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Volumn 15, Issue 1, 2014, Pages

Improving clustering with metabolic pathway data

Author keywords

Clustering; Pathway data; SOM training

Indexed keywords

BIOINFORMATICS; CONFORMAL MAPPING; METABOLISM; PLANTS (BOTANY);

EID: 84899629924     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-101     Document Type: Article
Times cited : (7)

References (45)
  • 1
    • 25444476441 scopus 로고    scopus 로고
    • Systematic survey reveals general applicability of " guilt-by-association" within gene coexpression networks
    • 10.1186/1471-2105-6-227, 1239911, 16162296
    • Wolfe CJ, Kohane IS, Butte AJ. Systematic survey reveals general applicability of " guilt-by-association" within gene coexpression networks. BMC Bioinformatics 2005, 6:227-237. 10.1186/1471-2105-6-227, 1239911, 16162296.
    • (2005) BMC Bioinformatics , vol.6 , pp. 227-237
    • Wolfe, C.J.1    Kohane, I.S.2    Butte, A.J.3
  • 4
    • 77954396635 scopus 로고    scopus 로고
    • Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function
    • 10.1038/nprot.2010.82, 20539294
    • Tohge T, Fernie A. Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function. Nat Protoc 2010, 5(6):1210-1227. 10.1038/nprot.2010.82, 20539294.
    • (2010) Nat Protoc , vol.5 , Issue.6 , pp. 1210-1227
    • Tohge, T.1    Fernie, A.2
  • 7
    • 84870458934 scopus 로고    scopus 로고
    • Essentials of the self-organizing map
    • Kohonen T. Essentials of the self-organizing map. Neural Netw 2013, 37(37):52-65.
    • (2013) Neural Netw , vol.37 , Issue.37 , pp. 52-65
    • Kohonen, T.1
  • 8
    • 0033027794 scopus 로고    scopus 로고
    • Interpreting patterns of gene expression with self-organizing maps: Methods and applications to hematopoietic differentiation
    • 10.1073/pnas.96.6.2907, 15868, 10077610
    • Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander E, Golub T. Interpreting patterns of gene expression with self-organizing maps: Methods and applications to hematopoietic differentiation. Proc Natl Acad Sci USA 1999, 96:2907-2912. 10.1073/pnas.96.6.2907, 15868, 10077610.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 2907-2912
    • Tamayo, P.1    Slonim, D.2    Mesirov, J.3    Zhu, Q.4    Kitareewan, S.5    Dmitrovsky, E.6    Lander, E.7    Golub, T.8
  • 9
    • 2942511784 scopus 로고    scopus 로고
    • Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study
    • 10.1186/1471-2105-3-36, 138792, 12445336
    • Wang J, Delabie J, Aasheim H, Smeland E, Myklebost O. Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study. BMC Bioinformatics 2002, 3:36-46. 10.1186/1471-2105-3-36, 138792, 12445336.
    • (2002) BMC Bioinformatics , vol.3 , pp. 36-46
    • Wang, J.1    Delabie, J.2    Aasheim, H.3    Smeland, E.4    Myklebost, O.5
  • 10
    • 77954071738 scopus 로고    scopus 로고
    • Correlation Network Analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis
    • 10.1186/1752-0509-4-62, 2890501, 20465807
    • Allen E, Moing A, Ebbels TM, Maucourt M, Tomos AD, Rolin D, Hooks MA. Correlation Network Analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis. BMC Syst Biol 2010, 4:62-72. 10.1186/1752-0509-4-62, 2890501, 20465807.
    • (2010) BMC Syst Biol , vol.4 , pp. 62-72
    • Allen, E.1    Moing, A.2    Ebbels, T.M.3    Maucourt, M.4    Tomos, A.D.5    Rolin, D.6    Hooks, M.A.7
  • 12
    • 70449457160 scopus 로고    scopus 로고
    • Neural Network Model for Integration and Visualization of Introgressed Genome and Metabolite Data
    • Piscataway: IEEE Computational Intelligence Society
    • Stegmayer G, Milone D, Kamenetzky L, Lopez M, Carrari F. Neural Network Model for Integration and Visualization of Introgressed Genome and Metabolite Data. IEEE International Joint Conference on Neural Networks 2009, 3177-3183. Piscataway: IEEE Computational Intelligence Society.
