메뉴 건너뛰기




Volumn 42, Issue D1, 2014, Pages

GoMapMan: Integration, consolidation and visualization of plant gene annotations within the MapMan ontology

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARABIDOPSIS; ARTICLE; AUTOMATION; GENE FUNCTION; GENETIC DATABASE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; PLANT GENE; POTATO; PRIORITY JOURNAL; WEB BROWSER; COMPUTER GRAPHICS; GENE ONTOLOGY; GENETICS; INTERNET; MOLECULAR GENETICS; SYSTEM ANALYSIS; FACTUAL DATABASE; GENE MAPPING; GENE PRODUCT; GENETIC ANALYSIS; GOMAPMAN; KNOWLEDGE MANAGEMENT; MICROARRAY ANALYSIS; MOLECULAR DYNAMICS; ONLINE SYSTEM; PHYLOGENY; RICE; TOMATO; VALIDATION PROCESS;

EID: 84891815276     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1056     Document Type: Article
Times cited : (82)

References (42)
  • 1
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • The Gene Ontology Consortium.
    • The Gene Ontology Consortium. (2000) Gene ontology: tool for the unification of biology. Nat. Genet., 25, 25-29.
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
  • 2
    • 84874253819 scopus 로고    scopus 로고
    • Gene ontology annotations and resources
    • The Gene Ontology Consortium.
    • The Gene Ontology Consortium. (2013) Gene ontology annotations and resources. Nucleic Acids Res., 41, D530-D535.
    • (2013) Nucleic Acids Res. , vol.41
  • 4
    • 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., Blasing, O., Gibon, Y., Nagel, A., Meyer, S., Kruger, P., Selbig, J., Muller, L.A., Rhee, S.Y., Stitt, M. et al. (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    Blasing, O.2    Gibon, Y.3    Nagel, A.4    Meyer, S.5    Kruger, P.6    Selbig, J.7    Muller, L.A.8    Rhee, S.Y.9    Stitt, M.10
  • 5
    • 35348892233 scopus 로고    scopus 로고
    • Adaptation of the MapMan ontology to biotic stress responses: Application in solanaceous species
    • Rotter, A., Usadel, B., Baebler, S., Stitt, M. and Gruden, K. (2007) Adaptation of the MapMan ontology to biotic stress responses: application in solanaceous species. Plant Methods, 3, 1-9.
    • (2007) Plant Methods , vol.3 , pp. 1-9
    • Rotter, A.1    Usadel, B.2    Baebler, S.3    Stitt, M.4    Gruden, K.5
  • 6
    • 69449097345 scopus 로고    scopus 로고
    • Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: Extending mapman ontology for grapevine
    • Rotter, A., Camps, C., Lohse, M., Kappel, C., Pilati, S., Hren, M., Stitt, M., Coutos-Thevenot, P., Moser, C., Usadel, B. et al. (2009) Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: extending mapman ontology for grapevine. BMC Plant Biol., 9, 1-14.
    • (2009) BMC Plant Biol. , vol.9 , pp. 1-14
    • Rotter, A.1    Camps, C.2    Lohse, M.3    Kappel, C.4    Pilati, S.5    Hren, M.6    Stitt, M.7    Coutos-Thevenot, P.8    Moser, C.9    Usadel, B.10
  • 7
    • 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, 1-14.
    • (2012) Front. Genet. , vol.3 , pp. 1-14
    • Klie, S.1    Nikoloski, Z.2
  • 8
    • 68249092895 scopus 로고    scopus 로고
    • A guide to using mapman to visualize and compare omics data in plants: A case study in the crop species, maize
    • Usadel, B., Poree, F., Nagel, A., Lohse, M., Czedik-Eysenberg, A. and Stitt, M. (2009) A guide to using mapman to visualize and compare omics data in plants: a case study in the crop species, maize. Plant Cell Environ., 32, 1211-1229.
    • (2009) Plant Cell Environ. , vol.32 , pp. 1211-1229
    • Usadel, B.1    Poree, F.2    Nagel, A.3    Lohse, M.4    Czedik-Eysenberg, A.5    Stitt, M.6
  • 10
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • The Arabidopsis Genome Initiative.
    • The Arabidopsis Genome Initiative. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
    • (2000) Nature , vol.408 , pp. 796-815
  • 12
    • 37849023306 scopus 로고    scopus 로고
    • Assessing performance of orthology detection strategies applied to eukaryotic genomes
    • Chen, F., Mackey, A.J., Vermunt, J.K. and Roos, D.S. (2007) Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS One, 2, e383.
    • (2007) PLoS One , vol.2
    • Chen, F.1    MacKey, A.J.2    Vermunt, J.K.3    Roos, D.S.4
  • 13
    • 47249148373 scopus 로고    scopus 로고
    • Performance comparison of gene family clustering methods with expert curated gene family data set in Arabidopsis thaliana
    • Yang, K. and Zhang, L. (2008) Performance comparison of gene family clustering methods with expert curated gene family data set in Arabidopsis thaliana. Planta, 228, 439-447.
    • (2008) Planta , vol.228 , pp. 439-447
    • Yang, K.1    Zhang, L.2
  • 14
    • 62549146620 scopus 로고    scopus 로고
    • Protein function prediction-the power of multiplicity
    • Rentzsch, R. and Orengo, C.A. (2009) Protein function prediction-the power of multiplicity. Trends Biotechnol., 27, 210-219.
    • (2009) Trends Biotechnol. , vol.27 , pp. 210-219
    • Rentzsch, R.1    Orengo, C.A.2
