메뉴 건너뛰기




Volumn 10, Issue , 2009, Pages

Gene set-based module discovery in the breast cancer transcriptome

Author keywords

[No Author keywords available]

Indexed keywords

BREAST CANCER CELLS; CIS-REGULATORY ELEMENTS; REGULATORY CIRCUITS; REGULATORY MECHANISM; REGULATORY PROGRAM; TRANSCRIPTIONAL PROGRAM; TRANSCRIPTOME DATUM; TRIPLE-NEGATIVE BREAST CANCERS;

EID: 65449121469     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-71     Document Type: Article
Times cited : (29)

References (54)
  • 1
    • 34250887474 scopus 로고    scopus 로고
    • Taking gene-expression profiling to the clinic: When will molecular signatures become relevant to patient care?
    • 10.1038/nrc2173 17585334
    • Sotiriou C Piccart MJ Taking gene-expression profiling to the clinic: when will molecular signatures become relevant to patient care? Nat Rev Cancer 2007, 7:545-553. 10.1038/nrc2173 17585334
    • (2007) Nat Rev Cancer , vol.7 , pp. 545-553
    • Sotiriou, C.1    Piccart, M.J.2
  • 2
    • 54849425774 scopus 로고    scopus 로고
    • Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells
    • 2572072 18823535 10.1186/1471-2105-9-404
    • Niida A Smith AD Imoto S Tsutsumi S Aburatani H Zhang MQ Akiyama T Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells BMC Bioinformatics 9, 404. 2572072 18823535 10.1186/1471-2105-9-404
    • BMC Bioinformatics , vol.9 , pp. 404
    • Niida, A.1    Smith, A.D.2    Imoto, S.3    Tsutsumi, S.4    Aburatani, H.5    Zhang, M.Q.6    Akiyama, T.7
  • 3
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • 9843981 10.1073/pnas.95.25.14863
    • Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci USA 1998, 95:14863-14868. 24541 9843981 10.1073/pnas.95.25.14863
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 14863-14868
    • Eisen, M.B.1    Spellman, P.T.2    Brown, P.O.3    Botstein, D.4
  • 4
    • 1942453302 scopus 로고    scopus 로고
    • Predicting gene expression from sequence
    • 10.1016/S0092-8674(04)00304-6 15084257
    • Beer MA Tavazoie S Predicting gene expression from sequence Cell 2004, 117:185-198. 10.1016/S0092-8674(04)00304-6 15084257
    • (2004) Cell , vol.117 , pp. 185-198
    • Beer, M.A.1    Tavazoie, S.2
  • 6
    • 34447555782 scopus 로고    scopus 로고
    • Mining gene expression profiles: Expression signatures as cancer phenotypes
    • 10.1038/nrg2137 17607306
    • Nevins JR Potti A Mining gene expression profiles: Expression signatures as cancer phenotypes Nat Rev Genet 2007, 8:601-609. 10.1038/nrg2137 17607306
    • (2007) Nat Rev Genet , vol.8 , pp. 601-609
    • Nevins, J.R.1    Potti, A.2
  • 7
    • 20044388557 scopus 로고    scopus 로고
    • From signatures to models: Understanding cancer using microarrays
    • 10.1038/ng1561
    • Segal E Friedman N Kaminski N Regev A Koller D From signatures to models: Understanding cancer using microarrays Nat Genet 37 2005, (Suppl):S38-S45. 10.1038/ng1561
    • (2005) Nat Genet , vol.37 , Issue.SUPPL.
