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  • Andersson, A., Keskitalo, J., Sjödin, A. et al. (2004) A transcriptional timetable of autumn senescence. Genome Biol. 5, R24.
  • Ashburner, M., Ball, C.A., Blake, J.A. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 2529.
  • Ball, C.A., Brazma, A., Causton, H. et al. (2004) Submission of microarray data to public repositories. PLoS Biol. 2, E317.
  • Banerjee, N. and Zhang, M.Q. (2002) Functional genomics as applied to mapping transcription regulatory networks. Curr. Opin. Microbiol. 5, 313317.
  • Bhalerao, R., Keskitalo, J., Sterky, F. et al. (2003) Gene expression in autumn leaves. Plant Physiol. 131, 430442.
  • Brazma, A., Hingamp, P., Quackenbush, J. et al. (2001) Minimum information about a microarray experiment (MIAME) – toward standards for microarray data. Nat. Genet. 29, 365371.
  • Brazma, A., Parkinson, H., Sarkans, U. et al. (2003) ArrayExpress – a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 31, 6871.
  • Bylesjo, M., Eriksson, D., Sjodin, A., Sjostrom, M., Jansson, S., Antti, H. and Trygg, J. (2005) MASQOT: a method for cDNA microarray spot quality control. BMC Bioinformatics, 6, 250.
  • Chang, S., Puryear, J. and Cairney, J. (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep. 11, 113116.
  • Churchill, G.A. (2002) Fundamentals of experimental design for cDNA microarrays. Nat. Genet. 32, 490495.
  • Craigon, D.J., James, N., Okyere, J., Higgins, J., Jotham, J. and May, S. (2004) NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res. 32, D575D577.
  • Doyle, J.J. and Doyle, J.L. (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 1115.
  • Dudoit, S. and Yang, Y.H. (2002) Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In The Analysis of Gene Expression Data: Methods and Software (Parmigiani, G., Garett, E.S., Irizarry, R.A., Zeger, S.L. eds). New York: Springer, pp. 73101.
  • Edgar, R., Domrachev, M. and Lash, A.E. (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30, 207210.
  • Ewing, R.M., Ben Kahla, A., Poirot, O., Lopez, F., Audic, S. and Claverie, J.M. (1999) Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res. 9, 950959.
  • Futschik, M. and Crompton, T. (2004a) Model selection and efficiency testing for normalization of cDNA microarray data. Genome Biol. 5, R60.
  • Futschik, M.E. and Crompton, T. (2004b) OLIN: optimized normalization, visualization and quality testing of two-channel microarray data. Bioinformatics, 21, 17241726.
  • Gentleman, R.C., Carey, V.J., Bates, D.M. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80.
  • Gu, J. and Gu, X. (2003) Induced gene expression in human brain after the split from chimpanzee. Trends Genet. 19, 6365.
  • Hertzberg, M., Aspeborg, H., Schrader, J. et al. (2001) A transcriptional roadmap to wood formation. Proc. Natl Acad. Sci. USA, 98, 1473214737.
  • Hilson, P., Allemeersch, J., Altmann, T. et al. (2004) Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res. 14, 21762189.
  • Hosack, D.A., Dennis, G. Jr, Sherman, B.T., Lane, H.C. and Lempicki, R.A. (2003) Identifying biological themes within lists of genes with EASE. Genome Biol. 4, R70.
  • Huala, E., Dickerman, A.W., Garcia-Hernandez, M. et al. (2001) The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res. 29, 102105.
  • Ihaka, R. and Gentleman, R. (1996) R: a language for data analysis and graphics. J. Comput. Graph. Stat. 5, 299314.
  • Israelsson, M., Eriksson, M.E., Hertzberg, M., Aspeborg, H., Nilsson, P. and Moritz, T. (2003) Changes in gene expression in the wood-forming tissue of transgenic hybrid aspen with increased secondary growth. Plant Mol. Biol. 52, 893903.
