메뉴 건너뛰기




Volumn 34, Issue 10, 2013, Pages 2300-2308

Correlating transcriptional networks to breast cancer survival: A large-scale coexpression analysis

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR 2; INWARDLY RECTIFYING POTASSIUM CHANNEL; MESSENGER RNA; UBIQUITIN CONJUGATING ENZYME E2; UBIQUITIN CONJUGATING ENZYME E2S; UNCLASSIFIED DRUG;

EID: 84885131104     PISSN: 01433334     EISSN: 14602180     Source Type: Journal    
DOI: 10.1093/carcin/bgt208     Document Type: Article
Times cited : (327)

References (54)
  • 1
    • 69449090120 scopus 로고    scopus 로고
    • Thresholds for therapies: highlights of the St Gallen International Expert Consensus on the primary therapy of early breast cancer 2009
    • Goldhirsch, A. et al. (2009) Thresholds for therapies: highlights of the St Gallen International Expert Consensus on the primary therapy of early breast cancer 2009. Ann. Oncol., 20, 1319-1329.
    • (2009) Ann. Oncol. , vol.20 , pp. 1319-1329
    • Goldhirsch, A.1
  • 2
    • 0034680102 scopus 로고    scopus 로고
    • Molecular portraits of human breast tumours
    • Perou, C.M. et al. (2000) Molecular portraits of human breast tumours. Nature, 406, 747-752.
    • (2000) Nature , vol.406 , pp. 747-752
    • Perou, C.M.1
  • 3
    • 84861527388 scopus 로고    scopus 로고
    • The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
    • Curtis, C. 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
  • 4
    • 84877028141 scopus 로고    scopus 로고
    • Comprehensive molecular portraits of human breast tumours
    • Network, T.C.G.A. (2012) Comprehensive molecular portraits of human breast tumours. Nature, 490, 61-70.
    • (2012) Nature , vol.490 , pp. 61-70
    • Network, T.C.G.A.1
  • 5
    • 18244409687 scopus 로고    scopus 로고
    • Gene expression profiling predicts clinical outcome of breast cancer
    • van't Veer, L.J. et al. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature, 415, 530-536.
    • (2002) Nature , vol.415 , pp. 530-536
    • van't Veer, L.J.1
  • 6
    • 19944422061 scopus 로고    scopus 로고
    • A multigene assay to predict recurrence of tamoxifentreated, node-negative breast cancer
    • Paik, S. et al. (2004) A multigene assay to predict recurrence of tamoxifentreated, node-negative breast cancer. N. Engl. J. Med., 351, 2817-2826.
    • (2004) N. Engl. J. Med. , vol.351 , pp. 2817-2826
    • Paik, S.1
  • 7
    • 84859568179 scopus 로고    scopus 로고
    • Making sense out of massive data by going beyond differential expression
    • Schmid, P.R. et al. (2012) Making sense out of massive data by going beyond differential expression. Proc. Natl Acad. Sci. USA, 109, 5594-5599.
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 5594-5599
    • Schmid, P.R.1
  • 8
    • 3042694117 scopus 로고    scopus 로고
    • Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression
    • Rhodes, D.R. et al. (2004) Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc. Natl Acad. Sci. USA, 101, 9309-9314.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 9309-9314
    • Rhodes, D.R.1
  • 9
    • 34548127285 scopus 로고    scopus 로고
    • Large-scale integration of cancer microarray data identifies a robust common cancer signature
    • Xu, L. et al. (2007) Large-scale integration of cancer microarray data identifies a robust common cancer signature. BMC Bioinformatics, 8, 275.
    • (2007) BMC Bioinformatics , vol.8 , pp. 275
    • Xu, L.1
  • 10
    • 84871959921 scopus 로고    scopus 로고
    • Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis, and tissue microarray validation
    • Botling, J. et al. (2013) Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis, and tissue microarray validation. Clin. Cancer Res., 19, 194-204.