    • Segal, E.1    Friedman, N.2    Kaminski, N.3    Regev, A.4    Koller, D.5
  • 9
    • 33644875782 scopus 로고    scopus 로고
    • A new generation of JASPAR, the open-access repository for transcription factor binding site profiles
    • 1347477 16381983 10.1093/nar/gkj115
    • Vlieghe D Sandelin A De Bleser PJ Vleminckx K Wasserman WW van Roy F Lenhard B A new generation of JASPAR, the open-access repository for transcription factor binding site profiles Nucleic Acids Res 2006, 34:D95- D97. 1347477 16381983 10.1093/nar/gkj115
    • (2006) Nucleic Acids Res , vol.34
    • Vlieghe, D.1    Sandelin, A.2    De Bleser, P.J.3    Vleminckx, K.4    Wasserman, W.W.5    van Roy, F.6    Lenhard, B.7
  • 11
    • 33645809747 scopus 로고    scopus 로고
    • Coordinated binding of NF-kappaB family members in the response of human cells to lipopolysaccharide
    • 1426243 16595631 10.1073/pnas.0510996103
    • Schreiber J Jenner RG Murray HL Gerber GK Gifford DK Young RA Coordinated binding of NF-kappaB family members in the response of human cells to lipopolysaccharide Proc Natl Acad Sci USA 2006, 103:5899-5904. 1426243 16595631 10.1073/pnas.0510996103
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 5899-5904
    • Schreiber, J.1    Jenner, R.G.2    Murray, H.L.3    Gerber, G.K.4    Gifford, D.K.5    Young, R.A.6
  • 16
    • 26444546442 scopus 로고    scopus 로고
    • An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival
    • 1197273 16141321 10.1073/pnas.0506230102
    • Miller LD Smeds J George J Vega VB Vergara L Ploner A Pawitan Y Hall P Klaar S Liu ET Bergh J An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival Proc Natl Acad Sci USA 2005, 102:13550-13555. 1197273 16141321 10.1073/pnas.0506230102
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 13550-13555
    • Miller, L.D.1    Smeds, J.2    George, J.3    Vega, V.B.4    Vergara, L.5    Ploner, A.6    Pawitan, Y.7    Hall, P.8    Klaar, S.9    Liu, E.T.10    Bergh, J.11
  • 19
    • 0034730140 scopus 로고    scopus 로고
    • Singular value decomposition for genome-wide expression data processing and modeling
    • 27718 10963673 10.1073/pnas.97.18.10101
    • Alter O Brown PO Botstein D Singular value decomposition for genome-wide expression data processing and modeling Proc Natl Acad Sci USA 2000, 97:10101-10106. 27718 10963673 10.1073/pnas.97.18.10101
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 10101-10106
    • Alter, O.1    Brown, P.O.2    Botstein, D.3
  • 20
    • 34347219009 scopus 로고    scopus 로고
    • Metagene projection for cross-platform, cross-species characterization of global transcriptional states
    • 1838404 17389406 10.1073/pnas.0701068104
    • Tamayo P Scanfeld D Ebert BL Gillette MA Roberts CW Mesirov JP Metagene projection for cross-platform, cross-species characterization of global transcriptional states Proc Natl Acad Sci USA 2007, 104:5959-5964. 1838404 17389406 10.1073/pnas.0701068104
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 5959-5964
    • Tamayo, P.1    Scanfeld, D.2    Ebert, B.L.3    Gillette, M.A.4    Roberts, C.W.5    Mesirov, J.P.6
  • 21
    • 0035999975 scopus 로고    scopus 로고
    • Application of Bayesian Decomposition for analysing microarray data
    • 10.1093/bioinformatics/18.4.566 12016054
    • Moloshok TD Klevecz RR Grant JD Manion FJ Speier WF IV Ochs MF Application of Bayesian Decomposition for analysing microarray data Bioinformatics 2002, 18:566-575. 10.1093/bioinformatics/18.4.566 12016054
    • (2002) Bioinformatics , vol.18 , pp. 566-575
    • Moloshok, T.D.1    Klevecz, R.R.2    Grant, J.D.3    Manion, F.J.4    Speier IV, W.F.5    Ochs, M.F.6
  • 22
    • 29144442380 scopus 로고    scopus 로고
    • Multi-way clustering of microarray data using probabilistic sparse matrix factorization
    • 10.1093/bioinformatics/bti1041
