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Volumn 19, Issue 4, 2014, Pages 212-221

Towards revealing the functions of all genes in plants

Author keywords

Big data; Co expression; Co function; Function prediction; Networks; Omics

Indexed keywords

ALGORITHM; BIOLOGY; GENE REGULATORY NETWORK; GENETICS; PLANT;

EID: 84897374792     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2013.10.006     Document Type: Review
Times cited : (184)

References (101)
  • 1
    • 84862234802 scopus 로고    scopus 로고
    • The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
    • Lamesch P., et al. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. 2012, 40:D1202-D1210.
    • (2012) Nucleic Acids Res. , vol.40
    • Lamesch, P.1
  • 2
    • 78651270854 scopus 로고    scopus 로고
    • Gramene database in 2010: updates and extensions
    • Youens-Clark K., et al. Gramene database in 2010: updates and extensions. Nucleic Acids Res. 2011, 39:D1085-D1094.
    • (2011) Nucleic Acids Res. , vol.39
    • Youens-Clark, K.1
  • 3
    • 1542290452 scopus 로고    scopus 로고
    • Ontologies in biology: design, applications and future challenges
    • Bard J.B., Rhee S.Y. Ontologies in biology: design, applications and future challenges. Nat. Rev. Genet. 2004, 5:213-222.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 213-222
    • Bard, J.B.1    Rhee, S.Y.2
  • 4
    • 35948989284 scopus 로고    scopus 로고
    • The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
    • Smith B., et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 2007, 25:1251-1255.
    • (2007) Nat. Biotechnol. , vol.25 , pp. 1251-1255
    • Smith, B.1
  • 5
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25:25-29.
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 7
    • 58149202169 scopus 로고    scopus 로고
    • The Transporter Classification Database: recent advances
    • Saier M.H., et al. The Transporter Classification Database: recent advances. Nucleic Acids Res. 2009, 37:D274-D278.
    • (2009) Nucleic Acids Res. , vol.37
    • Saier, M.H.1
  • 8
    • 33750079855 scopus 로고    scopus 로고
    • Whole-plant growth stage ontology for angiosperms and its application in plant biology
    • Pujar A., et al. Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiol. 2006, 142:414-428.
    • (2006) Plant Physiol. , vol.142 , pp. 414-428
    • Pujar, A.1
  • 9
    • 34247192074 scopus 로고    scopus 로고
    • The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant
    • Ilic K., et al. The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol. 2007, 143:587-599.
    • (2007) Plant Physiol. , vol.143 , pp. 587-599
    • Ilic, K.1
  • 10
    • 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., et al. MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 2004, 37:914-939.
    • (2004) Plant J. , vol.37 , pp. 914-939
    • Thimm, O.1
  • 11
    • 45549107329 scopus 로고    scopus 로고
    • Use and misuse of the gene ontology annotations
    • Rhee S.Y., et al. Use and misuse of the gene ontology annotations. Nat. Rev. Genet. 2008, 9:509-515.
    • (2008) Nat. Rev. Genet. , vol.9 , pp. 509-515
    • Rhee, S.Y.1
  • 12
    • 76349125292 scopus 로고    scopus 로고
    • Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana
    • Lee I., et al. Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat. Biotechnol. 2010, 28:149-156.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 149-156
    • Lee, I.1
  • 13
    • 84870724279 scopus 로고    scopus 로고
    • Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks
    • Bassel G.W., et al. Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. Plant Cell 2012, 24:3859-3875.
    • (2012) Plant Cell , vol.24 , pp. 3859-3875
    • Bassel, G.W.1
  • 14
    • 0036500834 scopus 로고    scopus 로고
    • Reverse engineering of biological complexity
    • Csete M.E., Doyle J.C. Reverse engineering of biological complexity. Science 2002, 295:1664-1669.
    • (2002) Science , vol.295 , pp. 1664-1669
    • Csete, M.E.1    Doyle, J.C.2
  • 15
    • 34548606295 scopus 로고    scopus 로고
    • Recent progress in protein subcellular location prediction
    • Chou K.C., Shen H.B. Recent progress in protein subcellular location prediction. Anal. Biochem. 2007, 370:1-16.
