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Volumn 6, Issue 8, 2010, Pages

Use of data-biased random walks on graphs for the retrieval of context-specific networks from genomic data

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION; GENOME; RANDOM PROCESSES;

EID: 78049437880     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000889     Document Type: Article
Times cited : (83)

References (35)
  • 1
  • 3
    • 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
  • 5
    • 40949085272 scopus 로고    scopus 로고
    • Pathway analysis tools and toxicogenomics reference databases for risk assessment
    • Ganter B, Zidek N, Hewitt PR, Muller D, Vladimirova A (2008) Pathway analysis tools and toxicogenomics reference databases for risk assessment. Pharmacogenomics 9: 35-54.
    • (2008) Pharmacogenomics , vol.9 , pp. 35-54
    • Ganter, B.1    Zidek, N.2    Hewitt, P.R.3    Muller, D.4    Vladimirova, A.5
  • 6
    • 67649601037 scopus 로고    scopus 로고
    • RNAiCut: Automated detection of significant genes from functional genomic screens
    • Kaplow IM, Singh R, Friedman A, Bakal C, Perrimon N, et al. (2009) RNAiCut: automated detection of significant genes from functional genomic screens. Nat Methods 6: 476-477.
    • (2009) Nat Methods , vol.6 , pp. 476-477
    • Kaplow, I.M.1    Singh, R.2    Friedman, A.3    Bakal, C.4    Perrimon, N.5
  • 7
    • 65549138481 scopus 로고    scopus 로고
    • Identifying disease-specific genes based on their topological significance in protein networks
    • Dezso Z, Nikolsky Y, Nikolskaya T, Miller J, Cherba D, et al. (2009) Identifying disease-specific genes based on their topological significance in protein networks. BMC Syst Biol 3: 36.
    • (2009) BMC Syst Biol , vol.3 , pp. 36
    • Dezso, Z.1    Nikolsky, Y.2    Nikolskaya, T.3    Miller, J.4    Cherba, D.5
  • 9
    • 18944391092 scopus 로고    scopus 로고
    • Biological networks and analysis of experimental data in drug discovery
    • Nikolsky Y, Nikolskaya T, Bugrim A (2005) Biological networks and analysis of experimental data in drug discovery. Drug Discov Today 10: 653-662.
    • (2005) Drug Discov Today , vol.10 , pp. 653-662
    • Nikolsky, Y.1    Nikolskaya, T.2    Bugrim, A.3
  • 10
    • 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
  • 11
    • 65449141657 scopus 로고    scopus 로고
    • Identifying functional modules using expression profiles and confidence-scored protein interactions
    • Ulitsky I, Shamir R (2009) Identifying functional modules using expression profiles and confidence-scored protein interactions. Bioinformatics 25: 1158-1164.
    • (2009) Bioinformatics , vol.25 , pp. 1158-1164
    • Ulitsky, I.1    Shamir, R.2
  • 12
    • 1042302103 scopus 로고    scopus 로고
    • Early prediction of drug metabolism and toxicity: Systems biology approach and modeling
    • Bugrim A, Nikolskaya T, Nikolsky Y (2004) Early prediction of drug metabolism and toxicity: systems biology approach and modeling. Drug Discov Today 9: 127-135.
    • (2004) Drug Discov Today , vol.9 , pp. 127-135
    • Bugrim, A.1    Nikolskaya, T.2    Nikolsky, Y.3
  • 13
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102: 15545-15550.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 15545-15550
    • Subramanian, A.1    Tamayo, P.2    Mootha, V.K.3    Mukherjee, S.4    Ebert, B.L.5
  • 14
    • 33845884027 scopus 로고    scopus 로고
    • Integrative molecular concept modeling of prostate cancer progression
    • Tomlins SA, Mehra R, Rhodes DR, Cao X, Wang L, et al. (2007) Integrative molecular concept modeling of prostate cancer progression. Nat Genet 39: 41-51.
    • (2007) Nat Genet , vol.39 , pp. 41-51
    • Tomlins, S.A.1    Mehra, R.2    Rhodes, D.R.3    Cao, X.4    Wang, L.5
  • 15
    • 43349091946 scopus 로고    scopus 로고
    • Using GenMAPP and MAPPFinder to view microarray data on biological pathways and identify global trends in the data
    • Unit 75
    • Dahlquist KD (2004) Using GenMAPP and MAPPFinder to view microarray data on biological pathways and identify global trends in the data. Curr Protoc Bioinformatics Chapter 7: Unit 7 5.
    • (2004) Curr Protoc Bioinformatics Chapter , vol.7
    • Dahlquist, K.D.1
  • 18
    • 39549086558 scopus 로고    scopus 로고
    • Maps of random walks on complex networks reveal community structure
    • Rosvall M, Bergstrom CT (2008) Maps of random walks on complex networks reveal community structure. Proc Natl Acad Sci U S A 105: 1118-1123.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 1118-1123
    • Rosvall, M.1    Bergstrom, C.T.2
  • 24
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 27
  • 28
    • 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
  • 29
    • 39149095963 scopus 로고    scopus 로고
    • Assay for apoptosis using the mitochondrial probes, Rhodamine123 and 10-N-nonyl acridine orange
    • Ferlini C, Scambia G (2007) Assay for apoptosis using the mitochondrial probes, Rhodamine123 and 10-N-nonyl acridine orange. Nat Protoc 2: 3111-3114.
    • (2007) Nat Protoc , vol.2 , pp. 3111-3114
    • Ferlini, C.1    Scambia, G.2
  • 30
    • 33749080967 scopus 로고    scopus 로고
    • Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*
    • Barrett T, Edgar R (2006) Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*. Methods Mol Biol 338: 175-190.
    • (2006) Methods Mol Biol , vol.338 , pp. 175-190
    • Barrett, T.1    Edgar, R.2
  • 31
    • 33845209913 scopus 로고    scopus 로고
    • A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes
    • Neve RM, Chin K, Fridlyand J, Yeh J, Baehner FL, et al. (2006) A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 10: 515-527.
    • (2006) Cancer Cell , vol.10 , pp. 515-527
    • Neve, R.M.1    Chin, K.2    Fridlyand, J.3    Yeh, J.4    Baehner, F.L.5
  • 32
    • 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
  • 33
    • 17644427718 scopus 로고    scopus 로고
    • Causal proteinsignaling networks derived from multiparameter single-cell data
    • Sachs K, Perez O, Pe'er D, Lauffenburger DA, Nolan GP (2005) Causal proteinsignaling networks derived from multiparameter single-cell data. Science 308: 523-529.
    • (2005) Science , vol.308 , pp. 523-529
    • Sachs, K.1    Perez, O.2    Pe'er, D.3    Lauffenburger, D.A.4    Nolan, G.P.5
  • 34
    • 51049117937 scopus 로고    scopus 로고
    • Models from experiments: Combinatorial drug perturbations of cancer cells
    • Nelander S, Wang W, Nilsson B, She QB, Pratilas C, et al. (2008) Models from experiments: combinatorial drug perturbations of cancer cells. Mol Syst Biol 4: 216.
    • (2008) Mol Syst Biol , vol.4 , pp. 216
    • Nelander, S.1    Wang, W.2    Nilsson, B.3    She, Q.B.4    Pratilas, C.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.