메뉴 건너뛰기




Volumn 25, Issue 6, 2013, Pages 1917-1927

Data integration through proximity-based networks provides biological principles of organization across scales

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS THALIANA;

EID: 84880943554     PISSN: 10404651     EISSN: 1532298X     Source Type: Journal    
DOI: 10.1105/tpc.113.111039     Document Type: Review
Times cited : (14)

References (46)
  • 1
    • 78751624415 scopus 로고    scopus 로고
    • Connected spatial networks over random points and a route-length statistic
    • Aldous, D.J., and Shun, J. (2010). Connected spatial networks over random points and a route-length statistic. Stat. Sci. 25: 275-288.
    • (2010) Stat. Sci , vol.25 , pp. 275-288
    • Aldous, D.J.1    Shun, J.2
  • 3
    • 0029507498 scopus 로고
    • Local indicators of spatial association-LISA
    • Anselin, L. (1995). Local indicators of spatial association-LISA. Geogr. Anal. 27: 93-115.
    • (1995) Geogr. Anal , vol.27 , pp. 93-115
    • Anselin, L.1
  • 4
    • 77953233453 scopus 로고    scopus 로고
    • Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
    • Atwell, S., et al. (2010). Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465: 627-631.
    • (2010) Nature , vol.465 , pp. 627-631
    • Atwell, S.1
  • 5
    • 0037616338 scopus 로고    scopus 로고
    • Spatial econometric functions in R
    • Bivand, R.S. (2002). Spatial econometric functions in R. J. Geogr. Syst. 4: 405-421.
    • (2002) J. Geogr. Syst , vol.4 , pp. 405-421
    • Bivand, R.S.1
  • 7
    • 0004247074 scopus 로고
    • London: Applied Science Publishers
    • Clark, I. (1979). Practical Geostatistics. (London: Applied Science Publishers).
    • (1979) Practical Geostatistics
    • Clark, I.1
  • 9
    • 77955731065 scopus 로고    scopus 로고
    • Spurious correlations and inference in landscape genetics
    • Cushman, S.A., and Landguth, E.L. (2010). Spurious correlations and inference in landscape genetics. Mol. Ecol. 19: 3592-3602.
    • (2010) Mol. Ecol , vol.19 , pp. 3592-3602
    • Cushman, S.A.1    Landguth, E.L.2
  • 12
    • 0000960565 scopus 로고
    • The contiguity ratio and statistical mapping
    • Geary, R.C. (1954). The contiguity ratio and statistical mapping. The Incorporated Statistician 5: 115-127+129-146.
    • (1954) The Incorporated Statistician , vol.5
    • Geary, R.C.1
  • 13
    • 84977363017 scopus 로고
    • The analysis of spatial association by use of distance statistics
    • Getis, A., and Ord, J.K. (1992). The analysis of spatial association by use of distance statistics. Geogr. Anal. 24: 189-206.
    • (1992) Geogr. Anal , vol.24 , pp. 189-206
    • Getis, A.1    Ord, J.K.2
  • 14
    • 84861179768 scopus 로고    scopus 로고
    • Guilt by association is the exception rather than the rule in gene networks
    • Gillis, J., and Pavlidis, P. (2012). "Guilt by association" is the exception rather than the rule in gene networks. PLoS Comput. Biol. 8: e1002444.
    • (2012) PLoS Comput. Biol , vol.8
    • Gillis, J.1    Pavlidis, P.2
  • 15
    • 79951979882 scopus 로고    scopus 로고
    • The impact of multifunctional genes on "guilt by association" analysis
    • Gillis, J., and Pavlidis, P. (2011). The impact of multifunctional genes on "guilt by association" analysis. PLoS ONE 6: e17258.
    • (2011) PLoS ONE , vol.6
    • Gillis, J.1    Pavlidis, P.2
  • 16
    • 37649025929 scopus 로고    scopus 로고
    • The ecodist package for dissimilarity-based analysis of ecological data
    • Goslee, S.C., and Urban, D.L. (2007). The ecodist package for dissimilarity-based analysis of ecological data. J. Stat. Softw. 22: 1-19.
    • (2007) J. Stat. Softw , vol.22 , pp. 1-19
    • Goslee, S.C.1    Urban, D.L.2
  • 18
    • 79953296447 scopus 로고    scopus 로고
    • Coordinated histone modifications are associated with gene expression variation within and between species
    • Ha, M., Ng, D.W.-K., Li, W.-H., and Chen, Z.J. (2011). Coordinated histone modifications are associated with gene expression variation within and between species. Genome Res. 21: 590-598.
    • (2011) Genome Res , vol.21 , pp. 590-598
    • Ha, M.1    Ng, D.W.-K.2    Li, W.-H.3    Chen, Z.J.4
  • 19
    • 0346801873 scopus 로고    scopus 로고
    • The Gene Ontology (GO) database and informatics resource