    • (2007) Anal. Biochem. , vol.370 , pp. 1-16
    • Chou, K.C.1    Shen, H.B.2
  • 16
    • 0142106373 scopus 로고    scopus 로고
    • How well is enzyme function conserved as a function of pairwise sequence identity?
    • Tian W., Skolnick J. How well is enzyme function conserved as a function of pairwise sequence identity?. J. Mol. Biol. 2003, 333:863-882.
    • (2003) J. Mol. Biol. , vol.333 , pp. 863-882
    • Tian, W.1    Skolnick, J.2
  • 17
    • 0038699587 scopus 로고    scopus 로고
    • Global protein function prediction from protein-protein interaction networks
    • Vazquez A., et al. Global protein function prediction from protein-protein interaction networks. Nat. Biotechnol. 2003, 21:697-700.
    • (2003) Nat. Biotechnol. , vol.21 , pp. 697-700
    • Vazquez, A.1
  • 18
    • 84859165788 scopus 로고    scopus 로고
    • The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
    • Pagani I., et al. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2012, 40:D571-D579.
    • (2012) Nucleic Acids Res. , vol.40
    • Pagani, I.1
  • 19
    • 84860342753 scopus 로고    scopus 로고
    • Current challenges in de novo plant genome sequencing and assembly
    • Schatz M.C., et al. Current challenges in de novo plant genome sequencing and assembly. Genome Biol. 2012, 13:243.
    • (2012) Genome Biol. , vol.13 , pp. 243
    • Schatz, M.C.1
  • 20
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 21
    • 23144458473 scopus 로고    scopus 로고
    • InterProScan: protein domains identifier
    • Quevillon E., et al. InterProScan: protein domains identifier. Nucleic Acids Res. 2005, 33:W116-W120.
    • (2005) Nucleic Acids Res. , vol.33
    • Quevillon, E.1
  • 22
    • 0036308741 scopus 로고    scopus 로고
    • Enzyme function less conserved than anticipated
    • Rost B. Enzyme function less conserved than anticipated. J. Mol. Biol. 2002, 318:595-608.
    • (2002) J. Mol. Biol. , vol.318 , pp. 595-608
    • Rost, B.1
  • 23
    • 0031666414 scopus 로고    scopus 로고
    • Analogous enzymes: independent inventions in enzyme evolution
    • Galperin M.Y., et al. Analogous enzymes: independent inventions in enzyme evolution. Genome Res. 1998, 8:779-790.
    • (1998) Genome Res. , vol.8 , pp. 779-790
    • Galperin, M.Y.1
  • 24
    • 33845878246 scopus 로고    scopus 로고
    • Rate and polarity of gene fusion and fission in Oryza sativa and Arabidopsis thaliana
    • Nakamura Y., et al. Rate and polarity of gene fusion and fission in Oryza sativa and Arabidopsis thaliana. Mol. Biol. Evol. 2007, 24:110-121.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 110-121
    • Nakamura, Y.1
  • 25
    • 0038104857 scopus 로고    scopus 로고
    • Genomic gene clustering analysis of pathways in eukaryotes
    • Lee J.M., Sonnhammer E.L. Genomic gene clustering analysis of pathways in eukaryotes. Genome Res. 2003, 13:875-882.
    • (2003) Genome Res. , vol.13 , pp. 875-882
    • Lee, J.M.1    Sonnhammer, E.L.2
  • 26
    • 79953237139 scopus 로고    scopus 로고
    • From hormones to secondary metabolism: the emergence of metabolic gene clusters in plants
    • Chu H.Y., et al. From hormones to secondary metabolism: the emergence of metabolic gene clusters in plants. Plant J. 2011, 66:66-79.
    • (2011) Plant J. , vol.66 , pp. 66-79
    • Chu, H.Y.1
  • 27
    • 0033551248 scopus 로고    scopus 로고
    • Assigning protein functions by comparative genome analysis: protein phylogenetic profiles
    • Pellegrini M., et al. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. U.S.A. 1999, 96:4285-4288.
    • (1999) Proc. Natl. Acad. Sci. U.S.A. , vol.96 , pp. 4285-4288
    • Pellegrini, M.1
  • 28
    • 79958850343 scopus 로고    scopus 로고
    • Synergistic use of plant-prokaryote comparative genomics for functional annotations
    • Gerdes S., et al. Synergistic use of plant-prokaryote comparative genomics for functional annotations. BMC Genomics 2011, 12(Suppl. 1):S2.