  • 15
    • 84878819024 scopus 로고    scopus 로고
    • HOMECAT: Consensus homologs mapping for interspecific knowledge transfer and functional genomic data integration
    • Simone, Z., Erika, L., Michele, E., Valeria, P., Carlo, L. and Mario, B. (2013) HOMECAT: consensus homologs mapping for interspecific knowledge transfer and functional genomic data integration. Bioinformatics, 29, 1574-1576.
    • (2013) Bioinformatics , vol.29 , pp. 1574-1576
    • Simone, Z.1    Erika, L.2    Michele, E.3    Valeria, P.4    Carlo, L.5    Mario, B.6
  • 19
    • 79960422847 scopus 로고    scopus 로고
    • Genome sequence and analysis of the tuber crop potato
    • The Potato Genome Sequencing Consortium.
    • The Potato Genome Sequencing Consortium. (2011) Genome sequence and analysis of the tuber crop potato. Nature, 475, 189-195.
    • (2011) Nature , vol.475 , pp. 189-195
  • 20
    • 84863693752 scopus 로고    scopus 로고
    • The tomato genome sequence provides insights into fleshy fruit evolution
    • The Tomato Genome Consortium.
    • The Tomato Genome Consortium. (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485, 635-641.
    • (2012) Nature , vol.485 , pp. 635-641
  • 24
    • 84861801113 scopus 로고    scopus 로고
    • Biomine: Predicting links between biological entities using network models of heterogeneous databases
    • Eronen, L. and Toivonen, H. (2012) Biomine: predicting links between biological entities using network models of heterogeneous databases. BMC Bioinformatics, 13, 1-21.
    • (2012) BMC Bioinformatics , vol.13 , pp. 1-21
    • Eronen, L.1    Toivonen, H.2
  • 27
    • 80053201210 scopus 로고    scopus 로고
    • The what, where, how and why of gene ontology: A primer for bioinformaticians
    • Du Plessis, L., Skunca, N. and Dessimoz, C. (2011) The what, where, how and why of gene ontology: a primer for bioinformaticians. Brief. Bioinform., 12, 723-735.
    • (2011) Brief. Bioinform. , vol.12 , pp. 723-735
    • Du Plessis, L.1    Skunca, N.2    Dessimoz, C.3
  • 28
    • 59149102602 scopus 로고    scopus 로고
    • Phylogenetic and functional assessment of orthologs inference projects and methods
    • Altenhoff, A.M. and Dessimoz, C. (2009) Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput. Biol., 5, e1000262.
    • (2009) PLoS Comput. Biol. , vol.5
    • Altenhoff, A.M.1    Dessimoz, C.2
  • 30
    • 84881265576 scopus 로고    scopus 로고
    • Clustering evolving proteins into homologous families
    • Chan, C.X., Mahbob, M. and Ragan, M.A. (2013) Clustering evolving proteins into homologous families. BMC Bioinformatics, 14, 1-11.
    • (2013) BMC Bioinformatics , vol.14 , pp. 1-11
    • Chan, C.X.1    Mahbob, M.2    Ragan, M.A.3
  • 31
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • Li, L., Stoeckert, C.J. and Roos, D.S. (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res., 13, 2178-2189.
    • (2003) Genome Res. , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 32
    • 36549049268 scopus 로고    scopus 로고
    • Ortholog detection using the reciprocal smallest distance algorithm
    • Wall, D.P. and Deluca, T. (2007) Ortholog detection using the reciprocal smallest distance algorithm. Methods Mol. Biol., 396, 95-110.
    • (2007) Methods Mol. Biol. , vol.396 , pp. 95-110
    • Wall, D.P.1    Deluca, T.2
  • 34
    • 46649101347 scopus 로고    scopus 로고
    • SEGS: Search for enriched gene sets in microarray data
    • Trajkovski, I., Lavrac, N. and Tolar, J. (2008) SEGS: search for enriched gene sets in microarray data. J. Biomed. Inform., 41, 588-601.
    • (2008) J. Biomed. Inform. , vol.41 , pp. 588-601
    • Trajkovski, I.1    Lavrac, N.2    Tolar, J.3
  • 36
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li, W. and Godzik, A. (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 39
    • 0003500248 scopus 로고
    • Kaufmann, M. (ed.) Morgan Kaufmann, Publishers, San Mateo, CA
    • Quinlan, J.R. (1993) In: Kaufmann, M. (ed.), C4.5: Programs for Machine Learning. Morgan Kaufmann, Publishers, San Mateo, CA.
    • (1993) C4.5: Programs for Machine Learning
    • Quinlan, J.R.1
  • 40
    • 0002226683 scopus 로고    scopus 로고
    • Pajek-program for large network analysis
    • Batagelj, V. and Mrvar, A. (1998) Pajek-program for large network analysis. Connections, 21, 47-57.
    • (1998) Connections , vol.21 , pp. 47-57
    • Batagelj, V.1    Mrvar, A.2
  • 41
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang, D.W., Sherman, B.T. and Lempicki, R.A. (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
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 42
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
    • Huang, D.W., Sherman, B.T. and Lempicki, R.A. (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res., 37, 1-13.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 1-13
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.