    • (2013) Clin. Cancer Res. , vol.19 , pp. 194-204
    • Botling, J.1
  • 11
    • 62749199200 scopus 로고    scopus 로고
    • Meta-analysis and gene set enrichment relative to er status reveal elevated activity of MYC and E2F in the "basal" breast cancer subgroup
    • Alles, M.C. et al. (2009) Meta-analysis and gene set enrichment relative to er status reveal elevated activity of MYC and E2F in the "basal" breast cancer subgroup. PLoS One, 4, e4710.
    • (2009) PLoS One , vol.4
    • Alles, M.C.1
  • 12
    • 29244481995 scopus 로고    scopus 로고
    • Identification of GATA3 as a breast cancer prognostic marker by global gene expression meta-analysis
    • Mehra, R. et al. (2005) Identification of GATA3 as a breast cancer prognostic marker by global gene expression meta-analysis. Cancer Res., 65, 11259-11264.
    • (2005) Cancer Res. , vol.65 , pp. 11259-11264
    • Mehra, R.1
  • 13
    • 84879833107 scopus 로고    scopus 로고
    • BreastMark: an integrated approach to mining publicly available transcriptomic datasets relating to breast cancer outcome
    • in press.
    • Madden, S.F. et al. (2013) BreastMark: an integrated approach to mining publicly available transcriptomic datasets relating to breast cancer outcome. Breast Cancer Res., in press.
    • (2013) Breast Cancer Res.
    • Madden, S.F.1
  • 14
    • 79151483638 scopus 로고    scopus 로고
    • An online survival analysis tool to rapidly assess the effect of 22,277 genes on breast cancer prognosis using microarray data of 1,809 patients
    • Györffy, B. et al. (2010) An online survival analysis tool to rapidly assess the effect of 22,277 genes on breast cancer prognosis using microarray data of 1,809 patients. Breast Cancer Res. Treat., 123, 725-731.
    • (2010) Breast Cancer Res. Treat. , vol.123 , pp. 725-731
    • Györffy, B.1
  • 15
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • Stuart, J.M. et al. (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science, 302, 249-255.
    • (2003) Science , vol.302 , pp. 249-255
    • Stuart, J.M.1
  • 16
    • 33845231723 scopus 로고    scopus 로고
    • Conservation and evolution of gene coexpression networks in human and chimpanzee brains
    • Oldham, M.C. et al. (2006) Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc. Natl Acad. Sci. USA, 103, 17973-17978.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 17973-17978
    • Oldham, M.C.1
  • 17
    • 54949113578 scopus 로고    scopus 로고
    • Functional organization of the transcriptome in human brain
    • Oldham, M.C. et al. (2008) Functional organization of the transcriptome in human brain. Nat. Neurosci., 11, 1271-1282.
    • (2008) Nat. Neurosci. , vol.11 , pp. 1271-1282
    • Oldham, M.C.1
  • 18
    • 80052389765 scopus 로고    scopus 로고
    • Large scale microarray profiling and coexpression network analysis of CHO cells identifies transcriptional modules associated with growth and productivity
    • Clarke, C. et al. (2011) Large scale microarray profiling and coexpression network analysis of CHO cells identifies transcriptional modules associated with growth and productivity. J. Biotechnol., 155, 350-359.
    • (2011) J. Biotechnol. , vol.155 , pp. 350-359
    • Clarke, C.1
  • 19
    • 73649135801 scopus 로고    scopus 로고
    • Gene networks and microRNAs implicated in aggressive prostate cancer
    • Wang, L. et al. (2009) Gene networks and microRNAs implicated in aggressive prostate cancer. Cancer Res., 69, 9490-9497.
    • (2009) Cancer Res. , vol.69 , pp. 9490-9497
    • Wang, L.1
  • 20
    • 33751208636 scopus 로고    scopus 로고
    • Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target
    • Horvath, S. et al. (2006) Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target. Proc. Natl Acad. Sci. USA, 103, 17402-17407.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 17402-17407
    • Horvath, S.1
  • 21
    • 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. 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 Res., 10, R65.