    • (2011) BMC Genomics , vol.12 , Issue.SUPPL. 1
    • Gerdes, S.1
  • 29
    • 0036649020 scopus 로고    scopus 로고
    • Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters
    • Wu L.F., et al. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat. Genet. 2002, 31:255-265.
    • (2002) Nat. Genet. , vol.31 , pp. 255-265
    • Wu, L.F.1
  • 30
    • 84856276299 scopus 로고    scopus 로고
    • SLocX: predicting subcellular localization of Arabidopsis proteins leveraging gene expression data
    • Ryngajllo M., et al. SLocX: predicting subcellular localization of Arabidopsis proteins leveraging gene expression data. Front. Plant Sci. 2011, 2:43.
    • (2011) Front. Plant Sci. , vol.2 , pp. 43
    • Ryngajllo, M.1
  • 31
    • 20844445318 scopus 로고    scopus 로고
    • Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets
    • Persson S., et al. Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:8633-8638.
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 8633-8638
    • Persson, S.1
  • 32
    • 84864075061 scopus 로고    scopus 로고
    • Co-expression analysis identifies CRC and AP1 the regulator of Arabidopsis fatty acid biosynthesis
    • Han X., et al. Co-expression analysis identifies CRC and AP1 the regulator of Arabidopsis fatty acid biosynthesis. J. Integr. Plant Biol. 2012, 54:486-499.
    • (2012) J. Integr. Plant Biol. , vol.54 , pp. 486-499
    • Han, X.1
  • 33
    • 78650513671 scopus 로고    scopus 로고
    • Prephenate aminotransferase directs plant phenylalanine biosynthesis via arogenate
    • Maeda H., et al. Prephenate aminotransferase directs plant phenylalanine biosynthesis via arogenate. Nat. Chem. Biol. 2011, 7:19-21.
    • (2011) Nat. Chem. Biol. , vol.7 , pp. 19-21
    • Maeda, H.1
  • 34
    • 79959995342 scopus 로고    scopus 로고
    • Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice
    • Ficklin S.P., Feltus F.A. Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice. Plant Physiol. 2011, 156:1244-1256.
    • (2011) Plant Physiol. , vol.156 , pp. 1244-1256
    • Ficklin, S.P.1    Feltus, F.A.2
  • 35
    • 79959970191 scopus 로고    scopus 로고
    • Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice
    • Movahedi S., et al. Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice. Plant Physiol. 2011, 156:1316-1330.
    • (2011) Plant Physiol. , vol.156 , pp. 1316-1330
    • Movahedi, S.1
  • 36
    • 84866080959 scopus 로고    scopus 로고
    • BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species
    • Patel R.V., et al. BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species. Plant J. 2012, 71:1038-1050.
    • (2012) Plant J. , vol.71 , pp. 1038-1050
    • Patel, R.V.1
  • 37
    • 84875159954 scopus 로고    scopus 로고
    • Comparative study of RNA-seq- and microarray-derived coexpression networks in Arabidopsis thaliana
    • Giorgi F.M., et al. Comparative study of RNA-seq- and microarray-derived coexpression networks in Arabidopsis thaliana. Bioinformatics 2013, 29:717-724.
    • (2013) Bioinformatics , vol.29 , pp. 717-724
    • Giorgi, F.M.1
  • 38
    • 84897450120 scopus 로고    scopus 로고
    • Arabidopsis Interactome Mapping, C. Evidence for network evolution in an Arabidopsis interactome map. Science
    • Arabidopsis Interactome Mapping, C. (2011) Evidence for network evolution in an Arabidopsis interactome map. Science 333, 601-607.
    • (2011) , vol.333 , pp. 601-607
  • 39
    • 33644555054 scopus 로고    scopus 로고
    • Proteome survey reveals modularity of the yeast cell machinery
    • Gavin A.C., et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 2006, 440:631-636.
    • (2006) Nature , vol.440 , pp. 631-636
    • Gavin, A.C.1
  • 40
    • 84872192446 scopus 로고    scopus 로고
    • Proteome-wide protein interaction measurements of bacterial proteins of unknown function
    • Meier M., et al. Proteome-wide protein interaction measurements of bacterial proteins of unknown function. Proc. Natl. Acad. Sci. U.S.A. 2013, 110:477-482.
