • The application of gene co-expression network reconstruction based on CNVs and gene expression microarray data in breast cancer
    • Xu Y, Duanmu H, Chang Z, Zhang S, Li Z, et al. (2012) The application of gene co-expression network reconstruction based on CNVs and gene expression microarray data in breast cancer. Mol Biol Rep 39: 1627-1637.
    • (2012) Mol Biol Rep , vol.39 , pp. 1627-1637
    • Xu, Y.1    Duanmu, H.2    Chang, Z.3    Zhang, S.4    Li, Z.5
  • 11
    • 84856944883 scopus 로고    scopus 로고
    • An iterative network partition algorithm for accurate identification of dense network modules
    • Sun S, Dong X, Fu Y, Tian W (2012) An iterative network partition algorithm for accurate identification of dense network modules. Nucleic Acids Research 40: e18.
    • (2012) Nucleic Acids Research , vol.40
    • Sun, S.1    Dong, X.2    Fu, Y.3    Tian, W.4
  • 12
    • 77952687416 scopus 로고    scopus 로고
    • Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression
    • Shi Z, Derow CK, Zhang B (2010) Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression. BMC Syst Biol 4: 74.
    • (2010) BMC Syst Biol , vol.4 , pp. 74
    • Shi, Z.1    Derow, C.K.2    Zhang, B.3
  • 13
    • 34548776990 scopus 로고    scopus 로고
    • Identification of aberrant chromosomal regions from gene expression microarray studies applied to human breast cancer
    • DOI 10.1093/bioinformatics/btm340
    • Buness A, Kuner R, Ruschhaupt M, Poustka A, Sultmann H, et al. (2007) Identification of aberrant chromosomal regions from gene expression microarray studies applied to human breast cancer. Bioinformatics 23: 2273-2280. (Pubitemid 47423865)
    • (2007) Bioinformatics , vol.23 , Issue.17 , pp. 2273-2280
    • Buness, A.1    Kuner, R.2    Ruschhaupt, M.3    Poustka, A.4    Sultmann, H.5    Tresch, A.6
  • 15
    • 74049143935 scopus 로고    scopus 로고
    • Dissecting the dynamics of dysregulation of cellular processes in mouse mammary gland tumor
    • Mentzen WI, Floris M, de la Fuente A (2009) Dissecting the dynamics of dysregulation of cellular processes in mouse mammary gland tumor. Bmc Genomics 10: 601.
    • (2009) Bmc Genomics , vol.10 , pp. 601
    • Mentzen, W.I.1    Floris, M.2    De La Fuente, A.3
  • 16
    • 58149330982 scopus 로고    scopus 로고
    • Meta-analysis of gene expression profiles in breast cancer: Toward a unified understanding of breast cancer subtyping and prognosis signatures
    • Wirapati P, Sotiriou C, Kunkel S, Farmer P, Pradervand S, et al. (2008) Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures. Breast Cancer Research 10: R65.
    • (2008) Breast Cancer Research , vol.10
    • Wirapati, P.1    Sotiriou, C.2    Kunkel, S.3    Farmer, P.4    Pradervand, S.5
  • 17
    • 84866065824 scopus 로고    scopus 로고
    • Weighted frequent gene co-expression network mining to identify genes involved in genome stability
    • Zhang J, Lu K, Xiang Y, Islam M, Kotian S, et al. (2012) Weighted frequent gene co-expression network mining to identify genes involved in genome stability. PLoS Comput Biol 8: e1002656.
    • (2012) PLoS Comput Biol , vol.8
    • Zhang, J.1    Lu, K.2    Xiang, Y.3    Islam, M.4    Kotian, S.5
  • 19
    • 51349088017 scopus 로고    scopus 로고
    • Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes
    • Desmedt C, Haibe-Kains B, Wirapati P, Buyse M, Larsimont D, et al. (2008) Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes. Clinical Cancer Research 14: 5158-5165.