    • Dueck D Morris QD Frey BJ Multi-way clustering of microarray data using probabilistic sparse matrix factorization Bioinformatics Suppl 2005, 1:i144-i151. 10.1093/bioinformatics/bti1041
    • (2005) Bioinformatics Suppl , vol.1
    • Dueck, D.1    Morris, Q.D.2    Frey, B.J.3
  • 23
    • 0037810449 scopus 로고    scopus 로고
    • Subsystem identification through dimensionality reduction of large-scale gene expression data
    • 403744 12840046 10.1101/gr.903503
    • Kim PM Tidor B Subsystem identification through dimensionality reduction of large-scale gene expression data Genome Res 2003, 13:1706-1718. 403744 12840046 10.1101/gr.903503
    • (2003) Genome Res , vol.13 , pp. 1706-1718
    • Kim, P.M.1    Tidor, B.2
  • 24
    • 0032729435 scopus 로고    scopus 로고
    • Exploring expression data: Identification and analysis of coexpressed genes
    • 310826 10568750 10.1101/gr.9.11.1106
    • Heyer LJ Kruglyak S Yooseph S Exploring expression data: Identification and analysis of coexpressed genes Genome Res 1999, 9:1106-1115. 310826 10568750 10.1101/gr.9.11.1106
    • (1999) Genome Res , vol.9 , pp. 1106-1115
    • Heyer, L.J.1    Kruglyak, S.2    Yooseph, S.3
  • 25
    • 0036080361 scopus 로고    scopus 로고
    • Adaptive quality-based clustering of gene expression profiles
    • 10.1093/bioinformatics/18.5.735 12050070
    • De Smet F Mathys J Marchal K Thijs G De Moor B Moreau Y Adaptive quality-based clustering of gene expression profiles Bioinformatics 2002, 18:735-746. 10.1093/bioinformatics/18.5.735 12050070
    • (2002) Bioinformatics , vol.18 , pp. 735-746
    • De Smet, F.1    Mathys, J.2    Marchal, K.3    Thijs, G.4    De Moor, B.5    Moreau, Y.6
  • 26
    • 15244358503 scopus 로고    scopus 로고
    • Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
    • 10.1038/nature03441 15735639
    • Xie X Lu J Kulbokas EJ Golub TR Mootha V Lindblad-Toh K Lander ES Kellis M Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals Nature 2005, 434:338-345. 10.1038/nature03441 15735639
    • (2005) Nature , vol.434 , pp. 338-345
    • Xie, X.1    Lu, J.2    Kulbokas, E.J.3    Golub, T.R.4    Mootha, V.5    Lindblad-Toh, K.6    Lander, E.S.7    Kellis, M.8
  • 27
    • 33847172748 scopus 로고    scopus 로고
    • Statistical significance of cis-regulatory modules
    • 1796902 17241466 10.1186/1471-2105-8-19
    • Schones DE Smith AD Zhang MQ Statistical significance of cis-regulatory modules BMC Bioinformatics 2007, 8:19. 1796902 17241466 10.1186/ 1471-2105-8-19
    • (2007) BMC Bioinformatics , vol.8 , pp. 19
    • Schones, D.E.1    Smith, A.D.2    Zhang, M.Q.3
  • 28
    • 12344269924 scopus 로고    scopus 로고
    • GO::TermFinder?open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    • 10.1093/bioinformatics/bth456 15297299
    • Boyle EI Weng S Gollub J Jin H Botstein D Cherry JM Sherlock G GO::TermFinder?open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes Bioinformatics 2004, 20:3710-3715. 10.1093/bioinformatics/bth456 15297299
    • (2004) Bioinformatics , vol.20 , pp. 3710-3715
    • Boyle, E.I.1    Weng, S.2    Gollub, J.3    Jin, H.4    Botstein, D.5    Cherry, J.M.6    Sherlock, G.7
  • 30
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software environment for integrated models of biomolecular interaction networks
    • 403769 14597658 10.1101/gr.1239303
    • Shannon P Markiel A Ozier O Baliga NS Wang JT Ramage D Amin N Schwikowski B Ideker T Cytoscape: A software environment for integrated models of biomolecular interaction networks Genome Res 2003, 13:2498-504. 403769 14597658 10.1101/gr.1239303
    • (2003) Genome Res , vol.13 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.S.4    Wang, J.T.5    Ramage, D.6    Amin, N.7    Schwikowski, B.8    Ideker, T.9
  • 32
    • 10044254753 scopus 로고    scopus 로고
    • E2Fs link the control of G1/S and G2/M transcription
    • 533046 15510213 10.1038/sj.emboj.7600459