    • (2008) Breast Cancer Res. , vol.10
    • Wirapati, P.1
  • 22
    • 23944458138 scopus 로고    scopus 로고
    • A general framework for weighted gene co-expression network analysis
    • Article 17
    • Zhang, B. et al. (2005) A general framework for weighted gene co-expression network analysis. Stat. Appl. Genet. Mol. Biol., 4, Article 17.
    • (2005) Stat. Appl. Genet. Mol. Biol. , vol.4
    • Zhang, B.1
  • 23
    • 68149147400 scopus 로고    scopus 로고
    • The Gene expression Grade Index: a potential predictor of relapse for endocrine-treated breast cancer patients in the BIG 1-98 trial
    • Desmedt, C. et al. (2009) The Gene expression Grade Index: a potential predictor of relapse for endocrine-treated breast cancer patients in the BIG 1-98 trial. BMC Med. Genomics, 2, 40.
    • (2009) BMC Med. Genomics , vol.2 , pp. 40
    • Desmedt, C.1
  • 24
    • 34250652449 scopus 로고    scopus 로고
    • Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series
    • Desmedt, C. et al. (2007) Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series. Clin. Cancer Res., 13, 3207-3214.
    • (2007) Clin. Cancer Res. , vol.13 , pp. 3207-3214
    • Desmedt, C.1
  • 25
    • 44949121510 scopus 로고    scopus 로고
    • Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen
    • Loi, S. et al. (2008) Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. BMC Genomics, 9, 239.
    • (2008) BMC Genomics , vol.9 , pp. 239
    • Loi, S.1
  • 26
    • 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. (2005) 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) Proc. Natl Acad. Sci. USA , vol.102 , pp. 13550-13555
    • Miller, L.D.1
  • 27
    • 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. (2005) Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population- based cohorts. Breast Cancer Res., 7, R953-R964.
    • (2005) Breast Cancer Res. , vol.7
    • Pawitan, Y.1
  • 28
    • 79958728723 scopus 로고    scopus 로고
    • A gene expression signature identifies two prognostic subgroups of basal breast cancer
    • Sabatier, R. et al. (2011) A gene expression signature identifies two prognostic subgroups of basal breast cancer. Breast Cancer Res. Treat., 126, 407-420.
    • (2011) Breast Cancer Res. Treat. , vol.126 , pp. 407-420
    • Sabatier, R.1
  • 29
    • 44849101184 scopus 로고    scopus 로고
    • The humoral immune system has a key prognostic impact in node-negative breast cancer
    • Schmidt, M. et al. (2008) The humoral immune system has a key prognostic impact in node-negative breast cancer. Cancer Res., 68, 5405-5413.
    • (2008) Cancer Res. , vol.68 , pp. 5405-5413
    • Schmidt, M.1
  • 30
    • 13844310310 scopus 로고    scopus 로고
    • Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer
    • Wang, Y. et al. (2005) Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet, 365, 671-679.
    • (2005) Lancet , vol.365 , pp. 671-679
    • Wang, Y.1
  • 31
    • 67649230285 scopus 로고    scopus 로고
    • The 76-gene signature defines high-risk patients that benefit from adjuvant tamoxifen therapy
    • Zhang, Y. et al. (2009) The 76-gene signature defines high-risk patients that benefit from adjuvant tamoxifen therapy. Breast Cancer Res. Treat., 116, 303-309.
    • (2009) Breast Cancer Res. Treat. , vol.116 , pp. 303-309
    • Zhang, Y.1
  • 32
    • 79955121426 scopus 로고    scopus 로고
    • Correlation of microarray-based breast cancer molecular subtypes and clinical outcomes: implications for treatment optimization
    • Kao, K.J. et al. (2011) Correlation of microarray-based breast cancer molecular subtypes and clinical outcomes: implications for treatment optimization. BMC Cancer, 11, 143.
