메뉴 건너뛰기




Volumn 9, Issue 72, 2012, Pages 1625-1636

Implications of functional similarity for gene regulatory interactions

Author keywords

Functional similarity; Gene ontology; Gene regulatory networks

Indexed keywords

ESCHERICHIA COLI; GENE EXPRESSION; YEAST;

EID: 84863569195     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2011.0585     Document Type: Article
Times cited : (9)

References (39)
  • 1
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The Gene Ontology consortium
    • doi:10.1038/75556
    • Ashburner, M. et al. 2000 Gene ontology: tool for the unification of biology. The Gene Ontology consortium. Nat. Genet. 25, 25-29. (doi:10.1038/75556)
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 2
    • 75849158230 scopus 로고    scopus 로고
    • The Gene Ontology in 2010: Extensions and refinements
    • doi:10.1093/nar/gkp1018
    • Consortium, T. G. O. 2010 The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 38(Suppl. 1), D331-D335. (doi:10.1093/nar/ gkp1018)
    • (2010) Nucleic Acids Res , vol.38 , Issue.SUPPL. 1
    • Consortium, T.G.O.1
  • 3
    • 34547589578 scopus 로고    scopus 로고
    • DAVID Bioinformatics resources: Expanded annotation database and novel algorithms to better extract biology from large gene lists
    • doi:10.1093/nar/gkm415
    • Huang, D. W. et al. 2007 DAVID Bioinformatics resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 35(Suppl. 2), W169-W175. (doi:10.1093/nar/gkm415)
    • (2007) Nucleic Acids Res , vol.35 , Issue.SUPPL. 2
    • Huang, D.W.1
  • 4
    • 77954309042 scopus 로고    scopus 로고
    • Fast integration of heterogeneous data sources for predicting gene function with limited annotation
    • doi:10.1093/bioinformatics/btq262
    • Mostafavi, S. & Morris, Q. 2010 Fast integration of heterogeneous data sources for predicting gene function with limited annotation. Bioinformatics 26, 1759-1765. (doi:10.1093/bioinformatics/btq262)
    • (2010) Bioinformatics , vol.26 , pp. 1759-1765
    • Mostafavi, S.1    Morris, Q.2
  • 5
    • 0037767293 scopus 로고    scopus 로고
    • Predicting gene function from patterns of annotation
    • doi:10.1101/gr.440803
    • King, O. D., Foulger, R. E., Dwight, S. S., White, J. V. & Roth, F. P. 2003 Predicting gene function from patterns of annotation. Genome Res. 13, 896-904. (doi:10.1101/gr.440803)
    • (2003) Genome Res , vol.13 , pp. 896-904
    • King, O.D.1    Foulger, R.E.2    Dwight, S.S.3    White, J.V.4    Roth, F.P.5
  • 6
    • 77955039075 scopus 로고    scopus 로고
    • Learning transcriptional networks from the integration of ChIP-chip and expression data in a non-parametric model
    • doi:10.1093/bioinformatics/btq289
    • Youn, A., Reiss, D. J. & Stuetzle, W. 2010 Learning transcriptional networks from the integration of ChIP-chip and expression data in a non-parametric model. Bioinformatics 26, 1879-1886. (doi:10.1093/bioinformatics/ btq289)
    • (2010) Bioinformatics , vol.26 , pp. 1879-1886
    • Youn, A.1    Reiss, D.J.2    Stuetzle, W.3
  • 7
    • 9444239213 scopus 로고    scopus 로고
    • A probabilistic functional network of yeast genes
    • doi:10.1126/science.1099511
    • Lee, I., Date, S. V., Adai, A. T. & Marcotte, E. M. 2004 A probabilistic functional network of yeast genes. Science 306, 1555-1558. (doi:10.1126/science.1099511)
    • (2004) Science , vol.306 , pp. 1555-1558
    • Lee, I.1    Date, S.V.2    Adai, A.T.3    Marcotte, E.M.4
  • 8
    • 33646884801 scopus 로고    scopus 로고
    • Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes
    • doi:10.1086/504300
