메뉴 건너뛰기




Volumn 7, Issue 9, 2011, Pages

Protein networks as logic functions in development and cancer

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER CIRCUITS; DISEASES; GENES; ONCOGENIC VIRUSES;

EID: 80053446196     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002180     Document Type: Article
Times cited : (90)

References (70)
  • 4
    • 14644425319 scopus 로고    scopus 로고
    • Mechanisms of BCR-ABL in the pathogenesis of chronic myelogenous leukaemia
    • Ren R, (2005) Mechanisms of BCR-ABL in the pathogenesis of chronic myelogenous leukaemia. Nat Rev Cancer 5: 172-183.
    • (2005) Nat Rev Cancer , vol.5 , pp. 172-183
    • Ren, R.1
  • 5
    • 1242338856 scopus 로고    scopus 로고
    • Huntingtin-protein interactions and the pathogenesis of Huntington's disease
    • Li SH, Li XJ, (2004) Huntingtin-protein interactions and the pathogenesis of Huntington's disease. Trends Genet 20: 146-154.
    • (2004) Trends Genet , vol.20 , pp. 146-154
    • Li, S.H.1    Li, X.J.2
  • 7
    • 33748467781 scopus 로고    scopus 로고
    • cis-regulatory processing of Notch signaling input to the sea urchin glial cells missing gene during mesoderm specification
    • Ransick A, Davidson EH, (2006) cis-regulatory processing of Notch signaling input to the sea urchin glial cells missing gene during mesoderm specification. Dev Biol 297: 587-602.
    • (2006) Dev Biol , vol.297 , pp. 587-602
    • Ransick, A.1    Davidson, E.H.2
  • 8
    • 75749101495 scopus 로고    scopus 로고
    • Chromatin remodelling during development
    • Ho L, Crabtree GR, (2010) Chromatin remodelling during development. Nature 463: 474-484.
    • (2010) Nature , vol.463 , pp. 474-484
    • Ho, L.1    Crabtree, G.R.2
  • 9
    • 65249180173 scopus 로고    scopus 로고
    • An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency
    • Ho L, Ronan JL, Wu J, Staahl BT, Chen L, et al. (2009) An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. Proc Natl Acad Sci U S A 106: 5181-5186.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 5181-5186
    • Ho, L.1    Ronan, J.L.2    Wu, J.3    Staahl, B.T.4    Chen, L.5
  • 10
    • 34447249019 scopus 로고    scopus 로고
    • An essential switch in subunit composition of a chromatin remodeling complex during neural development
    • Lessard J, Wu JI, Ranish JA, Wan M, Winslow MM, et al. (2007) An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron 55: 201-215.
    • (2007) Neuron , vol.55 , pp. 201-215
    • Lessard, J.1    Wu, J.I.2    Ranish, J.A.3    Wan, M.4    Winslow, M.M.5
  • 11
    • 1042290351 scopus 로고    scopus 로고
    • The SWI/SNF complex--chromatin and cancer
    • Roberts CW, Orkin SH, (2004) The SWI/SNF complex--chromatin and cancer. Nat Rev Cancer 4: 133-142.
    • (2004) Nat Rev Cancer , vol.4 , pp. 133-142
    • Roberts, C.W.1    Orkin, S.H.2
  • 12
    • 6944244084 scopus 로고    scopus 로고
    • A module map showing conditional activity of expression modules in cancer
    • 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.
    • (2004) Nat Genet , vol.36 , pp. 1090-1098
    • Segal, E.1    Friedman, N.2    Koller, D.3    Regev, A.4
  • 13
    • 52149097555 scopus 로고    scopus 로고
    • Regulatory networks define phenotypic classes of human stem cell lines
    • Muller FJ, Laurent LC, Kostka D, Ulitsky I, Williams R, et al. (2008) Regulatory networks define phenotypic classes of human stem cell lines. Nature 455: 401-405.
    • (2008) Nature , vol.455 , pp. 401-405
    • Muller, F.J.1    Laurent, L.C.2    Kostka, D.3    Ulitsky, I.4    Williams, R.5
  • 14
    • 75149195336 scopus 로고    scopus 로고
    • The transcriptional network for mesenchymal transformation of brain tumours
    • Carro MS, Lim WK, Alvarez MJ, Bollo RJ, Zhao X, et al. (2009) The transcriptional network for mesenchymal transformation of brain tumours. Nature 463: 318-325.
