Nelson N, Yocum CF: Structure and function of photosystems I and II. Annual Review of Plant Biology. 2006, 57: 521-565. 10.1146/annurev.arplant.57.032905.105350.
Article
PubMed
CAS
Google Scholar
Fleming AJ: The control of leaf development. New Phytologist. 2005, 166: 9-20. 10.1111/j.1469-8137.2004.01292.x.
Article
PubMed
CAS
Google Scholar
Pien S, Wyrzykowska J, Mason S, Smart C, Fleming A: Local expression of expansin induces the entire process of leaf development and modifies leaf shape. Proceedings of the National Academy of Sciences, USA. 2001, 98 (20): 11812-11817. 10.1073/pnas.191380498.
Article
CAS
Google Scholar
Tsuge T, Tsukaya H, Uchimiya H: Two independent and polarized processes of cell elongation regulate leaf blade expansion in Arabidopsis thaliana (L.) Heynh. Development. 1996, 122 (5): 1589-1600.
PubMed
CAS
Google Scholar
Lee Y, Kim GT, Kim IJ, Park J, Kwak SS, Choi G, Chung WI: LONGIFOLIA1 and LONGIFOLIA2, two homologous genes, regulate longitudinal cell elongation in Arabidopsis. Development. 2006, 133 (21): 4305-4314. 10.1242/dev.02604.
Article
PubMed
CAS
Google Scholar
Tsukaya H, Tsuge T, Uchimiya H: The cotyledon: A superior system for studies of leaf development. Planta. 1994, 195 (2): 309-312. 10.1007/BF00199692.
Article
CAS
Google Scholar
Savaldi-Goldstein S, Peto C, Chory J: The epidermis both drives and restricts plant shoot growth. Nature. 2007, 446 (7132): 199-202. 10.1038/nature05618.
Article
PubMed
CAS
Google Scholar
Rae AM, Ferris R, Tallis MJ, Taylor G: Elucidating genomic regions determining enhanced leaf growth and delayed senescence in elevated CO2. Plant Cell and Environment. 2006, 29: 1730-1741. 10.1111/j.1365-3040.2006.01545.x.
Article
CAS
Google Scholar
Street NR, Skogstrom O, Sjodin A, Tucker J, Rodriguez-Acosta M, Nilsson P, Jansson S, Taylor G: The genetics and genomics of the drought response in Populus. Plant Journal. 2006, 48 (3): 321-341. 10.1111/j.1365-313X.2006.02864.x.
Article
PubMed
CAS
Google Scholar
Juenger T, Perez-Perez J, Bernal S, Micol J: Quantitative trait loci mapping of floral and leaf morphology traits in Arabidopsis thaliana: evidence for modular genetic architecture. Evolution and Development. 2005, 7 (3): 259-271. 10.1111/j.1525-142X.2005.05028.x.
Article
PubMed
CAS
Google Scholar
Wullschleger S, Yin T, Difazio S, Tschaplinski T, Gunter L, Davis M, Tuskan G: Phenotypic variation in growth and biomass distribution for two advanced-generation pedigrees of hybrid poplar. Canadian Journal of Forest Research. 2005, 35 (8): 1779-1789. 10.1139/x05-101.
Article
CAS
Google Scholar
El-Lithy M, Clerkx E, Ruys G, Koornneef M, Vreugdenhil D: Quantitative Trait Locus Analysis of Growth-Related Traits in a New Arabidopsis Recombinant Inbred Population. Plant Physiology. 2004, 135: 444-458. 10.1104/pp.103.036822.
Article
PubMed
CAS
PubMed Central
Google Scholar
Frary A, Fritz L, Tanksley S: A comparative study of the genetic bases of natural variation in tomato leaf, sepal, and petal morphology. Theoretical and Applied Genetics. 2004, 109 (3): 523-533. 10.1007/s00122-004-1669-x.
Article
PubMed
Google Scholar
Perez-Perez J, Serrano-Cartagena J, Micol J: Genetic Analysis of Natural Variations in the Architecture of Arabidopsis thaliana Vegetative Leaves. Genetics. 2002, 162 (2): 893-915.
PubMed
CAS
PubMed Central
Google Scholar
Jiang C, Wright RJ, Woo SS, Delmonte TA, Paterson AH: QTL analysis of leaf morphology in tetraploid Gossypium (cotton). Theoretical and Applied Genetics. 2000, 100 (3): 409-418. 10.1007/s001220050054.