    • Franke, L., Van Bakel, H., Fokkens, L., de Jong, E. D., Egmont-Petersen, M. & Wijmenga, C. 2006 Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am. J. Hum. Genet. 78, 1011-1025. (doi:10.1086/504300)
    • (2006) Am. J. Hum. Genet. , vol.78 , pp. 1011-1025
    • Franke, L.1    Van Bakel, H.2    Fokkens, L.3    De Jong, E.D.4    Egmont-Petersen, M.5    Wijmenga, C.6
  • 9
    • 69949134573 scopus 로고    scopus 로고
    • Reconstruct modular phenotype-specific gene networks by knowledge-driven matrix factorization
    • doi:10.1093/bioinformatics/btp376
    • Yang, X., Zhou, Y., Jin, R. & Chan, C. 2009 Reconstruct modular phenotype-specific gene networks by knowledge-driven matrix factorization. Bioinformatics 25, 2236-2243. (doi:10.1093/bioinformatics/btp376)
    • (2009) Bioinformatics , vol.25 , pp. 2236-2243
    • Yang, X.1    Zhou, Y.2    Jin, R.3    Chan, C.4
  • 10
    • 0038718854 scopus 로고    scopus 로고
    • The structure and function of complex networks
    • doi:10.1137/S003614450342480
    • Newman, M. E. J. 2003 The structure and function of complex networks. SIAM Rev. 45, 167-256. (doi:10.1137/S003614450342480)
    • (2003) SIAM Rev , vol.45 , pp. 167-256
    • Newman, M.E.J.1
  • 11
    • 0037174670 scopus 로고    scopus 로고
    • Network motifs: Simple building blocks of complex networks
    • doi:10.1126/science.298.5594.824
    • Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D. & Alon, U. 2002 Network motifs: simple building blocks of complex networks. Science 298, 824-827. (doi:10.1126/science.298.5594.824)
    • (2002) Science , vol.298 , pp. 824-827
    • Milo, R.1    Shen-Orr, S.2    Itzkovitz, S.3    Kashtan, N.4    Chklovskii, D.5    Alon, U.6
  • 12
    • 85040474279 scopus 로고    scopus 로고
    • Selection, tinkering, and emergence in complex networks
    • doi:10.1002/cplx.10055
    • Solé, R. V., Cancho, R. F., Montoya, J. M. & Valverde, S. 2002 Selection, tinkering, and emergence in complex networks. Complex 8, 20-33. (doi:10.1002/cplx.10055)
    • (2002) Complex , vol.8 , pp. 20-33
    • Solé, R.V.1    Cancho, R.F.2    Montoya, J.M.3    Valverde, S.4
  • 13
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • doi:10.1038/35075138
    • Jeong, H., Mason, S. P., Barabási, A. L. & Oltvai, Z. N. 2001 Lethality and centrality in protein networks. Nature 411, 41-42. (doi:10.1038/35075138)
    • (2001) Nature , vol.411 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabási, A.L.3    Oltvai, Z.N.4
  • 14
    • 0034943378 scopus 로고    scopus 로고
    • The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes
    • Wagner, A. 2001 The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol. Biol. Evol. 18, 1283-1292. (Pubitemid 32660673)
    • (2001) Molecular Biology and Evolution , vol.18 , Issue.7 , pp. 1283-1292
    • Wagner, A.1
  • 15
    • 14644396645 scopus 로고    scopus 로고
    • Functional cartography of complex metabolic networks
    • doi:10.1038/nature03288
    • Guimera, R. & Nunes Amaral, L. A. 2005 Functional cartography of complex metabolic networks. Nature 433, 895-900. (doi:10.1038/nature03288)
    • (2005) Nature , vol.433 , pp. 895-900
    • Guimera, R.1    Nunes Amaral, L.A.2
  • 16
    • 33748650631 scopus 로고    scopus 로고
    • Complex networks theory for analyzing metabolic networks
    • DOI 10.1007/s11434-006-2015-2
    • Zhao, J., Yu, H., Luo, J., Cao, Z. & Li, Y. 2006 Complex networks theory for analyzing metabolic networks. Chin. Sci. Bull. 51, 1529-1537. (Pubitemid 44432167)
    • (2006) Chinese Science Bulletin , vol.51 , Issue.13 , pp. 1529-1537