    • (2009) IEEE International Joint Conference on Neural Networks , pp. 3177-3183
    • Stegmayer, G.1    Milone, D.2    Kamenetzky, L.3    Lopez, M.4    Carrari, F.5
  • 13
    • 77957007197 scopus 로고    scopus 로고
    • *omeSOM: a software for integration, clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants
    • 10.1186/1471-2105-11-438, 2942854, 20796314
    • Milone D, Stegmayer G, Kamenetzky L, Lopez M, Giovannoni J, Lee JM, Carrari F. *omeSOM: a software for integration, clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants. BMC Bioinformatics 2010, 11:438-448. 10.1186/1471-2105-11-438, 2942854, 20796314.
    • (2010) BMC Bioinformatics , vol.11 , pp. 438-448
    • Milone, D.1    Stegmayer, G.2    Kamenetzky, L.3    Lopez, M.4    Giovannoni, J.5    Lee, J.M.6    Carrari, F.7
  • 14
    • 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
    • 10.1111/j.1365-3040.2009.01978.x, 19389052
    • Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eysenberg A, Stitt M. A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plant Cell Environ 2009, 32:1211-1229. 10.1111/j.1365-3040.2009.01978.x, 19389052.
    • (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
  • 15
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology
    • 10.1038/75556, 3037419, 10802651
    • Ashburner M. Gene ontology: tool for the unification of biology. Nat Genet 2000, 25:25-9. 10.1038/75556, 3037419, 10802651.
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 16
    • 10244264786 scopus 로고    scopus 로고
    • The CRASSS plug-in for integrating annotation data with hierarchical clustering results
    • 10.1093/bioinformatics/bth362, 15201188
    • Buehler E, Sachs J, Shao K, Bagchi A, Ungar L. The CRASSS plug-in for integrating annotation data with hierarchical clustering results. Bioinformatics 2004, 20(17):3266-3269. 10.1093/bioinformatics/bth362, 15201188.
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3266-3269
    • Buehler, E.1    Sachs, J.2    Shao, K.3    Bagchi, A.4    Ungar, L.5
  • 17
    • 22744458472 scopus 로고    scopus 로고
    • Pathways to the analysis of microarray data
    • 10.1016/j.tibtech.2005.05.011, 15950303
    • Curtis RK, Oresic M, Vidal-Puig A. Pathways to the analysis of microarray data. Trends Biotechnol 2005, 23(8):429-435. 10.1016/j.tibtech.2005.05.011, 15950303.
    • (2005) Trends Biotechnol , vol.23 , Issue.8 , pp. 429-435
    • Curtis, R.K.1    Oresic, M.2    Vidal-Puig, A.3
  • 18
    • 33646584520 scopus 로고    scopus 로고
    • GOurmet: a tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions
    • 10.1186/1471-2105-7-1, 1360682, 16393334
    • Doherty J, Carmichael L, Mills J. GOurmet: a tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions. BMC Bioinformatics 2006, 7:1-9. 10.1186/1471-2105-7-1, 1360682, 16393334.
    • (2006) BMC Bioinformatics , vol.7 , pp. 1-9
    • Doherty, J.1    Carmichael, L.2    Mills, J.3
  • 19
    • 2942601249 scopus 로고    scopus 로고
    • Selection of informative clusters from hierarchical cluster tree with gene classes
    • 10.1186/1471-2105-5-32, 407846, 15043761
    • Toronen P. Selection of informative clusters from hierarchical cluster tree with gene classes. BMC Bioinformatics 2004, 5:32. 10.1186/1471-2105-5-32, 407846, 15043761.
    • (2004) BMC Bioinformatics , vol.5 , pp. 32
    • Toronen, P.1
  • 21
    • 8844263749 scopus 로고    scopus 로고
    • A statistical framework for genomic data fusion
    • 10.1093/bioinformatics/bth294, 15130933
    • Lanckriet GRG, Bie TD, Cristianini N, Jordan MI, Noble WS. A statistical framework for genomic data fusion. Bioinformatics 2004, 20(16):2626-2635. 10.1093/bioinformatics/bth294, 15130933.