  • Kanehisa, M. and Goto, S. (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 2730.
  • Kennedy, G.C. and Wilson, I.W. (2004) Plant functional genomics: opportunities in microarray databases and data mining. Funct. Plant Biol. 31, 295314.
  • Kerr, M.K. and Churchill, G.A. (2001) Statistical design and the analysis of gene expression microarray data. Genet. Res. 77, 123128.
  • Kerr, M.K., Martin, M. and Churchill, G.A. (2000) Analysis of variance for gene expression microarray data. J. Comput. Biol. 7, 819837.
  • Kohler, A., Delaruelle, C., Martin, D., Encelot, N. and Martin, F. (2003) The poplar root transcriptome: analysis of 7000 expressed sequence tags. FEBS Lett. 542, 3741.
  • Kroll, T.C. and Wolfl, S. (2002) Ranking: a closer look on globalisation methods for normalisation of gene expression arrays. Nucleic Acids Res. 30, e50.
  • Lafarguette, F., Leple, J.C., Dejardin, A., Laurans, F., Costa, G., Lesage-Descauses, M.C. and Pilate, G. (2004) Poplar genes encoding fasciclin-like arabinogalactan proteins are highly expressed in tension wood. New Phytol. 164, 107121.
  • Lockhart, D.J., Dong, H., Byrne, M.C. et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14, 16751680.
  • Lonnstedt, I. and Speed, T. (2002) Replicated microarray data. Stat. Sin. 12, 3146.
  • Mewes, H.W., Heumann, K., Kaps, A., Mayer, K., Pfeiffer, F., Stocker, S. and Frishman, D. (1999) MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 27, 4448.
  • Moreau, C., Aksenov, N., Lorenzo, M., Segerman, B., Funk, C., Nilsson, P., Jansson, S. and Tuominen, H. (2005) A genomic approach to investigate developmental cell death in woody tissues of Populus trees. Genome Biol. 6, R34.
  • Mueller, L.A., Zhang, P. and Rhee, S.Y. (2003) AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol. 132, 453460.
  • Nanjo, T., Futamura, N., Nishiguchi, M., Igasaki, T., Shinozaki, K. and Shinohara, K. (2004) Characterization of full-length enriched expressed sequence tags of stress-treated poplar leaves. Plant Cell Physiol. 45, 17381748.
  • Pearson, W.R. and Lipman, D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 24442448.
  • Penkett, C.J. and Bahler, G. (2004) Navigating public microarray databases. Comp. Funct. Genomics 5, 471479.
  • Rishi, A.S., Munir, S., Kapur, V., Nelson, N.D. and Goyal, A. (2004) Identification and analysis of safener-inducible expressed sequence tags in Populus using a cDNA microarray. Planta, 220, 296306.
  • Ryden, P., Andersson, H., Landfors, M., Naslund, L., Hartmanova, B., Noppa, L. and Sjostedt, A. (2006) Evaluation of microarray data normalization procedures using spike-in experiments. BMC Bioinformatics, 7, 300.
  • Saal, L.H., Troein, C., Vallon-Christersson, J., Gruvberger, S., Borg, A. and Peterson, C. (2002) BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. Genome Biol. 3, SOFTWARE0003.
  • Schena, M., Shalon, D., Davis, R.W. and Brown, P.O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270, 467470.
  • Schmid, M., Davison, T.S., Henz, S.R., Pape, U.J., Demar, M., Vingron, M., Scholkopf, B., Weigel, D. and Lohmann, J.U. (2005) A gene expression map of Arabidopsis thaliana development. Nat. Genet. 37, 501506.
  • Schoof, H., Zaccaria, P., Gundlach, H., Lemcke, K., Rudd, S., Kolesov, G., Arnold, R., Mewes, H.W. and Mayer, K.F. (2002) MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome. Nucleic Acids Res. 30, 9193.