    • (2011) BMC Cancer , vol.11 , pp. 143
    • Kao, K.J.1
  • 33
    • 67649300721 scopus 로고    scopus 로고
    • Genes that mediate breast cancer metastasis to the brain
    • Bos, P.D. 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
  • 34
    • 77957555408 scopus 로고    scopus 로고
    • Genome profiling of ERBB2-amplified breast cancers
    • Sircoulomb, F. et al. (2010) Genome profiling of ERBB2-amplified breast cancers. BMC Cancer, 10, 539.
    • (2010) BMC Cancer , vol.10 , pp. 539
    • Sircoulomb, F.1
  • 35
    • 84876666154 scopus 로고    scopus 로고
    • Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis
    • Nagalla, S. 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
  • 36
    • 0142121516 scopus 로고    scopus 로고
    • Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    • Irizarry, R.A. et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 249-264.
    • (2003) Biostatistics , vol.4 , pp. 249-264
    • Irizarry, R.A.1
  • 37
    • 33845432928 scopus 로고    scopus 로고
    • Adjusting batch effects in microarray expression data using empirical Bayes methods
    • Johnson, W.E. et al. (2007) Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics, 8, 118-127.
    • (2007) Biostatistics , vol.8 , pp. 118-127
    • Johnson, W.E.1
  • 38
    • 0037478605 scopus 로고    scopus 로고
    • Repeated observation of breast tumor subtypes in independent gene expression data sets
    • Sorlie, T. et al. (2003) Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc. Natl Acad. Sci. USA, 100, 8418-8423.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 8418-8423
    • Sorlie, T.1
  • 39
    • 33646874546 scopus 로고    scopus 로고
    • The molecular portraits of breast tumors are conserved across microarray platforms
    • Hu, Z. et al. (2006) The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics, 7, 96.
    • (2006) BMC Genomics , vol.7 , pp. 96
    • Hu, Z.1
  • 40
    • 62449131093 scopus 로고    scopus 로고
    • Supervised risk predictor of breast cancer based on intrinsic subtypes
    • Parker, J.S. 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
  • 41
    • 46949098575 scopus 로고    scopus 로고
    • Drug metabolism-related genes as potential biomarkers: analysis of expression in normal and tumour breast tissue
    • Martinez, V. et al. (2008) Drug metabolism-related genes as potential biomarkers: analysis of expression in normal and tumour breast tissue. Breast Cancer Res. Treat., 110, 521-530.
    • (2008) Breast Cancer Res. Treat. , vol.110 , pp. 521-530
    • Martinez, V.1
  • 42
    • 60549111634 scopus 로고    scopus 로고
    • WGCNA: an R package for weighted correlation network analysis
    • Langfelder, P. et al. (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics, 9, 559.
    • (2008) BMC Bioinformatics , vol.9 , pp. 559
    • Langfelder, P.1
  • 43
    • 68949098307 scopus 로고    scopus 로고
    • Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells
    • Mason, M.J. et al. (2009) Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells. BMC Genomics, 10, 327.
    • (2009) BMC Genomics , vol.10 , pp. 327
    • Mason, M.J.1
  • 44
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical organization of modularity in metabolic networks
    • Ravasz, E. et al. (2002) Hierarchical organization of modularity in metabolic networks. Science, 297, 1551-1555.
    • (2002) Science , vol.297 , pp. 1551-1555
    • Ravasz, E.1
  • 45
    • 50949084896 scopus 로고    scopus 로고
    • Geometric interpretation of gene coexpression network analysis
    • Horvath, S. et al. (2008) Geometric interpretation of gene coexpression network analysis. PLoS Comput. Biol., 4, e1000117.