Article
CAS
Google Scholar
Wu R, Stettler R: Quantitative genetics of growth and development in Populus. III. Phenotypic plasticity of crown structure and function. Heredity. 1998, 81 (3): 299-310. 10.1046/j.1365-2540.1998.00397.x.
Article
Google Scholar
Wu R, Bradshaw HD, Stettler RF: Molecular genetics of growth and development in Populus (Salicaceae). 5. Mapping quantitative trait loci affecting leaf variation. American Journal of Botany. 1997, 84 (2): 143-153. 10.2307/2446076.
Article
PubMed
CAS
Google Scholar
Hay A, Tsiantis M: The genetic basis for differences in leaf form between Arabidopsis thaliana and its wild relative Cardamine hirsuta. Nature Genetics. 2006, 38 (8): 942-947. 10.1038/ng1835.
Article
PubMed
CAS
Google Scholar
Ingvarsson P: Nucleotide Polymorphism and Linkage Disequilibrium Within and Among Natural Populations of European Aspen (Populus tremula L., Salicaceae). Genetics. 2005, 169 (2): 945-953. 10.1534/genetics.104.034959.
Article
PubMed
CAS
PubMed Central
Google Scholar
Jansen RC, Nap JP: Genetical genomics: the added value from segregation. Trends in Genetics. 2001, 17 (7): 388-391. 10.1016/S0168-9525(01)02310-1.
Article
PubMed
CAS
Google Scholar
Bing N, Hoeschele I: Genetical genomics analysis of a yeast segregant population for transcription network inference. Genetics. 2005, 170 (2): 533-542. 10.1534/genetics.105.041103.
Article
PubMed
CAS
PubMed Central
Google Scholar
Deutsch S, Lyle R, Dermitzakis E, Attar H, Subrahmanyan L, Gehrig C, Parand L, Gagnebin M, Rougemont J, Jongeneel V, Antonarakis S: Gene expression variation and expression quantitative trait mapping of human chromosome 21 genes. Human Molecular Genetics. 2005, 14 (23): 3741-3749. 10.1093/hmg/ddi404.
Article
PubMed
CAS
Google Scholar
Ghazalpour A, Doss S, Zhang B, Wang S, Plaisier C, Castellanos R, Brozell A, Schadt EE, Drake TA, Lusis AJ, Horvath S: Integrating Genetic and Network Analysis to Characterize Genes Related to Mouse Weight. PLoS Genetics. 2006, 2 (8): e130-10.1371/journal.pgen.0020130.
Article
PubMed
PubMed Central
Google Scholar
Kliebenstein D, West M, van Leeuwen H, Loudet O, Doerge RW, Dina : Identification of QTLs controlling gene expression networks defined a priori. BMC Bioinformatics. 2006, 7: 308-10.1186/1471-2105-7-308.
Article
PubMed
PubMed Central
Google Scholar
West M, Kim K, Kliebenstein D, van Leeuwen H, Michelmore R, Doerge RW, St Clair D: Global eQTL Mapping Reveals the Complex Genetic Architecture of Transcript-Level Variation in Arabidopsis. Genetics. 2007, 175 (3): 1441-1450. 10.1534/genetics.106.064972.
Article
PubMed
CAS
PubMed Central
Google Scholar
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics. 2001, 29 (4): 365-371. 10.1038/ng1201-365.
Article
PubMed
CAS
Google Scholar
Kerr MK, Martin M, Churchill GA: Analysis of variance for gene expression microarray data. Journal of Computational Biology. 2000, 7 (6): 819-837. 10.1089/10665270050514954.
Article
PubMed
CAS
Google Scholar
Smyth G: Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004, 3: Article 3
Google Scholar
Bylesjo M, Eriksson D, Kusano M, Moritz T, Trygg J: Data integration in plant biology: the O2PLS method for combined modeling of transcript and metabolite data. Plant Journal. 2007, 52: 1181-1191.
Article
PubMed
Google Scholar
Bylesjo M, Eriksson D, Sjodin A, Jansson S, Moritz T, Trygg J: Orthogonal projections to latent structures as a strategy for microarray data normalization. BMC Bioinformatics. 2007, 8: 207-10.1186/1471-2105-8-207.