    • (2009) Nature , vol.463 , pp. 318-325
    • Carro, M.S.1    Lim, W.K.2    Alvarez, M.J.3    Bollo, R.J.4    Zhao, X.5
  • 15
    • 77649299348 scopus 로고    scopus 로고
    • An atlas of combinatorial transcriptional regulation in mouse and man
    • Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, et al. (2010) An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140: 744-752.
    • (2010) Cell , vol.140 , pp. 744-752
    • Ravasi, T.1    Suzuki, H.2    Cannistraci, C.V.3    Katayama, S.4    Bajic, V.B.5
  • 16
    • 77953255983 scopus 로고    scopus 로고
    • A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers
    • Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, et al. (2010) A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol 6: 377.
    • (2010) Mol Syst Biol , vol.6 , pp. 377
    • Lefebvre, C.1    Rajbhandari, P.2    Alvarez, M.J.3    Bandaru, P.4    Lim, W.K.5
  • 17
    • 0000801240 scopus 로고    scopus 로고
    • Discovering regulatory and signalling circuits in molecular interaction networks
    • Ideker T, Ozier O, Schwikowski B, Siegel AF, (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18 (Suppl 1): S233-240.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Ideker, T.1    Ozier, O.2    Schwikowski, B.3    Siegel, A.F.4
  • 18
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
    • Segal E, Shapira M, Regev A, Pe'er D, Botstein D, et al. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 34: 166-176.
    • (2003) Nat Genet , vol.34 , pp. 166-176
    • Segal, E.1    Shapira, M.2    Regev, A.3    Pe'er, D.4    Botstein, D.5
  • 21
    • 37849022459 scopus 로고    scopus 로고
    • Identification of key processes underlying cancer phenotypes using biologic pathway analysis
    • Efroni S, Schaefer CF, Buetow KH, (2007) Identification of key processes underlying cancer phenotypes using biologic pathway analysis. PLoS One 2: e425.
    • (2007) PLoS One , vol.2
    • Efroni, S.1    Schaefer, C.F.2    Buetow, K.H.3
  • 23
    • 34548742517 scopus 로고    scopus 로고
    • Identification of functional modules using network topology and high-throughput data
    • Ulitsky I, Shamir R, (2007) Identification of functional modules using network topology and high-throughput data. BMC Syst Biol 1: 8.
    • (2007) BMC Syst Biol , vol.1 , pp. 8
    • Ulitsky, I.1    Shamir, R.2
  • 24
    • 67049160152 scopus 로고    scopus 로고
    • Learning on weighted hypergraphs to integrate protein interactions and gene expressions for cancer outcome prediction
    • Washington, DC, USA, IEEE Computer Society
    • Hwang T, Tian Z, Kocher J, Kuang R, (2008) Learning on weighted hypergraphs to integrate protein interactions and gene expressions for cancer outcome prediction. Proceedings of the 2008 Eighth IEEE International Conference on Data Mining Washington, DC, USA IEEE Computer Society pp. 293-302.
    • (2008) Proceedings of the 2008 Eighth IEEE International Conference on Data Mining , pp. 293-302
    • Hwang, T.1    Tian, Z.2    Kocher, J.3    Kuang, R.4
  • 25
  • 27
    • 59849125136 scopus 로고    scopus 로고
    • Dynamic modularity in protein interaction networks predicts breast cancer outcome
    • Taylor IW, Linding R, Warde-Farley D, Liu Y, Pesquita C, et al. (2009) Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol 27: 199-204.
    • (2009) Nat Biotechnol , vol.27 , pp. 199-204
    • Taylor, I.W.1    Linding, R.2    Warde-Farley, D.3    Liu, Y.4    Pesquita, C.5
  • 29
    • 76749148657 scopus 로고    scopus 로고
    • An integrative -omics approach to identify functional sub-networks in human colorectal cancer
    • Nibbe RK, Koyuturk M, Chance MR, (2010) An integrative-omics approach to identify functional sub-networks in human colorectal cancer. PLoS Comput Biol 6: e1000639.