    • (2008) PLoS Comput. Biol. , vol.4
    • Horvath, S.1
  • 46
    • 79954519039 scopus 로고    scopus 로고
    • FNV: light-weight flash-based network and pathway viewer
    • Dannenfelser, R. et al. (2011) FNV: light-weight flash-based network and pathway viewer. Bioinformatics, 27, 1181-1182.
    • (2011) Bioinformatics , vol.27 , pp. 1181-1182
    • Dannenfelser, R.1
  • 47
    • 34648829133 scopus 로고    scopus 로고
    • An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer
    • Teschendorff, A.E. et al. (2007) An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer. Genome Biol., 8, R157.
    • (2007) Genome Biol. , vol.8
    • Teschendorff, A.E.1
  • 48
    • 63349086623 scopus 로고    scopus 로고
    • PDLIM4, an actin binding protein, suppresses prostate cancer cell growth
    • Vanaja, D.K. et al. (2009) PDLIM4, an actin binding protein, suppresses prostate cancer cell growth. Cancer Invest., 27, 264-272.
    • (2009) Cancer Invest. , vol.27 , pp. 264-272
    • Vanaja, D.K.1
  • 49
    • 84862191974 scopus 로고    scopus 로고
    • Methylation of HIN-1, RASSF1A, RIL and CDH13 in breast cancer is associated with clinical characteristics, but only RASSF1A methylation is associated with outcome
    • Xu, J. et al. (2012) Methylation of HIN-1, RASSF1A, RIL and CDH13 in breast cancer is associated with clinical characteristics, but only RASSF1A methylation is associated with outcome. BMC Cancer, 12, 243.
    • (2012) BMC Cancer , vol.12 , pp. 243
    • Xu, J.1
  • 50
    • 81055137232 scopus 로고    scopus 로고
    • FOXM1: From cancer initiation to progression and treatment
    • Koo, C.Y. et al. (2012) FOXM1: From cancer initiation to progression and treatment. Biochim. Biophys. Acta, 1819, 28-37.
    • (2012) Biochim. Biophys. Acta , vol.1819 , pp. 28-37
    • Koo, C.Y.1
  • 51
    • 33947651745 scopus 로고    scopus 로고
    • LRIG inhibitors of growth factor signalling - double- edged swords in human cancer?
    • Hedman, H. et al. (2007) LRIG inhibitors of growth factor signalling - double- edged swords in human cancer? Eur. J. Cancer, 43, 676-682.
    • (2007) Eur. J. Cancer , vol.43 , pp. 676-682
    • Hedman, H.1
  • 52
    • 80054706404 scopus 로고    scopus 로고
    • Lrig1 is an estrogen-regulated growth suppressor and correlates with longer relapse-free survival in ERa-positive breast cancer
    • Krig, S.R. et al. (2011) Lrig1 is an estrogen-regulated growth suppressor and correlates with longer relapse-free survival in ERa-positive breast cancer. Mol. Cancer Res., 9, 1406-1417.
    • (2011) Mol. Cancer Res. , vol.9 , pp. 1406-1417
    • Krig, S.R.1
  • 53
    • 84863248798 scopus 로고    scopus 로고
    • LRIG1 modulates cancer cell sensitivity to Smac mimetics by regulating TNFa expression and receptor tyrosine kinase signaling
    • Bai, L. et al. (2012) LRIG1 modulates cancer cell sensitivity to Smac mimetics by regulating TNFa expression and receptor tyrosine kinase signaling. Cancer Res., 72, 1229-1238.
    • (2012) Cancer Res. , vol.72 , pp. 1229-1238
    • Bai, L.1
  • 54
    • 84859196824 scopus 로고    scopus 로고
    • The pan-ErbB negative regulator Lrig1 is an intestinal stem cell marker that functions as a tumor suppressor
    • Powell, A.E. et al. (2012) The pan-ErbB negative regulator Lrig1 is an intestinal stem cell marker that functions as a tumor suppressor. Cell, 149, 146-158.
    • (2012) Cell , vol.149 , pp. 146-158
    • Powell, A.E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.