    • Zhu W Giangrande PH Nevins JR E2Fs link the control of G1/S and G2/M transcription EMBO J 2004, 23:4615-4626. 533046 15510213 10.1038/ sj.emboj.7600459
    • (2004) EMBO J , vol.23 , pp. 4615-4626
    • Zhu, W.1    Giangrande, P.H.2    Nevins, J.R.3
  • 33
    • 0035515347 scopus 로고    scopus 로고
    • The ETS-domain transcription factor family
    • 10.1038/35099076 11715049
    • Sharrocks AD The ETS-domain transcription factor family Nat Rev Mol Cell Biol 2001, 2:827-837. 10.1038/35099076 11715049
    • (2001) Nat Rev Mol Cell Biol , vol.2 , pp. 827-837
    • Sharrocks, A.D.1
  • 34
    • 18344372018 scopus 로고    scopus 로고
    • The RUNX genes: Gain or loss of function in cancer
    • 10.1038/nrc1607 15864279
    • Blyth K Cameron ER Neil JC The RUNX genes: Gain or loss of function in cancer Nat Rev Cancer 2005, 5:376-387. 10.1038/nrc1607 15864279
    • (2005) Nat Rev Cancer , vol.5 , pp. 376-387
    • Blyth, K.1    Cameron, E.R.2    Neil, J.C.3
  • 35
    • 33845768987 scopus 로고    scopus 로고
    • Integrating cell-signalling pathways with NF-kappaB and IKK function
    • 10.1038/nrm2083 17183360
    • Perkins ND Integrating cell-signalling pathways with NF-kappaB and IKK function Nat Rev Mol Cell Biol 2007, 8:49-62. 10.1038/nrm2083 17183360
    • (2007) Nat Rev Mol Cell Biol , vol.8 , pp. 49-62
    • Perkins, N.D.1
  • 36
    • 33748051738 scopus 로고    scopus 로고
    • IRFs: Master regulators of signalling by Toll-like receptors and cytosolic pattern-recognition receptors
    • 10.1038/nri1900 16932750
    • Honda K Taniguchi T IRFs: Master regulators of signalling by Toll-like receptors and cytosolic pattern-recognition receptors Nat Rev Immunol 2006, 6:644-658. 10.1038/nri1900 16932750
    • (2006) Nat Rev Immunol , vol.6 , pp. 644-658
    • Honda, K.1    Taniguchi, T.2
  • 37
    • 34247625135 scopus 로고    scopus 로고
    • Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells
    • 1855231 17437993 10.1101/gad.1524107
    • Tan J Yang X Zhuang L Jiang X Chen W Lee PL Karuturi RK Tan PB Liu ET Yu Q Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells Genes Dev 2007, 21:1050-1063. 1855231 17437993 10.1101/gad.1524107
    • (2007) Genes Dev , vol.21 , pp. 1050-1063
    • Tan, J.1    Yang, X.2    Zhuang, L.3    Jiang, X.4    Chen, W.5    Lee, P.L.6    Karuturi, R.K.7    Tan, P.B.8    Liu, E.T.9    Yu, Q.10
  • 38
    • 0142105414 scopus 로고    scopus 로고
    • EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer
    • 213796 14532106 10.1093/emboj/cdg542
    • Bracken AP Pasini D Capra M Prosperini E Colli E Helin K EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer EMBO J 2003, 22:5323-5335. 213796 14532106 10.1093/ emboj/cdg542
    • (2003) EMBO J , vol.22 , pp. 5323-5335
    • Bracken, A.P.1    Pasini, D.2    Capra, M.3    Prosperini, E.4    Colli, E.5    Helin, K.6
  • 39
    • 42649112047 scopus 로고    scopus 로고
    • An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors
    • 10.1038/ng.127 18443585
    • Ben-Porath I Thomson MW Carey VJ Ge R Bell GW Regev A Weinberg RA An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors Nature Genet 2008, 40:499-507. 10.1038/ng.127 18443585
    • (2008) Nature Genet , vol.40 , pp. 499-507
    • Ben-Porath, I.1    Thomson, M.W.2    Carey, V.J.3    Ge, R.4    Bell, G.W.5    Regev, A.6    Weinberg, R.A.7
  • 41
    • 33749148764 scopus 로고    scopus 로고
    • Modularity of the transcriptional response of protein complexes in yeast
    • 10.1016/j.jmb.2006.06.024 16973176
    • Simonis N Gonze D Orsi C van Helden J Wodak SJ Modularity of the transcriptional response of protein complexes in yeast J Mol Biol 2006, 363:589-610. 10.1016/j.jmb.2006.06.024 16973176
    • (2006) J Mol Biol , vol.363 , pp. 589-610
    • Simonis, N.1    Gonze, D.2    Orsi, C.3    van Helden, J.4    Wodak, S.J.5
  • 42
    • 0141792394 scopus 로고    scopus 로고
    • Correlating protein-DNA and protein-protein interaction networks