    • (2008) Clinical Cancer Research , vol.14 , pp. 5158-5165
    • Desmedt, C.1    Haibe-Kains, B.2    Wirapati, P.3    Buyse, M.4    Larsimont, D.5
  • 20
    • 63349091533 scopus 로고    scopus 로고
    • A robust classifier of high predictive value to identify good prognosis patients in ER-negative breast cancer
    • Teschendorff AE, Caldas C (2008) A robust classifier of high predictive value to identify good prognosis patients in ER-negative breast cancer. Breast Cancer Research 10: R73.
    • (2008) Breast Cancer Research , vol.10
    • Teschendorff, A.E.1    Caldas, C.2
  • 21
    • 33646874546 scopus 로고    scopus 로고
    • The molecular portraits of breast tumors are conserved across microarray platforms
    • Hu ZY, Fan C, Oh DS, Marron JS, He XP, et al. (2006) The molecular portraits of breast tumors are conserved across microarray platforms. Bmc Genomics 7.
    • (2006) Bmc Genomics , pp. 7
    • Hu, Z.Y.1    Fan, C.2    Oh, D.S.3    Marron, J.S.4    He, X.P.5
  • 22
    • 33745259517 scopus 로고    scopus 로고
    • Cell-type specific gene expression profiles of leukocytes in human peripheral blood
    • Palmer C, Diehn M, Alizadeh AA, Brown PO (2006) Cell-type specific gene expression profiles of leukocytes in human peripheral blood. Bmc Genomics 7: 115.
    • (2006) Bmc Genomics , vol.7 , pp. 115
    • Palmer, C.1    Diehn, M.2    Alizadeh, A.A.3    Brown, P.O.4
  • 25
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4: 44-57.
    • (2009) Nature Protocols , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 26
    • 79959923522 scopus 로고    scopus 로고
    • g:Profiler-a web server for functional interpretation of gene lists (2011 update)
    • Reimand J, Arak T, Vilo J (2011) g:Profiler-a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Research 39: W307-315.
    • (2011) Nucleic Acids Research , vol.39
    • Reimand, J.1    Arak, T.2    Vilo, J.3
  • 27
    • 84860390189 scopus 로고    scopus 로고
    • Endocrine resistance in breast cancer: New roles for ErbB3 and ErbB4
    • Sutherland RL (2011) Endocrine resistance in breast cancer: new roles for ErbB3 and ErbB4. Breast Cancer Research 13: 106.
    • (2011) Breast Cancer Research , vol.13 , pp. 106
    • Sutherland, R.L.1
  • 28
    • 77955656804 scopus 로고    scopus 로고
    • Gene expression profiling of response to mTOR inhibitor everolimus in pre-operatively treated post-menopausal women with oestrogen receptor-positive breast cancer
    • Sabine VS, Sims AH, Macaskill EJ, Renshaw L, Thomas JS, et al. (2010) Gene expression profiling of response to mTOR inhibitor everolimus in pre-operatively treated post-menopausal women with oestrogen receptor-positive breast cancer. Breast Cancer Res Treat 122: 419-428.
    • (2010) Breast Cancer Res Treat , vol.122 , pp. 419-428
    • Sabine, V.S.1    Sims, A.H.2    Macaskill, E.J.3    Renshaw, L.4    Thomas, J.S.5
  • 29
    • 84876666154 scopus 로고    scopus 로고
    • Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis
    • Nagalla S, Chou JW, Willingham MC, Ruiz J, Vaughn JP, et al. (2013) Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis. Genome Biol 14: R34.
    • (2013) Genome Biol , vol.14
    • Nagalla, S.1    Chou, J.W.2    Willingham, M.C.3    Ruiz, J.4    Vaughn, J.P.5
  • 30
    • 84871949633 scopus 로고    scopus 로고
    • Molecular pathways: Involvement of immune pathways in the therapeutic response and outcome in breast cancer
    • Andre F, Dieci MV, Dubsky P, Sotiriou C, Curigliano G, et al. (2013) Molecular pathways: involvement of immune pathways in the therapeutic response and outcome in breast cancer. Clin Cancer Res 19: 28-33.