    • Zhao, J.1    Yu, H.2    Luo, J.3    Cao, Z.W.4    Li, Y.5
  • 17
    • 38549140094 scopus 로고    scopus 로고
    • RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
    • doi:10.1093/nar/gkm994
    • Gama-Castro, S. et al. 2008 RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucl. Acids Res. 36(Suppl. 1), D120-D124. (doi:10.1093/nar/gkm994)
    • (2008) Nucl. Acids Res. , vol.36 , Issue.SUPPL. 1
    • Gama-Castro, S.1
  • 18
    • 0038478096 scopus 로고    scopus 로고
    • Semantic similarity measures as tools for exploring the Gene Ontology
    • Lord, P. W., Stevens, R. D., Brass, A. & Goble, C. A. 2003 Semantic similarity measures as tools for exploring the Gene Ontology. Pac. Symp. Biocomput. 8, 601-612.
    • (2003) Pac. Symp. Biocomput. , vol.8 , pp. 601-612
    • Lord, P.W.1    Stevens, R.D.2    Brass, A.3    Goble, C.A.4
  • 19
    • 41349115432 scopus 로고    scopus 로고
    • The DAVID gene functional classification tool: A novel biological module-centric algorithm to functionally analyze large gene lists
    • doi:10.1186/gb-2007-8-9-r183
    • Huang, D. W. et al. 2007 The DAVID gene functional classification tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol. 8, R183. (doi:10.1186/gb-2007-8-9-r183)
    • (2007) Genome Biol , vol.8
    • Huang, D.W.1
  • 20
    • 33846400424 scopus 로고    scopus 로고
    • Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
    • doi:10.1371/journal.pbio.0050008
    • Faith, J. J., Hayete, B., Thaden, J. T., Mogno, I., Wierzbowski, J., Cottarel, G., Kasif, S., Collins, J. J. & Gardner, T. S. 2007 Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 5, e8. (doi:10.1371/journal.pbio. 0050008)
    • (2007) PLoS Biol , vol.5
    • Faith, J.J.1    Hayete, B.2    Thaden, J.T.3    Mogno, I.4    Wierzbowski, J.5    Cottarel, G.6    Kasif, S.7    Collins, J.J.8    Gardner, T.S.9
  • 21
    • 0034887203 scopus 로고    scopus 로고
    • Creating the Gene Ontology resource: Design and implementation
    • The Gene Ontology Consortium 2001 Creating the Gene Ontology resource: design and implementation. Genome Res. 11, 1425-1433.
    • (2001) Genome Res , vol.11 , pp. 1425-1433
  • 22
    • 65549085067 scopus 로고    scopus 로고
    • Power-law distributions in empirical data
    • Clauset, A., Shalizi, C. R. & Newman, M. E. J. 2009 Power-law distributions in empirical data. SIAM Rev. 51, 661-703.
    • (2009) SIAM Rev. , vol.51 , pp. 661-703
    • Clauset, A.1    Shalizi, C.R.2    Newman, M.E.J.3
  • 23
    • 68249087607 scopus 로고    scopus 로고
    • Semantic similarity in biomedical ontologies
    • doi:10.1371/journal.pcbi.1000443
    • Pesquita, C., Faria, D., Falcão, A. O., Lord, P. & Couto, F. M. 2009 Semantic similarity in biomedical ontologies. PLoS Comput. Biol. 5, e1000443. (doi:10.1371/journal.pcbi.1000443)
    • (2009) PLoS Comput. Biol. , vol.5
    • Pesquita, C.1    Faria, D.2    Falcão, A.O.3    Lord, P.4    Couto, F.M.5
  • 24
    • 67849110934 scopus 로고    scopus 로고
    • Fast gene ontology based clustering for microarray experiments
    • doi:10.1186/1756-0381-1-11
    • Ovaska, K., Laakso, M. & Hautaniemi, S. 2008 Fast gene ontology based clustering for microarray experiments. BioData Mining 1, 11. (doi:10.1186/1756-0381-1-11)
    • (2008) BioData Mining , vol.1 , pp. 11
    • Ovaska, K.1    Laakso, M.2    Hautaniemi, S.3
  • 28
    • 33748335463 scopus 로고    scopus 로고
    • A new measure for functional similarity of gene products based on gene ontology
    • doi:10.1186/1471-2105-7-302