    • (2013) Proc. Natl. Acad. Sci. U.S.A. , vol.110 , pp. 477-482
    • Meier, M.1
  • 41
    • 0035044077 scopus 로고    scopus 로고
    • Assessment of prediction accuracy of protein function from protein-protein interaction data
    • Hishigaki H., et al. Assessment of prediction accuracy of protein function from protein-protein interaction data. Yeast 2001, 18:523-531.
    • (2001) Yeast , vol.18 , pp. 523-531
    • Hishigaki, H.1
  • 42
    • 78651328883 scopus 로고    scopus 로고
    • The BioGRID Interaction Database: 2011 update
    • Stark C., et al. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res. 2011, 39:D698-D704.
    • (2011) Nucleic Acids Res. , vol.39
    • Stark, C.1
  • 43
    • 36949000237 scopus 로고    scopus 로고
    • Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps
    • Huang H., et al. Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. PLoS Comput. Biol. 2007, 3:e214.
    • (2007) PLoS Comput. Biol. , vol.3
    • Huang, H.1
  • 44
    • 33847744247 scopus 로고    scopus 로고
    • How complete are current yeast and human protein-interaction networks?
    • Hart G.T., et al. How complete are current yeast and human protein-interaction networks?. Genome Biol. 2006, 7:120.
    • (2006) Genome Biol. , vol.7 , pp. 120
    • Hart, G.T.1
  • 45
    • 53349117774 scopus 로고    scopus 로고
    • High-quality binary protein interaction map of the yeast interactome network
    • Yu H., et al. High-quality binary protein interaction map of the yeast interactome network. Science 2008, 322:104-110.
    • (2008) Science , vol.322 , pp. 104-110
    • Yu, H.1
  • 46
    • 78649703966 scopus 로고    scopus 로고
    • Rewiring of genetic networks in response to DNA damage
    • Bandyopadhyay S., et al. Rewiring of genetic networks in response to DNA damage. Science 2010, 330:1385-1389.
    • (2010) Science , vol.330 , pp. 1385-1389
    • Bandyopadhyay, S.1
  • 47
    • 84874113985 scopus 로고    scopus 로고
    • A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility
    • Bassik M.C., et al. A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility. Cell 2013, 152:909-922.
    • (2013) Cell , vol.152 , pp. 909-922
    • Bassik, M.C.1
  • 48
    • 81755177857 scopus 로고    scopus 로고
    • Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways
    • Babu M., et al. Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways. PLoS Genet. 2011, 7:e1002377.
    • (2011) PLoS Genet. , vol.7
    • Babu, M.1
  • 49
    • 70349622576 scopus 로고    scopus 로고
    • From information to knowledge: new technologies for defining gene function
    • Collins S.R., et al. From information to knowledge: new technologies for defining gene function. Nat. Methods 2009, 6:721-723.
    • (2009) Nat. Methods , vol.6 , pp. 721-723
    • Collins, S.R.1
  • 50
    • 38349100452 scopus 로고    scopus 로고
    • A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
    • Brylinski M., Skolnick J. A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:129-134.
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 129-134
    • Brylinski, M.1    Skolnick, J.2
  • 51
    • 77954065271 scopus 로고    scopus 로고
    • I-TASSER: a unified platform for automated protein structure and function prediction
    • Roy A., et al. I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc. 2010, 5:725-738.
    • (2010) Nat. Protoc. , vol.5 , pp. 725-738
    • Roy, A.1
  • 52
    • 80555142938 scopus 로고    scopus 로고
    • The Proteome Folding Project: proteome-scale prediction of structure and function
    • Drew K., et al. The Proteome Folding Project: proteome-scale prediction of structure and function. Genome Res. 2011, 21:1981-1994.
    • (2011) Genome Res. , vol.21 , pp. 1981-1994
    • Drew, K.1
  • 53
    • 84897583926 scopus 로고    scopus 로고
    • Progress and challenges in the computational prediction of gene function using networks
    • Pavlidis P., Gillis J. Progress and challenges in the computational prediction of gene function using networks. F1000 Res. 2012, 1:1-14.
    • (2012) F1000 Res. , vol.1 , pp. 1-14
    • Pavlidis, P.1    Gillis, J.2
  • 54
    • 77949532033 scopus 로고    scopus 로고
    • CORNET: a user-friendly tool for data mining and integration
    • De Bodt S., et al. CORNET: a user-friendly tool for data mining and integration. Plant Physiol. 2010, 152:1167-1179.