    • (2004) Bioinformatics , vol.20 , Issue.16 , pp. 2626-2635
    • Lanckriet, G.R.G.1    Bie, T.D.2    Cristianini, N.3    Jordan, M.I.4    Noble, W.S.5
  • 23
    • 67649840899 scopus 로고    scopus 로고
    • Seeing the forest for the trees: using the Gene Ontology to restructure hierarchical clustering
    • Dotan-Cohen D, Kasif S, Melkman AA. Seeing the forest for the trees: using the Gene Ontology to restructure hierarchical clustering. Bioinformatics 2009, 35(14):1789-1795.
    • (2009) Bioinformatics , vol.35 , Issue.14 , pp. 1789-1795
    • Dotan-Cohen, D.1    Kasif, S.2    Melkman, A.A.3
  • 25
    • 0038014879 scopus 로고    scopus 로고
    • Co-clustering of biological networks and gene expression data
    • Oxford: Oxford University Press
    • Hanisch D, Zien A, Zimmer R, Lengauer T. Co-clustering of biological networks and gene expression data. ISMB (Supplement of Bioinformatics) 2002, 145-154. Oxford: Oxford University Press.
    • (2002) ISMB (Supplement of Bioinformatics) , pp. 145-154
    • Hanisch, D.1    Zien, A.2    Zimmer, R.3    Lengauer, T.4
  • 26
    • 3142749026 scopus 로고    scopus 로고
    • A knowledge-based clustering algorithm driven by gene ontology
    • 10.1081/BIP-200025659, 15468759
    • Cheng J, Cline M, Martin J, Finkelstein D, Awad T, Kulp D, Siani-Rose MA. A knowledge-based clustering algorithm driven by gene ontology. J Biopharm Stat 2004, 14(3):687-700. 10.1081/BIP-200025659, 15468759.
    • (2004) J Biopharm Stat , vol.14 , Issue.3 , pp. 687-700
    • Cheng, J.1    Cline, M.2    Martin, J.3    Finkelstein, D.4    Awad, T.5    Kulp, D.6    Siani-Rose, M.A.7
  • 27
    • 33646895693 scopus 로고    scopus 로고
    • Incorporating biological knowledge into distance-based clustering analysis of microarray gene expression data
    • 10.1093/bioinformatics/btl065, 16500932
    • Huang D, Pan W. Incorporating biological knowledge into distance-based clustering analysis of microarray gene expression data. Bioinformatics 2006, 22(10):1259-1268. 10.1093/bioinformatics/btl065, 16500932.
    • (2006) Bioinformatics , vol.22 , Issue.10 , pp. 1259-1268
    • Huang, D.1    Pan, W.2
  • 28
    • 4344660263 scopus 로고    scopus 로고
    • A memetic co-clustering algorithm for gene expression profiles and biological annotation
    • Piscataway: IEEE Press
    • Speer N, Spieth C, Zell A. A memetic co-clustering algorithm for gene expression profiles and biological annotation. Proc. of Congress on Evolutionary Computation (CEC), Volume 2 2004, 1631-8. Piscataway: IEEE Press.
    • (2004) Proc. of Congress on Evolutionary Computation (CEC), Volume 2 , pp. 1631-1638
    • Speer, N.1    Spieth, C.2    Zell, A.3
  • 29
    • 76849109688 scopus 로고    scopus 로고
    • Data-fusion in clustering microarray data: Balancing discovery and interpretability
    • Kustra R, Zagdanski A. Data-fusion in clustering microarray data: Balancing discovery and interpretability. IEEE/ACM Trans Comput Biol Bioinform 2010, 7:50-63.
    • (2010) IEEE/ACM Trans Comput Biol Bioinform , vol.7 , pp. 50-63
    • Kustra, R.1    Zagdanski, A.2
  • 30
    • 80052151544 scopus 로고    scopus 로고
    • GO-based functional dissimilarity of gene sets
    • 10.1186/1471-2105-12-360, 3248071, 21884611
    • Diaz N, Ruiz J. GO-based functional dissimilarity of gene sets. BMC Bioinformatics 2011, 12:360+. 10.1186/1471-2105-12-360, 3248071, 21884611.
    • (2011) BMC Bioinformatics , vol.12
    • Diaz, N.1    Ruiz, J.2
  • 31
    • 36949014067 scopus 로고    scopus 로고
    • Hierarchical tree snipping: clustering guided by prior knowledge
    • 10.1093/bioinformatics/btm526, 17989094