    • (2013) Clin Cancer Res , vol.19 , pp. 28-33
    • Andre, F.1    Dieci, M.V.2    Dubsky, P.3    Sotiriou, C.4    Curigliano, G.5
  • 31
    • 77957759237 scopus 로고    scopus 로고
    • A multigene predictor of metastatic outcome in early stage hormone receptor-negative and triple-negative breast cancer
    • Yau C, Esserman L, Moore DH, Waldman F, Sninsky J, et al. (2010) A multigene predictor of metastatic outcome in early stage hormone receptor-negative and triple-negative breast cancer. Breast Cancer Res 12: R85.
    • (2010) Breast Cancer Res , vol.12
    • Yau, C.1    Esserman, L.2    Moore, D.H.3    Waldman, F.4    Sninsky, J.5
  • 32
    • 62449131093 scopus 로고    scopus 로고
    • Supervised risk predictor of breast cancer based on intrinsic subtypes
    • Parker JS, Mullins M, Cheang MC, Leung S, Voduc D, et al. (2009) Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol 27: 1160-1167.
    • (2009) J Clin Oncol , vol.27 , pp. 1160-1167
    • Parker, J.S.1    Mullins, M.2    Cheang, M.C.3    Leung, S.4    Voduc, D.5
  • 37
    • 59349092369 scopus 로고    scopus 로고
    • Risk estimation of distant metastasis in node-negative, estrogen receptor-positive breast cancer patients using an RT-PCR based prognostic expression signature
    • Tutt A, Wang A, Rowland C, Gillett C, Lau K, et al. (2008) Risk estimation of distant metastasis in node-negative, estrogen receptor-positive breast cancer patients using an RT-PCR based prognostic expression signature. Bmc Cancer 8.
    • (2008) Bmc Cancer , pp. 8
    • Tutt, A.1    Wang, A.2    Rowland, C.3    Gillett, C.4    Lau, K.5
  • 38
    • 33748967069 scopus 로고    scopus 로고
    • Of extracellular matrix, scaffolds, and signaling: Tissue architecture regulates development, homeostasis, and cancer
    • Nelson CM, Bissell MJ (2006) Of extracellular matrix, scaffolds, and signaling: Tissue architecture regulates development, homeostasis, and cancer. Annual Review of Cell and Developmental Biology 22: 287-309.
    • (2006) Annual Review of Cell and Developmental Biology , vol.22 , pp. 287-309
    • Nelson, C.M.1    Bissell, M.J.2
  • 39
    • 84865191389 scopus 로고    scopus 로고
    • Chemotherapy response and recurrence-free survival in neoadjuvant breast cancer depends on biomarker profiles: Results from the I-SPY 1 TRIAL (CALGB 150007/150012; ACRIN 6657)
    • Esserman LJ, Berry DA, Cheang MC, Yau C, Perou CM, et al. (2012) Chemotherapy response and recurrence-free survival in neoadjuvant breast cancer depends on biomarker profiles: results from the I-SPY 1 TRIAL (CALGB 150007/150012; ACRIN 6657). Breast Cancer Res Treat 132: 1049-1062.
    • (2012) Breast Cancer Res Treat , vol.132 , pp. 1049-1062
    • Esserman, L.J.1    Berry, D.A.2    Cheang, M.C.3    Yau, C.4    Perou, C.M.5
  • 40
    • 79551710060 scopus 로고    scopus 로고
    • Gene pathways associated with prognosis and chemotherapy sensitivity in molecular subtypes of breast cancer
    • Iwamoto T, Bianchini G, Booser D, Qi Y, Coutant C, et al. (2011) Gene pathways associated with prognosis and chemotherapy sensitivity in molecular subtypes of breast cancer. J Natl Cancer Inst 103: 264-272.