    • (2010) Plant Physiol. , vol.152 , pp. 1167-1179
    • De Bodt, S.1
  • 55
    • 77954269901 scopus 로고    scopus 로고
    • The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
    • Warde-Farley D., et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res. 2010, 38:W214-W220.
    • (2010) Nucleic Acids Res. , vol.38
    • Warde-Farley, D.1
  • 56
    • 84864657071 scopus 로고    scopus 로고
    • Inferring gene functions through dissection of relevance networks: interleaving the intra- and inter-species views
    • Klie S., et al. Inferring gene functions through dissection of relevance networks: interleaving the intra- and inter-species views. Mol. Biosyst. 2012, 8:2233-2241.
    • (2012) Mol. Biosyst. , vol.8 , pp. 2233-2241
    • Klie, S.1
  • 57
    • 84874663959 scopus 로고    scopus 로고
    • A large-scale evaluation of computational protein function prediction
    • Radivojac P., et al. A large-scale evaluation of computational protein function prediction. Nat. Methods 2013, 10:221-227.
    • (2013) Nat. Methods , vol.10 , pp. 221-227
    • Radivojac, P.1
  • 58
    • 67149123401 scopus 로고    scopus 로고
    • Computational reconstruction of protein-protein interaction networks: algorithms and issues
    • Franzosa E., et al. Computational reconstruction of protein-protein interaction networks: algorithms and issues. Methods Mol. Biol. 2009, 541:89-100.
    • (2009) Methods Mol. Biol. , vol.541 , pp. 89-100
    • Franzosa, E.1
  • 59
    • 84897441471 scopus 로고    scopus 로고
    • Predicting gene function using omics data: from data preparation to data integration
    • Springer, D. Kihara (Ed.)
    • Tian W., et al. Predicting gene function using omics data: from data preparation to data integration. Protein Function Prediction for Omics Era 2011, 215-242. Springer. D. Kihara (Ed.).
    • (2011) Protein Function Prediction for Omics Era , pp. 215-242
    • Tian, W.1
  • 60
    • 77349119213 scopus 로고    scopus 로고
    • Predicting gene function using hierarchical multi-label decision tree ensembles
    • Schietgat L., et al. Predicting gene function using hierarchical multi-label decision tree ensembles. BMC Bioinformatics 2010, 11:2.
    • (2010) BMC Bioinformatics , vol.11 , pp. 2
    • Schietgat, L.1
  • 61
    • 84878083062 scopus 로고    scopus 로고
    • Protein function prediction by massive integration of evolutionary analyses and multiple data sources
    • Cozzetto D., et al. Protein function prediction by massive integration of evolutionary analyses and multiple data sources. BMC Bioinformatics 2013, 14(Suppl. 3):S1.
    • (2013) BMC Bioinformatics , vol.14 , Issue.SUPPL. 3
    • Cozzetto, D.1
  • 62
    • 78650539578 scopus 로고    scopus 로고
    • Network-based function prediction and interactomics: the case for metabolic enzymes
    • Janga S.C., et al. Network-based function prediction and interactomics: the case for metabolic enzymes. Metab. Eng. 2011, 13:1-10.
    • (2011) Metab. Eng. , vol.13 , pp. 1-10
    • Janga, S.C.1
  • 63
    • 84870305264 scopus 로고    scopus 로고
    • Wisdom of crowds for robust gene network inference
    • Marbach D., et al. Wisdom of crowds for robust gene network inference. Nat. Methods 2012, 9:796-804.
    • (2012) Nat. Methods , vol.9 , pp. 796-804
    • Marbach, D.1
  • 64
    • 84876544295 scopus 로고    scopus 로고
    • SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis
    • Tanz S.K., et al. SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis. Nucleic Acids Res. 2013, 41:D1185-D1191.
    • (2013) Nucleic Acids Res. , vol.41
    • Tanz, S.K.1
  • 65
    • 77956684350 scopus 로고    scopus 로고
    • Combining machine learning and homology-based approaches to accurately predict subcellular localization in Arabidopsis
    • Kaundal R., et al. Combining machine learning and homology-based approaches to accurately predict subcellular localization in Arabidopsis. Plant Physiol. 2010, 154:36-54.