    • Schlicker, A., Domingues, F., Rahnenfuhrer, J. & Lengauer, T. 2006 A new measure for functional similarity of gene products based on gene ontology. BMC Bioinform. 7, 302. (doi:10.1186/1471-2105-7-302)
    • (2006) BMC Bioinform , vol.7 , pp. 302
    • Schlicker, A.1    Domingues, F.2    Rahnenfuhrer, J.3    Lengauer, T.4
  • 31
    • 33645821454 scopus 로고    scopus 로고
    • Assessing semantic similarity measures for the characterization of human regulatory pathways
    • doi:10.1093/bioinformatics/btl042
    • Guo, X., Liu, R., Shriver, C. D., Hu, H. & Liebman, M. N. 2006 Assessing semantic similarity measures for the characterization of human regulatory pathways. Bioinformatics 22, 967-973. (doi:10.1093/bioinformatics/ btl042)
    • (2006) Bioinformatics , vol.22 , pp. 967-973
    • Guo, X.1    Liu, R.2    Shriver, C.D.3    Hu, H.4    Liebman, M.N.5
  • 32
    • 47149083877 scopus 로고    scopus 로고
    • Metrics for GO based protein semantic similarity: A systematic evaluation
    • Pesquita, C., Faria, D., Bastos, H., Ferreira, A., Falcao, A. & Couto, F. 2008 Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinform. 9(Suppl. 5), S4.
    • (2008) BMC Bioinform , vol.9 , Issue.SUPPL. 5
    • Pesquita, C.1    Faria, D.2    Bastos, H.3    Ferreira, A.4    Falcao, A.5    Couto, F.6
  • 33
    • 34547763236 scopus 로고    scopus 로고
    • A transversal approach to predict gene product networks from ontology-based similarity
    • doi:10.1186/1471-2105-8-235
    • Chabalier, J., Mosser, J. & Burgun, A. 2007 A transversal approach to predict gene product networks from ontology-based similarity. BMC Bioinform. 8, 235. (doi:10.1186/1471-2105-8-235)
    • (2007) BMC Bioinform , vol.8 , pp. 235
    • Chabalier, J.1    Mosser, J.2    Burgun, A.3
  • 34
  • 35
    • 0033655775 scopus 로고    scopus 로고
    • Mutual information relevance networks: Functional genomic clustering using pairwise entropy measurements
    • Butte, A. J. & Kohane, I. S. 2000 Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac. Symp. Biocomput. 5, 418-429.
    • (2000) Pac. Symp. Biocomput. , vol.5 , pp. 418-429
    • Butte, A.J.1    Kohane, I.S.2
  • 36
    • 3242806720 scopus 로고    scopus 로고
    • An integrative genomics approach to the reconstruction of gene networks in segregating populations
    • doi:10.1159/000078209
    • Zhu, J. et al. 2004 An integrative genomics approach to the reconstruction of gene networks in segregating populations. Cytogenet. Genome Res. 105, 363-374. (doi:10.1159/000078209)
    • (2004) Cytogenet. Genome Res. , vol.105 , pp. 363-374
    • Zhu, J.1
  • 38
    • 41549138299 scopus 로고    scopus 로고
    • An improved, bias-reduced probabilistic functional gene network of bakers yeast, Saccharomyces cerevisiae
    • doi:10.1371/journal.pone.0000988
    • Lee, I., Li, Z. & Marcotte, E. M. 2007 An improved, bias-reduced probabilistic functional gene network of bakers yeast, Saccharomyces cerevisiae. PLoS ONE 2, e988. (doi:10.1371/journal.pone.0000988)
    • (2007) PLoS ONE , vol.2
    • Lee, I.1    Li, Z.2    Marcotte, E.M.3
  • 39
    • 33645769260 scopus 로고    scopus 로고
    • An improved map of conserved regulatory sites for Saccharomyces cerevisiae
    • doi:10.1186/1471-2105-7-113
    • MacIsaac, K. D., Wang, T., Gordon, D. B., Gifford, D. K., Stormo, G. D. & Fraenkel, E. 2006 An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinform. 7, 113. (doi:10.1186/1471-2105-7-113)
    • (2006) BMC Bioinform , vol.7 , pp. 113
    • MacIsaac, K.D.1    Wang, T.2    Gordon, D.B.3    Gifford, D.K.4    Stormo, G.D.5    Fraenkel, E.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.