    • Dotan-Cohen D, Melkman AA, Kasif S. Hierarchical tree snipping: clustering guided by prior knowledge. Bioinformatics 2007, 23(24):3335-3342. 10.1093/bioinformatics/btm526, 17989094.
    • (2007) Bioinformatics , vol.23 , Issue.24 , pp. 3335-3342
    • Dotan-Cohen, D.1    Melkman, A.A.2    Kasif, S.3
  • 32
    • 14644399780 scopus 로고    scopus 로고
    • Clustering of diverse genomic data using information fusion
    • 10.1093/bioinformatics/bti186, 15608052
    • Kasturi J, Acharya R. Clustering of diverse genomic data using information fusion. Bioinformatics 2005, 21(4):423-429. 10.1093/bioinformatics/bti186, 15608052.
    • (2005) Bioinformatics , vol.21 , Issue.4 , pp. 423-429
    • Kasturi, J.1    Acharya, R.2
  • 33
    • 84874298500 scopus 로고    scopus 로고
    • Assessing identity, redundancy and confounds in Gene Ontology annotations over time
    • 2013. doi:10.1093/bioinformatics/bts727.
    • Gillis J, Pavlidis P. Assessing identity, redundancy and confounds in Gene Ontology annotations over time. Bioinformatics 2013, 2013. doi:10.1093/bioinformatics/bts727.
    • (2013) Bioinformatics
    • Gillis, J.1    Pavlidis, P.2
  • 34
    • 70349335150 scopus 로고    scopus 로고
    • Piscataway: Wiley and IEEE Press
    • Xu R, Wunsch DC. Clustering 2009, Piscataway: Wiley and IEEE Press.
    • (2009) Clustering
    • Xu, R.1    Wunsch, D.C.2
  • 37
    • 25144456056 scopus 로고    scopus 로고
    • Computational cluster validation in post-genomic data analysis
    • 10.1093/bioinformatics/bti517, 15914541
    • Handl J, Knowles J, Kell DB. Computational cluster validation in post-genomic data analysis. Bioinformatics 2005, 21(15):3201-3212. 10.1093/bioinformatics/bti517, 15914541.
    • (2005) Bioinformatics , vol.21 , Issue.15 , pp. 3201-3212
    • Handl, J.1    Knowles, J.2    Kell, D.B.3
  • 39
    • 84872809389 scopus 로고    scopus 로고
    • KEGG PATHWAY Database
    • KEGG PATHWAY Database. http://www.genome.jp/kegg/pathway.html.
  • 40
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • 10.1093/nar/28.1.27, 102409, 10592173
    • Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30. 10.1093/nar/28.1.27, 102409, 10592173.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 41
    • 78649592081 scopus 로고    scopus 로고
    • Interaction with Diurnal and Circadian regulation results in dynamic metabolic and transcriptional changes during cold acclimation in Arabidopsis
    • Espinoza C, Degenkolbe T, Caldana C, Zuther E, Leisse A, Willmitzer L, Hincha D, Hannah M. Interaction with Diurnal and Circadian regulation results in dynamic metabolic and transcriptional changes during cold acclimation in Arabidopsis. PloS one 2010, 5(11):1-19.
    • (2010) PloS one , vol.5 , Issue.11 , pp. 1-19
    • Espinoza, C.1    Degenkolbe, T.2    Caldana, C.3    Zuther, E.4    Leisse, A.5    Willmitzer, L.6    Hincha, D.7    Hannah, M.8
  • 42
    • 0035532141 scopus 로고    scopus 로고
    • Estimating the number of clusters in a dataset via the Gap statistic
    • Tibshirani R, Walther G, Hastie T. Estimating the number of clusters in a dataset via the Gap statistic. J R Stat Soc B 2001, 63:411-423.
    • (2001) J R Stat Soc B , vol.63 , pp. 411-423
    • Tibshirani, R.1    Walther, G.2    Hastie, T.3
  • 45
    • 84899653881 scopus 로고    scopus 로고
    • Role of protein kinases, phosphatases and 14-3-3 proteins in the control of primary plant metabolism
    • Plaxton WC, McManus MT, Moorhead GBG, Templeton GW, Tran HT. Role of protein kinases, phosphatases and 14-3-3 proteins in the control of primary plant metabolism. Ann Plant Rev 2007, 22:121-149.
    • (2007) Ann Plant Rev , vol.22 , pp. 121-149
    • Plaxton, W.C.1    McManus, M.T.2    Moorhead, G.B.G.3    Templeton, G.W.4    Tran, H.T.5


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