    • (2010) PLoS Comput Biol , vol.6
    • Nibbe, R.K.1    Koyuturk, M.2    Chance, M.R.3
  • 30
    • 78149460182 scopus 로고    scopus 로고
    • DEGAS: de novo discovery of dysregulated pathways in human diseases
    • Ulitsky I, Krishnamurthy A, Karp RM, Shamir R, (2010) DEGAS: de novo discovery of dysregulated pathways in human diseases. PLoS One 5: e13367.
    • (2010) PLoS One , vol.5
    • Ulitsky, I.1    Krishnamurthy, A.2    Karp, R.M.3    Shamir, R.4
  • 31
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman L, (2001) Random forests. Machine Learning 45: 5-32.
    • (2001) Machine Learning , vol.45 , pp. 5-32
    • Breiman, L.1
  • 33
    • 0020300879 scopus 로고
    • Decision Trees and Diagrams
    • Moret BME, (1982) Decision Trees and Diagrams. ACM Computing Surveys 14: 593-623.
    • (1982) ACM Computing Surveys , vol.14 , pp. 593-623
    • Moret, B.M.E.1
  • 35
    • 67349166946 scopus 로고    scopus 로고
    • Detecting gene-gene interactions that underlie human diseases
    • Cordell HJ, (2009) Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet 10: 392-404.
    • (2009) Nat Rev Genet , vol.10 , pp. 392-404
    • Cordell, H.J.1
  • 37
    • 0033958662 scopus 로고    scopus 로고
    • Smad1 domains interacting with Hoxc-8 induce osteoblast differentiation
    • Yang X, Ji X, Shi X, Cao X, (2000) Smad1 domains interacting with Hoxc-8 induce osteoblast differentiation. J Biol Chem 275: 1065-1072.
    • (2000) J Biol Chem , vol.275 , pp. 1065-1072
    • Yang, X.1    Ji, X.2    Shi, X.3    Cao, X.4
  • 39
    • 78249235739 scopus 로고    scopus 로고
    • The Mammalian Phenotype Ontology: enabling robust annotation and comparative analysis
    • Smith CL, Eppig JT, (2009) The Mammalian Phenotype Ontology: enabling robust annotation and comparative analysis. Wiley Interdiscip Rev Syst Biol Med 1: 390-399.
    • (2009) Wiley Interdiscip Rev Syst Biol Med , vol.1 , pp. 390-399
    • Smith, C.L.1    Eppig, J.T.2
  • 40
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5
  • 41
    • 0037137519 scopus 로고    scopus 로고
    • A gene-expression signature as a predictor of survival in breast cancer
    • van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, et al. (2002) A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 347: 1999-2009.
    • (2002) N Engl J Med , vol.347 , pp. 1999-2009
    • van de Vijver, M.J.1    He, Y.D.2    van't Veer, L.J.3    Dai, H.4    Hart, A.A.5
  • 42
    • 13844310310 scopus 로고    scopus 로고
    • Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer
    • Wang Y, Klijn JG, Zhang Y, Sieuwerts AM, Look MP, 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    Klijn, J.G.2    Zhang, Y.3    Sieuwerts, A.M.4    Look, M.P.5
  • 43
    • 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 HS, Kharbanda S, Chen R, Forrest WF, Soriano RH, et al. (2006) 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) Cancer Cell , vol.9 , pp. 157-173
    • Phillips, H.S.1    Kharbanda, S.2    Chen, R.3    Forrest, W.F.4    Soriano, R.H.5
  • 44
    • 0037434785 scopus 로고    scopus 로고
    • CCAAT/enhancer binding protein beta (C/EBPbeta)-2 transforms normal mammary epithelial cells and induces epithelial to mesenchymal transition in culture
    • Bundy LM, Sealy L, (2003) CCAAT/enhancer binding protein beta (C/EBPbeta)-2 transforms normal mammary epithelial cells and induces epithelial to mesenchymal transition in culture. Oncogene 22: 869-883.