    • (2010) Plant Physiol. , vol.154 , pp. 36-54
    • Kaundal, R.1
  • 66
    • 75149162948 scopus 로고    scopus 로고
    • TransportTP: a two-phase classification approach for membrane transporter prediction and characterization
    • Li H., et al. TransportTP: a two-phase classification approach for membrane transporter prediction and characterization. BMC Bioinformatics 2009, 10:418.
    • (2009) BMC Bioinformatics , vol.10 , pp. 418
    • Li, H.1
  • 67
    • 33947252154 scopus 로고    scopus 로고
    • Network-based prediction of protein function
    • Sharan R., et al. Network-based prediction of protein function. Mol. Syst. Biol. 2007, 3:88.
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 88
    • Sharan, R.1
  • 68
    • 25144456056 scopus 로고    scopus 로고
    • Computational cluster validation in post-genomic data analysis
    • Handl J., et al. Computational cluster validation in post-genomic data analysis. Bioinformatics 2005, 21:3201-3212.
    • (2005) Bioinformatics , vol.21 , pp. 3201-3212
    • Handl, J.1
  • 69
    • 33645830948 scopus 로고    scopus 로고
    • CFinder: locating cliques and overlapping modules in biological networks
    • Adamcsek B., et al. CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics 2006, 22:1021-1023.
    • (2006) Bioinformatics , vol.22 , pp. 1021-1023
    • Adamcsek, B.1
  • 70
    • 63449107173 scopus 로고    scopus 로고
    • A general modular framework for gene set enrichment analysis
    • Ackermann M., Strimmer K. A general modular framework for gene set enrichment analysis. BMC Bioinformatics 2009, 10:47.
    • (2009) BMC Bioinformatics , vol.10 , pp. 47
    • Ackermann, M.1    Strimmer, K.2
  • 71
    • 0346156102 scopus 로고    scopus 로고
    • Detection of functional modules from protein interaction networks
    • Pereira-Leal J.B., et al. Detection of functional modules from protein interaction networks. Proteins 2004, 54:49-57.
    • (2004) Proteins , vol.54 , pp. 49-57
    • Pereira-Leal, J.B.1
  • 72
    • 3042523388 scopus 로고    scopus 로고
    • Predicting protein complex membership using probabilistic network reliability
    • Asthana S., et al. Predicting protein complex membership using probabilistic network reliability. Genome Res. 2004, 14:1170-1175.
    • (2004) Genome Res. , vol.14 , pp. 1170-1175
    • Asthana, S.1
  • 73
    • 77951991485 scopus 로고    scopus 로고
    • Reverse genetics techniques: engineering loss and gain of gene function in plants
    • Gilchrist E., Haughn G. Reverse genetics techniques: engineering loss and gain of gene function in plants. Brief. Funct. Genomics 2010, 9:103-110.
    • (2010) Brief. Funct. Genomics , vol.9 , pp. 103-110
    • Gilchrist, E.1    Haughn, G.2
  • 74
    • 27344448597 scopus 로고    scopus 로고
    • Feature selection and the class imbalance problem in predicting protein function from sequence
    • Al-Shahib A., et al. Feature selection and the class imbalance problem in predicting protein function from sequence. Appl. Bioinformatics 2005, 4:195-203.
    • (2005) Appl. Bioinformatics , vol.4 , pp. 195-203
    • Al-Shahib, A.1
  • 75
    • 84875275808 scopus 로고    scopus 로고
    • On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE
    • Graur D., et al. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol. Evol. 2013, 5:578-590.
    • (2013) Genome Biol. Evol. , vol.5 , pp. 578-590
    • Graur, D.1
  • 76
    • 84883746688 scopus 로고    scopus 로고
    • Machine learning and genome annotation: a match meant to be?
    • Yip K.Y., et al. Machine learning and genome annotation: a match meant to be?. Genome Biol. 2013, 14:205.
    • (2013) Genome Biol. , vol.14 , pp. 205
    • Yip, K.Y.1
  • 77
    • 77957726465 scopus 로고    scopus 로고
    • Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology
    • Ning K., et al. Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology. BMC Bioinformatics 2010, 11:505.