    • (2011) J Natl Cancer Inst , vol.103 , pp. 264-272
    • Iwamoto, T.1    Bianchini, G.2    Booser, D.3    Qi, Y.4    Coutant, C.5
  • 41
    • 79953300698 scopus 로고    scopus 로고
    • The seed and soil hypothesis revisited - The role of tumor-stroma interactions in metastasis to different organs
    • Langley RR, Fidler IJ (2011) The seed and soil hypothesis revisited-the role of tumor-stroma interactions in metastasis to different organs. International Journal of Cancer 128: 2527-2535.
    • (2011) International Journal of Cancer , vol.128 , pp. 2527-2535
    • Langley, R.R.1    Fidler, I.J.2
  • 42
    • 67649300721 scopus 로고    scopus 로고
    • Genes that mediate breast cancer metastasis to the brain
    • Bos PD, Zhang XH, Nadal C, Shu W, Gomis RR, et al. (2009) Genes that mediate breast cancer metastasis to the brain. Nature 459: 1005-1009.
    • (2009) Nature , vol.459 , pp. 1005-1009
    • Bos, P.D.1    Zhang, X.H.2    Nadal, C.3    Shu, W.4    Gomis, R.R.5
  • 43
    • 68549085276 scopus 로고    scopus 로고
    • Tissue architecture and function: Dynamic reciprocity via extra- and intra-cellular matrices
    • Xu R, Boudreau A, Bissell MJ (2009) Tissue architecture and function: dynamic reciprocity via extra- and intra-cellular matrices. Cancer Metastasis Rev 28: 167-176.
    • (2009) Cancer Metastasis Rev , vol.28 , pp. 167-176
    • Xu, R.1    Boudreau, A.2    Bissell, M.J.3
  • 44
    • 84877737214 scopus 로고    scopus 로고
    • Development of a prognostic model for breast cancer survival in an open challenge environment
    • Cheng WY, Ou Yang TH, Anastassiou D (2013) Development of a prognostic model for breast cancer survival in an open challenge environment. Sci Transl Med 5: 181ra150.
    • (2013) Sci Transl Med , vol.5
    • Cheng, W.Y.1    Ou Yang, T.H.2    Anastassiou, D.3
  • 46
    • 29144535372 scopus 로고    scopus 로고
    • Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data
    • Dai MH, Wang PL, Boyd AD, Kostov G, Athey B, et al. (2005) Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Research 33.
    • (2005) Nucleic Acids Research , pp. 33
    • Dai, M.H.1    Wang, P.L.2    Boyd, A.D.3    Kostov, G.4    Athey, B.5
  • 49
    • 77649269338 scopus 로고    scopus 로고
    • The bimodality index: A criterion for discovering and ranking bimodal signatures from cancer gene expression profiling data
    • Wang J, Wen S, Symmans WF, Pusztai L, Coombes KR (2009) The bimodality index: a criterion for discovering and ranking bimodal signatures from cancer gene expression profiling data. Cancer Inform 7: 199-216.
    • (2009) Cancer Inform , vol.7 , pp. 199-216
    • Wang, J.1    Wen, S.2    Symmans, W.F.3    Pusztai, L.4    Coombes, K.R.5
  • 51
    • 0000120766 scopus 로고
    • Estimating the diension of a model
    • Schwarz GE (1978) Estimating the diension of a model. Annals of Statistics 6: 461-464.
    • (1978) Annals of Statistics , vol.6 , pp. 461-464
    • Schwarz, G.E.1
  • 53
    • 84864507889 scopus 로고    scopus 로고
    • A Package for Survival Analysis in S
    • version 2.36-14
    • Therneau T (2012) A Package for Survival Analysis in S. R package version 2.36-14.
    • (2012) R Package
    • Therneau, T.1


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