    • (2003) Oncogene , vol.22 , pp. 869-883
    • Bundy, L.M.1    Sealy, L.2
  • 45
    • 13444263403 scopus 로고    scopus 로고
    • Stat5 promotes homotypic adhesion and inhibits invasive characteristics of human breast cancer cells
    • Sultan AS, Xie J, LeBaron MJ, Ealley EL, Nevalainen MT, et al. (2005) Stat5 promotes homotypic adhesion and inhibits invasive characteristics of human breast cancer cells. Oncogene 24: 746-760.
    • (2005) Oncogene , vol.24 , pp. 746-760
    • Sultan, A.S.1    Xie, J.2    LeBaron, M.J.3    Ealley, E.L.4    Nevalainen, M.T.5
  • 46
    • 77956929098 scopus 로고    scopus 로고
    • Heat-shock transcription factor HSF1 has a critical role in human epidermal growth factor receptor-2-induced cellular transformation and tumorigenesis
    • Meng L, Gabai VL, Sherman MY, (2010) Heat-shock transcription factor HSF1 has a critical role in human epidermal growth factor receptor-2-induced cellular transformation and tumorigenesis. Oncogene 29: 5204-5213.
    • (2010) Oncogene , vol.29 , pp. 5204-5213
    • Meng, L.1    Gabai, V.L.2    Sherman, M.Y.3
  • 47
    • 0346969980 scopus 로고    scopus 로고
    • Dendrite development regulated by CREST, a calcium-regulated transcriptional activator
    • Aizawa H, Hu SC, Bobb K, Balakrishnan K, Ince G, et al. (2004) Dendrite development regulated by CREST, a calcium-regulated transcriptional activator. Science 303: 197-202.
    • (2004) Science , vol.303 , pp. 197-202
    • Aizawa, H.1    Hu, S.C.2    Bobb, K.3    Balakrishnan, K.4    Ince, G.5
  • 49
    • 0034614637 scopus 로고    scopus 로고
    • The hallmarks of cancer
    • Hanahan D, Weinberg RA, (2000) The hallmarks of cancer. Cell 100: 57-70.
    • (2000) Cell , vol.100 , pp. 57-70
    • Hanahan, D.1    Weinberg, R.A.2
  • 50
    • 29144504350 scopus 로고    scopus 로고
    • Functional and physical communication between oncoproteins and tumor suppressors
    • Prochownik EV, (2005) Functional and physical communication between oncoproteins and tumor suppressors. Cell Mol Life Sci 62: 2438-2459.
    • (2005) Cell Mol Life Sci , vol.62 , pp. 2438-2459
    • Prochownik, E.V.1
  • 51
    • 13444282534 scopus 로고    scopus 로고
    • Outcome signature genes in breast cancer: is there a unique set?
    • Ein-Dor L, Kela I, Getz G, Givol D, Domany E, (2005) Outcome signature genes in breast cancer: is there a unique set? Bioinformatics 21: 171-178.
    • (2005) Bioinformatics , vol.21 , pp. 171-178
    • Ein-Dor, L.1    Kela, I.2    Getz, G.3    Givol, D.4    Domany, E.5
  • 52
    • 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, (2006) Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci U S A 103: 5923-5928.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 5923-5928
    • Ein-Dor, L.1    Zuk, O.2    Domany, E.3
  • 53
    • 79952659846 scopus 로고    scopus 로고
    • Boosting Signal-to-Noise in Complex Biology: Prior Knowledge Is Power
    • Ideker T, Dutkowski J, Hood L, (2011) Boosting Signal-to-Noise in Complex Biology: Prior Knowledge Is Power. Cell 144: 860-863.
    • (2011) Cell , vol.144 , pp. 860-863
    • Ideker, T.1    Dutkowski, J.2    Hood, L.3
  • 54
    • 23344431857 scopus 로고    scopus 로고
    • Group 13 HOX proteins interact with the MH2 domain of R-Smads and modulate Smad transcriptional activation functions independent of HOX DNA-binding capability
    • Williams TM, Williams ME, Heaton JH, Gelehrter TD, Innis JW, (2005) Group 13 HOX proteins interact with the MH2 domain of R-Smads and modulate Smad transcriptional activation functions independent of HOX DNA-binding capability. Nucleic Acids Res 33: 4475-4484.