    • (2010) BMC Bioinformatics , vol.11 , pp. 505
    • Ning, K.1
  • 78
    • 77952253818 scopus 로고    scopus 로고
    • Genes encoding hub and bottleneck enzymes of the Arabidopsis metabolic network preferentially retain homeologs through whole genome duplication
    • Wu X., Qi X. Genes encoding hub and bottleneck enzymes of the Arabidopsis metabolic network preferentially retain homeologs through whole genome duplication. BMC Evol. Biol. 2010, 10:145.
    • (2010) BMC Evol. Biol. , vol.10 , pp. 145
    • Wu, X.1    Qi, X.2
  • 79
    • 60949085866 scopus 로고    scopus 로고
    • Evolutionary constraints on hub and non-hub proteins in human protein interaction network: insight from protein connectivity and intrinsic disorder
    • Manna B., et al. Evolutionary constraints on hub and non-hub proteins in human protein interaction network: insight from protein connectivity and intrinsic disorder. Gene 2009, 434:50-55.
    • (2009) Gene , vol.434 , pp. 50-55
    • Manna, B.1
  • 80
    • 3042848952 scopus 로고    scopus 로고
    • Evidence for dynamically organized modularity in the yeast protein-protein interaction network
    • Han J.D., et al. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 2004, 430:88-93.
    • (2004) Nature , vol.430 , pp. 88-93
    • Han, J.D.1
  • 81
    • 79954486228 scopus 로고    scopus 로고
    • Connectedness of PPI network neighborhoods identifies regulatory hub proteins
    • Fox A.D., et al. Connectedness of PPI network neighborhoods identifies regulatory hub proteins. Bioinformatics 2011, 27:1135-1142.
    • (2011) Bioinformatics , vol.27 , pp. 1135-1142
    • Fox, A.D.1
  • 82
    • 1242319556 scopus 로고    scopus 로고
    • The metabolic world of Escherichia coli is not small
    • Arita M. The metabolic world of Escherichia coli is not small. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:1543-1547.
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 1543-1547
    • Arita, M.1
  • 83
    • 84861179768 scopus 로고    scopus 로고
    • Guilt by association" is the exception rather than the rule in gene networks
    • Gillis J., Pavlidis P. Guilt by association" is the exception rather than the rule in gene networks. PLoS Comput. Biol. 2012, 8:e1002444.
    • (2012) PLoS Comput. Biol. , vol.8
    • Gillis, J.1    Pavlidis, P.2
  • 84
    • 25444527443 scopus 로고    scopus 로고
    • Improved prediction of critical residues for protein function based on network and phylogenetic analyses
    • Thibert B., et al. Improved prediction of critical residues for protein function based on network and phylogenetic analyses. BMC Bioinformatics 2005, 6:213.
    • (2005) BMC Bioinformatics , vol.6 , pp. 213
    • Thibert, B.1
  • 85
    • 84876472005 scopus 로고    scopus 로고
    • P(3)DB: an integrated database for plant protein phosphorylation
    • Yao Q., et al. P(3)DB: an integrated database for plant protein phosphorylation. Front. Plant Sci. 2012, 3:206.
    • (2012) Front. Plant Sci. , vol.3 , pp. 206
    • Yao, Q.1
  • 86
    • 84864003584 scopus 로고    scopus 로고
    • Prediction of chemical-protein interactions network with weighted network-based inference method
    • Cheng F., et al. Prediction of chemical-protein interactions network with weighted network-based inference method. PLoS ONE 2012, 7:e41064.
    • (2012) PLoS ONE , vol.7
    • Cheng, F.1
  • 88
    • 84866130570 scopus 로고    scopus 로고
    • A network-based approach for predicting missing pathway interactions
    • Navlakha S., et al. A network-based approach for predicting missing pathway interactions. PLoS Comput. Biol. 2012, 8:e1002640.
    • (2012) PLoS Comput. Biol. , vol.8
    • Navlakha, S.1
  • 89
    • 84879330505 scopus 로고    scopus 로고
    • An overview of the BioCreative 2012 Workshop Track III: interactive text mining task
    • bas056
    • Arighi C.N., et al. An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database (Oxford) 2013, 2013:bas056.
    • (2013) Database (Oxford) , vol.2013
    • Arighi, C.N.1
  • 90
    • 84883362840 scopus 로고    scopus 로고
    • Using the iPlant collaborative discovery environment
    • Oliver S.L., et al. Using the iPlant collaborative discovery environment. Curr. Protoc. Bioinformatics 2013, 42:1-26.