    • 10.1016/j.jmb.2003.08.004 14516744
    • Manke T Bringas R Vingron M Correlating protein-DNA and protein-protein interaction networks J Mol Biol 2003, 333:75-85. 10.1016/ j.jmb.2003.08.004 14516744
    • (2003) J Mol Biol , vol.333 , pp. 75-85
    • Manke, T.1    Bringas, R.2    Vingron, M.3
  • 43
    • 3042822267 scopus 로고    scopus 로고
    • Cancer and the chemokine network
    • 10.1038/nrc1388 15229479
    • Balkwill F Cancer and the chemokine network Nat Rev Cancer 2004, 4:540-550. 10.1038/nrc1388 15229479
    • (2004) Nat Rev Cancer , vol.4 , pp. 540-550
    • Balkwill, F.1
  • 45
    • 33745847481 scopus 로고    scopus 로고
    • Interferon regulatory factor 8 regulates RANTES gene transcription in cooperation with interferon regulatory factor-1, NF-kappaB, and PU.1
    • 10.1074/jbc.M602059200 16707500
    • Liu J Ma X Interferon regulatory factor 8 regulates RANTES gene transcription in cooperation with interferon regulatory factor-1, NF-kappaB, and PU.1 J Biol Chem 2006, 281:19188-19195. 10.1074/ jbc.M602059200 16707500
    • (2006) J Biol Chem , vol.281 , pp. 19188-19195
    • Liu, J.1    Ma, X.2
  • 47
    • 6944244084 scopus 로고    scopus 로고
    • A module map showing conditional activity of expression modules in cancer
    • 10.1038/ng1434 15448693
    • Segal E Friedman N Koller D Regev A A module map showing conditional activity of expression modules in cancer Nat Genet 2004, 36:1090-1098. 10.1038/ng1434 15448693
    • (2004) Nat Genet , vol.36 , pp. 1090-1098
    • Segal, E.1    Friedman, N.2    Koller, D.3    Regev, A.4
  • 50
    • 38749102349 scopus 로고    scopus 로고
    • Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis
    • 2217565 18021416 10.1186/1471-2105-8-453
    • Kim TM Chung YJ Rhyu MG Jung MH Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis BMC Bioinformatics 2007, 8:453. 2217565 18021416 10.1186/1471-2105-8-453
    • (2007) BMC Bioinformatics , vol.8 , pp. 453
    • Kim, T.M.1    Chung, Y.J.2    Rhyu, M.G.3    Jung, M.H.4
  • 51
    • 9644268153 scopus 로고    scopus 로고
    • Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays
    • 10.1038/ng1473 15543148
    • Mukherjee S Berger MF Jona G Wang XS Muzzey D Snyder M Young RA Bulyk ML Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays Nat Genet 2004, 36:1331-1339. 10.1038/ng1473 15543148
    • (2004) Nat Genet , vol.36 , pp. 1331-1339
    • Mukherjee, S.1    Berger, M.F.2    Jona, G.3    Wang, X.S.4    Muzzey, D.5    Snyder, M.6    Young, R.A.7    Bulyk, M.L.8
  • 52
    • 33750882505 scopus 로고    scopus 로고
    • Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
    • 10.1038/nbt1246 16998473
    • Berger MF Philippakis AA Qureshi AM He FS Estep PW 3rd Bulyk ML Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities Nat Biotechnol 2006, 24:1429-1435. 10.1038/nbt1246 16998473
    • (2006) Nat Biotechnol , vol.24 , pp. 1429-1435
    • Berger, M.F.1    Philippakis, A.A.2    Qureshi, A.M.3    He, F.S.4    Estep III, P.W.5    Bulyk, M.L.6
  • 53
    • 34249026300 scopus 로고    scopus 로고
    • High-resolution profiling of histone methylations in the human genome
    • 10.1016/j.cell.2007.05.009 17512414
    • Barski A Cuddapah S Cui K Roh TY Schones DE Wang Z Wei G Chepelev I Zhao K High-resolution profiling of histone methylations in the human genome Cell 2007, 129:823-837. 10.1016/j.cell.2007.05.009 17512414
    • (2007) Cell , vol.129 , pp. 823-837
    • Barski, A.1    Cuddapah, S.2    Cui, K.3    Roh, T.Y.4    Schones, D.E.5    Wang, Z.6    Wei, G.7    Chepelev, I.8    Zhao, K.9
  • 54
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • 10.1126/science.1141319 17540862
    • Johnson DS Mortazavi A Myers RM Wold B Genome-wide mapping of in vivo protein-DNA interactions Science 2007, 316:1497-1502. 10.1126/ science.1141319 17540862
    • (2007) Science , vol.316 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.