    • (2005) Nucleic Acids Res , vol.33 , pp. 4475-4484
    • Williams, T.M.1    Williams, M.E.2    Heaton, J.H.3    Gelehrter, T.D.4    Innis, J.W.5
  • 57
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang da W, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
    • (2009) Nat Protoc , vol.4 , pp. 44-57
    • da Huang, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 61
    • 33847172327 scopus 로고    scopus 로고
    • Clustering by passing messages between data points
    • Frey BJ, Dueck D, (2007) Clustering by passing messages between data points. Science 315: 972-976.
    • (2007) Science , vol.315 , pp. 972-976
    • Frey, B.J.1    Dueck, D.2
  • 62
    • 38449101120 scopus 로고    scopus 로고
    • Integration of biological networks and gene expression data using Cytoscape
    • Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2: 2366-2382.
    • (2007) Nat Protoc , vol.2 , pp. 2366-2382
    • Cline, M.S.1    Smoot, M.2    Cerami, E.3    Kuchinsky, A.4    Landys, N.5
  • 63
    • 77954468404 scopus 로고    scopus 로고
    • MODEVO: exploring modularity and evolution of protein interaction networks
    • Wozniak M, Tiuryn J, Dutkowski J, (2010) MODEVO: exploring modularity and evolution of protein interaction networks. Bioinformatics 26: 1790-1791.
    • (2010) Bioinformatics , vol.26 , pp. 1790-1791
    • Wozniak, M.1    Tiuryn, J.2    Dutkowski, J.3
  • 64
    • 0031724589 scopus 로고    scopus 로고
    • TAL1 and LIM-only proteins synergistically induce retinaldehyde dehydrogenase 2 expression in T-cell acute lymphoblastic leukemia by acting as cofactors for GATA3
    • Ono Y, Fukuhara N, Yoshie O, (1998) TAL1 and LIM-only proteins synergistically induce retinaldehyde dehydrogenase 2 expression in T-cell acute lymphoblastic leukemia by acting as cofactors for GATA3. Mol Cell Biol 18: 6939-6950.
    • (1998) Mol Cell Biol , vol.18 , pp. 6939-6950
    • Ono, Y.1    Fukuhara, N.2    Yoshie, O.3
  • 66
    • 16844370003 scopus 로고    scopus 로고
    • HOXA9 activates transcription of the gene encoding gp91Phox during myeloid differentiation
    • Bei L, Lu Y, Eklund EA, (2005) HOXA9 activates transcription of the gene encoding gp91Phox during myeloid differentiation. J Biol Chem 280: 12359-12370.
    • (2005) J Biol Chem , vol.280 , pp. 12359-12370
    • Bei, L.1    Lu, Y.2    Eklund, E.A.3
  • 67
    • 34247608645 scopus 로고    scopus 로고
    • HOXA10 controls osteoblastogenesis by directly activating bone regulatory and phenotypic genes
    • Hassan MQ, Tare R, Lee SH, Mandeville M, Weiner B, et al. (2007) HOXA10 controls osteoblastogenesis by directly activating bone regulatory and phenotypic genes. Mol Cell Biol 27: 3337-3352.
    • (2007) Mol Cell Biol , vol.27 , pp. 3337-3352
    • Hassan, M.Q.1    Tare, R.2    Lee, S.H.3    Mandeville, M.4    Weiner, B.5
  • 68
    • 0033604898 scopus 로고    scopus 로고
    • IkappaB-alpha enhances transactivation by the HOXB7 homeodomain-containing protein
    • Chariot A, Princen F, Gielen J, Merville MP, Franzoso G, et al. (1999) IkappaB-alpha enhances transactivation by the HOXB7 homeodomain-containing protein. J Biol Chem 274: 5318-5325.
    • (1999) J Biol Chem , vol.274 , pp. 5318-5325
    • Chariot, A.1    Princen, F.2    Gielen, J.3    Merville, M.P.4    Franzoso, G.5
  • 70
    • 0037447462 scopus 로고    scopus 로고
    • Sox10 and Pax3 physically interact to mediate activation of a conserved c-RET enhancer
    • Lang D, Epstein JA, (2003) Sox10 and Pax3 physically interact to mediate activation of a conserved c-RET enhancer. Hum Mol Genet 12: 937-945.
    • (2003) Hum Mol Genet , vol.12 , pp. 937-945
    • Lang, D.1    Epstein, J.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.