    • (2013) Curr. Protoc. Bioinformatics , vol.42 , pp. 1-26
    • Oliver, S.L.1
  • 91
    • 0036007687 scopus 로고    scopus 로고
    • Metabolomics - the link between genotypes and phenotypes
    • Fiehn O. Metabolomics - the link between genotypes and phenotypes. Plant Mol. Biol. 2002, 48:155-171.
    • (2002) Plant Mol. Biol. , vol.48 , pp. 155-171
    • Fiehn, O.1
  • 92
    • 84863669875 scopus 로고    scopus 로고
    • Systematic identification of functional plant modules through the integration of complementary data sources
    • Heyndrickx K.S., Vandepoele K. Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol. 2012, 159:884-901.
    • (2012) Plant Physiol. , vol.159 , pp. 884-901
    • Heyndrickx, K.S.1    Vandepoele, K.2
  • 93
    • 79951562208 scopus 로고    scopus 로고
    • ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants
    • Obayashi T., et al. ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. Plant Cell Physiol. 2011, 52:213-219.
    • (2011) Plant Cell Physiol. , vol.52 , pp. 213-219
    • Obayashi, T.1
  • 94
    • 78650982710 scopus 로고    scopus 로고
    • Genome-wide computational function prediction of Arabidopsis proteins by integration of multiple data sources
    • Kourmpetis Y.A., et al. Genome-wide computational function prediction of Arabidopsis proteins by integration of multiple data sources. Plant Physiol. 2011, 155:271-281.
    • (2011) Plant Physiol. , vol.155 , pp. 271-281
    • Kourmpetis, Y.A.1
  • 95
    • 77952799294 scopus 로고    scopus 로고
    • CoP: a database for characterizing co-expressed gene modules with biological information in plants
    • Ogata Y., et al. CoP: a database for characterizing co-expressed gene modules with biological information in plants. Bioinformatics 2010, 26:1267-1268.
    • (2010) Bioinformatics , vol.26 , pp. 1267-1268
    • Ogata, Y.1
  • 96
    • 76449090623 scopus 로고    scopus 로고
    • GO-At: in silico prediction of gene function in Arabidopsis thaliana by combining heterogeneous data
    • Bradford J.R., et al. GO-At: in silico prediction of gene function in Arabidopsis thaliana by combining heterogeneous data. Plant J. 2010, 61:713-721.
    • (2010) Plant J. , vol.61 , pp. 713-721
    • Bradford, J.R.1
  • 97
    • 79955581503 scopus 로고    scopus 로고
    • PlaNet: combined sequence and expression comparisons across plant networks derived from seven species
    • Mutwil M., et al. PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. Plant Cell 2011, 23:895-910.
    • (2011) Plant Cell , vol.23 , pp. 895-910
    • Mutwil, M.1
  • 98
    • 80054969308 scopus 로고    scopus 로고
    • Functional network construction in Arabidopsis using rule-based machine learning on large-scale data sets
    • Bassel G.W., et al. Functional network construction in Arabidopsis using rule-based machine learning on large-scale data sets. Plant Cell 2011, 23:3101-3116.
    • (2011) Plant Cell , vol.23 , pp. 3101-3116
    • Bassel, G.W.1
  • 99
    • 70449657085 scopus 로고    scopus 로고
    • STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data
    • Jupiter D., et al. STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data. BMC Bioinformatics 2009, 10:332.
    • (2009) BMC Bioinformatics , vol.10 , pp. 332
    • Jupiter, D.1
  • 100
    • 84876515907 scopus 로고    scopus 로고
    • STRING v9.1: protein-protein interaction networks, with increased coverage and integration
    • Franceschini A., et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 2013, 41:D808-D815.
    • (2013) Nucleic Acids Res. , vol.41
    • Franceschini, A.1
  • 101
    • 75949087420 scopus 로고    scopus 로고
    • VirtualPlant: a software platform to support systems biology research
    • Katari M.S., et al. VirtualPlant: a software platform to support systems biology research. Plant Physiol. 2010, 152:500-515.
    • (2010) Plant Physiol. , vol.152 , pp. 500-515
    • Katari, M.S.1


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