    • Gene Ontology Consortium, Database issue
    • Harris, M.A., et al; Gene Ontology Consortium (2004). The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32 (Database issue): D258-D261.
    • (2004) Nucleic Acids Res , vol.32
    • Harris, M.A.1
  • 20
    • 84856270364 scopus 로고    scopus 로고
    • Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel
    • Horton, M.W., et al. (2012). Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nat. Genet. 44: 212-216.
    • (2012) Nat. Genet , vol.44 , pp. 212-216
    • Horton, M.W.1
  • 21
    • 0026924875 scopus 로고
    • Relative neighborhood graphs and their relatives
    • Jaromczyk, J.W., and Toussaint, G.T. (1992). Relative neighborhood graphs and their relatives. Proc. IEEE 80: 1502-1517.
    • (1992) Proc. IEEE , vol.80 , pp. 1502-1517
    • Jaromczyk, J.W.1    Toussaint, G.T.2
  • 23
    • 70349999416 scopus 로고    scopus 로고
    • Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis
    • Kinoshita, K., and Obayashi, T. (2009). Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis. Bioinformatics 25: 2677-2684.
    • (2009) Bioinformatics , vol.25 , pp. 2677-2684
    • Kinoshita, K.1    Obayashi, T.2
  • 24
  • 25
    • 84875133914 scopus 로고    scopus 로고
    • The choice between MapMan and Gene Ontology for automated gene function prediction in plant science
    • Klie, S., and Nikoloski, Z. (2012). The choice between MapMan and Gene Ontology for automated gene function prediction in plant science. Front. Genet. 3: 115.
    • (2012) Front. Genet , vol.3 , pp. 115
    • Klie, S.1    Nikoloski, Z.2
  • 26
    • 46749110034 scopus 로고    scopus 로고
    • FactoMineR: An R package for multivariate analysis
    • Lê, S., Josse, J., and Husson, F. (2008). FactoMineR: An R package for multivariate analysis. J. Stat. Softw. 25: 1-18.
    • (2008) J. Stat. Softw , vol.25 , pp. 1-18
    • Lê, S.1    Josse, J.2    Husson, F.3
  • 27
    • 76349125292 scopus 로고    scopus 로고
    • Rational association of genes with traits using a genomescale gene network for Arabidopsis thaliana
    • Lee, I., Ambaru, B., Thakkar, P., Marcotte, E.M., and Rhee, S.Y. (2010). Rational association of genes with traits using a genomescale gene network for Arabidopsis thaliana. Nat. Biotechnol. 28: 149-156.
    • (2010) Nat. Biotechnol , vol.28 , pp. 149-156
    • Lee, I.1    Ambaru, B.2    Thakkar, P.3    Marcotte, E.M.4    Rhee, S.Y.5
  • 28
    • 0014054519 scopus 로고
    • The detection of disease clustering and a generalized regression approach
    • Mantel, N. (1967). The detection of disease clustering and a generalized regression approach. Cancer Res. 27: 209-220.
    • (1967) Cancer Res , vol.27 , pp. 209-220
    • Mantel, N.1
  • 29
    • 0037022862 scopus 로고    scopus 로고
    • Order and disorder in the nucleus
    • Marshall, W.F. (2002). Order and disorder in the nucleus. Curr. Biol. 12: R185-R192.
    • (2002) Curr. Biol , vol.12
    • Marshall, W.F.1
  • 30
    • 76549254593 scopus 로고
    • Notes on continuous stochastic phenomena
    • Moran, P.A.P. (1950). Notes on continuous stochastic phenomena. Biometrika 37: 17-23.
    • (1950) Biometrika , vol.37 , pp. 17-23
    • Moran, P.A.P.1
  • 32
    • 18744389789 scopus 로고    scopus 로고
    • Assortative mixing in networks
    • Newman, M.E. (2002). Assortative mixing in networks. Phys. Rev. Lett. 89: 208701.
    • (2002) Phys. Rev. Lett , vol.89 , pp. 208701
    • Newman, M.E.1
  • 33
    • 0034628487 scopus 로고    scopus 로고
    • Guilt-by-association goes global
    • Oliver, S. (2000). Guilt-by-association goes global. Nature 403: 601-603.
    • (2000) Nature , vol.403 , pp. 601-603
    • Oliver, S.1
  • 34
    • 77649215261 scopus 로고    scopus 로고
    • The scale of population structure in Arabidopsis thaliana
    • Platt, A., et al. (2010). The scale of population structure in Arabidopsis thaliana. PLoS Genet. 6: e1000843.
    • (2010) PLoS Genet , vol.6
    • Platt, A.1
  • 35
    • 0037287259 scopus 로고    scopus 로고
    • Mantel and partial Mantel tests suggest some factors that may control the local distribution of Aster laurentianus at Îles de la Madeleine, Québec
    • Reynolds, C.E., and Houle, G. (2003). Mantel and partial Mantel tests suggest some factors that may control the local distribution of Aster laurentianus at Îles de la Madeleine, Québec. Plant Ecol. 164: 19-27.
