GeneCAT—novel webtools that combine BLAST and co-expression analyses
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Tài liệu tham khảo
Parkinson, 2007, ArrayExpress—a public database of microarray experiments and gene expression profiles, Nucleic Acids Res., 35, D747, 10.1093/nar/gkl995
Zimmermann, 2004, GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox, Plant Physiol., 136, 2621, 10.1104/pp.104.046367
Manfield, 2006, Arabidopsis co-expression tool (ACT): web server tools for microarray-based gene expression analysis, Nucleic Acids Res., 34, W504, 10.1093/nar/gkl204
Toufighi, 2005, The Botany array resource: e-Northerns, expression angling, and promoter analyses, Plant J., 43, 153, 10.1111/j.1365-313X.2005.02437.x
Steinhauser, 2004, CSB.DB: a comprehensive systems-biology database, Bioinformatics, 20, 3647, 10.1093/bioinformatics/bth398
Obayashi, 2007, ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis, Nucleic Acids Res., 35, 869, 10.1093/nar/gkl783
Geisler-Lee, 2004, A predicted interactome for Arabidopsis, Plant Physiol., 45, 317
Stuart, 2003, A gene-coexpression network for global discovery of conserved genetic modules, Science, 302, 249, 10.1126/science.1087447
Bergmann, 2004, Similarities and differences in genome-wide expression data of six organisms, PLoS Biol., 2, E9, 10.1371/journal.pbio.0020009
Brown, 2005, Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics, Plant Cell, 17, 2281, 10.1105/tpc.105.031542
Persson, 2005, Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets, Proc. Natl Acad. Sci. USA, 102, 8633, 10.1073/pnas.0503392102
Wei, 2006, Transcriptional coordination of the metabolic network in Arabidopsis, Plant Physiol., 142, 762, 10.1104/pp.106.080358
Hirai, 2007, Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis, Proc. Natl Acad. Sci. USA, 104, 6478, 10.1073/pnas.0611629104
Fredslund, 2006, PHY.FI: fast and easy online creation and manipulation of phylogeny color figures, BMC Bioinform., 7, 315, 10.1186/1471-2105-7-315
Rhee, 2003, The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community, Nucleic Acids Res., 31, 224, 10.1093/nar/gkg076
Schmid, 2005, A gene expression map of Arabidopsis thaliana development, Nat. Genet., 37, 501, 10.1038/ng1543
Shen, 2005, BarleyBase—an expression profiling database for plant genomics, Nucleic Acids Res., 33, D614, 10.1093/nar/gki123
Druka, 2006, An atlas of gene expression from seed to seed through Barley development, Funct. Integr. Genomics, 6, 202, 10.1007/s10142-006-0025-4
Somerville, 2006, Cellulose synthesis in higher plants, Annu. Rev. Cell Dev. Biol., 22, 53, 10.1146/annurev.cellbio.22.022206.160206
Arioli, 1998, Molecular analysis of cellulose biosynthesis in Arabidopsis, Science, 279, 10.1126/science.279.5351.717
Fagard, 2000, PROCUSTE1 encodes a cellulose synthase required for normal cell elongation specifically in roots and dark-grown hypocotyls of Arabidopsis, Plant Cell, 12, 2409, 10.1105/tpc.12.12.2409
Persson, 2007, Genetic evidence for three unique components in primary cell-wall cellulose synthase complexes in Arabidopsis, Proc. Natl Acad. Sci. USA, 104, 15566, 10.1073/pnas.0706592104
Turner, 1997, Collapsed xylem phenotype of Arabidopsis identifies mutants deficient in cellulose deposition in the secondary cell wall, Plant Cell, 9, 689, 10.1105/tpc.9.5.689
Burton, 2004, The CesA gene family of Barley. Quantitative analysis of transcripts reveals two groups of co-expressed genes, Plant Physiol., 134, 224, 10.1104/pp.103.032904
Desprez, 2007, Organization of cellulose synthase complexes involved in primary cell wall synthesis in Arabidopsis thaliana, Proc. Natl Acad. Sci. USA, 104, 15572, 10.1073/pnas.0706569104
Jen, 2006, The Arabidopsis co-expression tool (ACT): a WWW-based tool and database for microarray-based gene expression analysis, Plant J., 46, 336, 10.1111/j.1365-313X.2006.02681.x
Aoki, 2007, Approaches for extracting practical information from gene coexpression networks in plant biology, Plant Cell Physiol., 48, 381, 10.1093/pcp/pcm013
Franke, 2007, Suberin—a biopolyester forming apoplastic plant interfaces, Curr. Opin. Plant Biol., 10, 252, 10.1016/j.pbi.2007.04.004
Muraoka, 2006, A eukaryotic factor required for accumulation of the chloroplast NAD(P)H dehydrogenase complex in Arabidopsis, Plant Physiol., 142, 1683, 10.1104/pp.106.088682