  • Schrader, J., Moyle, R., Bhalerao, R., Hertzberg, M., Lundeberg, J., Nilsson, P. and Bhalerao, R.P. (2004a) Cambial meristem dormancy in trees involves extensive remodelling of the transcriptome. Plant J. 40, 173187.
  • Schrader, J., Nilsson, J., Mellerowicz, E., Berglund, A., Nilsson, P., Hertzberg, M. and Sandberg, G. (2004b) A high-resolution transcript profile across the wood-forming meristem of poplar identifies potential regulators of cambial stem cell identity. Plant Cell, 16, 22782292.
  • Smith, C.M., Rodriguez-Buey, M., Karlsson, J. and Campbell, M.M. (2004) The response of the poplar transcriptome to wounding and subsequent infection by a viral pathogen. New Phytol. 164, 123136.
  • Smyth, G. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, No 1, Article 3.
  • Sterky, F., Regan, S., Karlsson, J. et al. (1998) Gene discovery in the wood-forming tissues of poplar: analysis of 5692 expressed sequence tags. Proc. Natl Acad. Sci. USA, 95, 1333013335.
  • Sterky, F., Bhalerao, R.R., Unneberg, P. et al. (2004) A Populus EST resource for plant functional genomics. Proc. Natl Acad. Sci. USA, 101, 1395113956.
  • Stoeckert, C.J. Jr, Causton, H.C. and Ball, C.A. (2002) Microarray databases: standards and ontologies. Nat. Genet. 32, S469S473.
  • Tarca, A.L., Cooke, J.E. and Mackay, J. (2005) A robust neural networks approach for spatial and intensity dependent normalization of cDNA microarray data. Bioinformatics, 21, 26742683.
  • Taylor, G., Street, N.R., Tricker, P.J., Sjödin, A., Graham, L., Skogström, O., Calfapietra, C., Scarascia-Mugnozza, G. and Jansson, S. (2005) The transcriptome of Populus in elevated CO2. New Phytol. 167, 143154.
  • Thimm, O., Blasing, O., Gibon, Y., Nagel, A., Meyer, S., Kruger, P., Selbig, J., Muller, 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, 914939.
  • Tuskan, G., DiFazio, S., Jansson, S. et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313, 15961604.
  • Usadel, B., Nagel, A., Thimm, O. 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, 11951204.
  • Vinciotti, V., Khanin, R., D'Alimonte, D. et al. (2005) An experimental evaluation of a loop versus a reference design for two-channel microarrays. Bioinformatics, 21, 492501.
  • Wang, J., Delabie, J., Aasheim, H., Smeland, E. and Myklebost, O. (2002) Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study. BMC Bioinformatics, 3, 36.
  • Wilson, D.L., Buckley, M.J., Helliwell, C.A. and Wilson, I.W. (2003) New normalization methods for cDNA microarray data. Bioinformatics, 19, 13251332.
  • Wit, E. and McClure, J. (2004) Statistics for Microarrays: Design, Analysis and Inference. Chichester: Wiley.
  • Wit, E., Nobile, A. and Khanin, R. (2005) Near-optimal designs for dual-channel microarray studies. Appl. Stat. 54, 817830.
  • Wold, S., Esbensen, K. and Geladi, P. (1987) Principal component analysis. Chemom. Intell. Lab. Syst. 2, 3752.
  • Wu, R. and Stettler, R.F. (1994) Quantitative genetics of growth and development in Populus.1. A three-generation comparison of tree architecture during the first 2 years of growth. Theor. Appl. Genet. 89, 10461054.
  • Yang, Y.H. and Speed, T. (2002) Design issues for cDNA microarray experiments. Nat. Rev. Genet. 3, 579588.
  • Yang, Y.H., Dudoit, S., Luu, P., Lin, D.M., Peng, V., Ngai, J. and Speed, T.P. (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30, e15.
  • Zimmermann, P., Hirsch-Hoffmann, M., Hennig, L. and Gruissem, W. (2004) GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol. 136, 26212632.