    • (2003) Plant Ecol , vol.164 , pp. 19-27
    • Reynolds, C.E.1    Houle, G.2
  • 36
    • 0002062430 scopus 로고    scopus 로고
    • geoR: A package for geostatistical analysis
    • Ribeiro, P.J., Jr., and Diggle, P.J. (2001). geoR: A package for geostatistical analysis. R-News 1: 15-18.
    • (2001) R-News , vol.1 , pp. 15-18
    • Ribeiro Jr., P.J.1    Diggle, P.J.2
  • 37
    • 0001400228 scopus 로고
    • A unifying tool for linear multivariate statistical methods: The RV coefficient
    • Robert, P., and Escoufier, Y. (1976). A unifying tool for linear multivariate statistical methods: The RV coefficient. J. R. Stat. Soc. Ser. C Appl. Stat. 25: 257-265.
    • (1976) J. R. Stat. Soc. Ser. C Appl. Stat , vol.25 , pp. 257-265
    • Robert, P.1    Escoufier, Y.2
  • 38
    • 84963034277 scopus 로고
    • Multiple regression and correlation extensions of the mantel test of matrix correspondence
    • Smouse, P.E., Long, J.C., and Sokal, R.R. (1986). Multiple regression and correlation extensions of the mantel test of matrix correspondence. Syst. Zool. 35: 627-632.
    • (1986) Syst. Zool , vol.35 , pp. 627-632
    • Smouse, P.E.1    Long, J.C.2    Sokal, R.R.3
  • 39
    • 84856023505 scopus 로고    scopus 로고
    • Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle
    • Sobetzko, P., Travers, A., and Muskhelishvili, G. (2012). Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle. Proc. Natl. Acad. Sci. USA 109: E42-E50.
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109
    • Sobetzko, P.1    Travers, A.2    Muskhelishvili, G.3
  • 40
    • 12144291195 scopus 로고    scopus 로고
    • MAPMAN: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
    • Thimm, O., Bläsing, O., Gibon, Y., Nagel, A., Meyer, S., Krüger, P., Selbig, J., Müller, L.A., Rhee, S.Y., and Stitt, M. (2004). MAPMAN: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 37: 914-939.
    • (2004) Plant J , vol.37 , pp. 914-939
    • Thimm, O.1    Bläsing, O.2    Gibon, Y.3    Nagel, A.4    Meyer, S.5    Krüger, P.6    Selbig, J.7    Müller, L.A.8    Rhee, S.Y.9    Stitt, M.10
  • 41
    • 0019213414 scopus 로고
    • The relative neighbourhood graph of a finite planar set
    • Toussaint, G.T. (1980). The relative neighbourhood graph of a finite planar set. Pattern Recognit. 12: 261-268.
    • (1980) Pattern Recognit , vol.12 , pp. 261-268
    • Toussaint, G.T.1
  • 42
    • 27244453164 scopus 로고    scopus 로고
    • Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses
    • Usadel, B., et al. (2005). Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses. Plant Physiol. 138: 1195-1204.
    • (2005) Plant Physiol , vol.138 , pp. 1195-1204
    • Usadel, B.1
  • 43
    • 38249014219 scopus 로고
    • The gamma-neighborhood graph
    • Veltkamp, R.C. (1992). The gamma-neighborhood graph. Comput. Geom. 1: 227-246.
    • (1992) Comput. Geom , vol.1 , pp. 227-246
    • Veltkamp, R.C.1
  • 44
    • 25444476441 scopus 로고    scopus 로고
    • Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks
    • Wolfe, C.J., Kohane, I.S., and Butte, A.J. (2005). Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinformatics 6: 227.
    • (2005) BMC Bioinformatics , vol.6 , pp. 227
    • Wolfe, C.J.1    Kohane, I.S.2    Butte, A.J.3
  • 45
    • 0036790999 scopus 로고    scopus 로고
    • Transitive functional annotation by shortest-path analysis of gene expression data
    • Zhou, X., Kao, M.-C.J., and Wong, W.H. (2002). Transitive functional annotation by shortest-path analysis of gene expression data. Proc. Natl. Acad. Sci. USA 99: 12783-12788.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 12783-12788
    • Zhou, X.1    Kao, M.-C.J.2    Wong, W.H.3
  • 46
    • 0035056709 scopus 로고    scopus 로고
    • Chromosomal organization governs the timing of cell type-specific gene expression required for spore formation in Bacillus subtilis
    • Zupancic, M.L., Tran, H., and Hofmeister, A.E.M. (2001). Chromosomal organization governs the timing of cell type-specific gene expression required for spore formation in Bacillus subtilis. Mol. Microbiol. 39: 1471-1481.
    • (2001) Mol. Microbiol , vol.39 , pp. 1471-1481
    • Zupancic, M.L.1    Tran, H.2    Hofmeister, A.E.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.