Article
PubMed
PubMed Central
Google Scholar
Sjodin A, Wissel K, Bylesjo M, Trygg J, Jansson S: Global expression profiling in leaves of free-growing aspen. BMC Plant Biology. 2008,
Google Scholar
Zhou Y, Young JA, Santrosyan A, Chen K, Yan SF, Winzeler EA: In silico gene function prediction using ontology-based pattern identification. Bioinformatics. 2005, 21 (7): 1237-1245. 10.1093/bioinformatics/bti111.
Article
PubMed
Google Scholar
Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences, USA. 1998, 95 (25): 14863-14868. 10.1073/pnas.95.25.14863.
Article
CAS
Google Scholar
Soukas A, Cohen P, Socci N, Friedman J: Leptin-specific patterns of gene expression in white adipose tissue. Genes & Development. 2000, 14 (8): 963-980.
CAS
Google Scholar
Kohonen T: Self-organized formation of topologically correct feature maps. Biological Cybernetics. 1982, 43: 59-69. 10.1007/BF00337288.
Article
Google Scholar
Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, Barkai N: Revealing modular organization in the yeast transcriptional network. Nature Genetics. 2002, 31 (4): 370-377.
PubMed
CAS
Google Scholar
Ihmels J, Bergmann S, Barkai N: Defining transcription modules using large-scale gene expression data. Bioinformatics. 2004, 20 (13): 1993-2003. 10.1093/bioinformatics/bth166.
Article
PubMed
CAS
Google Scholar
Subramanian A, Tamayo P, Mootha V, Mukherjee S, Ebert B, Gillette M, Paulovich A, Pomeroy S, Golub T, Lander E, Mesirov J: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, USA. 2005, 102 (43): 15545-15550. 10.1073/pnas.0506580102.
Article
CAS
Google Scholar
Zhang B, Horvath S: A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol. 2005, 4: Article17-
PubMed
Google Scholar
Yip A, Horvath S: Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics. 2007, 8: 22-10.1186/1471-2105-8-22.
Article
PubMed
PubMed Central
Google Scholar
Dong J, Horvath S: Understanding Network Concepts in Modules. BMC Systems Biology. 2007, 1: 24-10.1186/1752-0509-1-24.
Article
PubMed
PubMed Central
Google Scholar
Wellmer F, Riechmann JL: Gene network analysis in plant development by genomic technologies. International Journal of Developmental Biology. 2005, 49 (5–6): 745-759. 10.1387/ijdb.051991fw.
Article
PubMed
CAS
Google Scholar
Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A: Reverse engineering cellular networks. Nature Protocols. 2006, 1 (2): 662-671. 10.1038/nprot.2006.106.
Article
PubMed
CAS
Google Scholar
Wang Y, Joshi T, Zhang XS, Xu D, Chen L: Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics. 2006, 22 (19): 2413-2420. 10.1093/bioinformatics/btl396.
Article
PubMed
CAS
Google Scholar
Ernst J, Vainas O, Harbison CT, Simon I, Bar-Joseph Z: Reconstructing dynamic regulatory maps. Molecular Systems Biology. 2007, 3: 74-10.1038/msb4100115.
Article
PubMed
PubMed Central
Google Scholar
Wittkopp PJ: Variable gene expression in eukaryotes: a network perspective. Journal of Experimental Biology. 2007, 210 (Pt 9): 1567-1575. 10.1242/jeb.002592.
Article
PubMed
CAS
Google Scholar
Bansal M, Belcastro V, Ambesi-Impiombato A, di Bernardo D: How to infer gene networks from expression profiles. Molecular Systems Biology. 2007, 3: 78-
Article
PubMed
PubMed Central
Google Scholar
Sjodin A, Bylesjo M, Skogstrom O, Eriksson D, Nilsson P, Ryden P, Jansson S, Karlsson J: UPSC-BASE-Populus transcriptomics online. Plant Journal. 2006, 48 (5): 806-817. 10.1111/j.1365-313X.2006.02920.x.
Article
PubMed
Google Scholar
Trygg J, Wold S: Orthogonal projections to latent structures (O-PLS). Journal of Chemometrics. 2002, 16: 119-128. 10.1002/cem.695.
Article
CAS
Google Scholar
Bylesjo M, Rantalainen M, Cloarec O, Nicholson J, Holmes E, Trygg J: OPLS discriminant analysis: combining the strengths of PLS-DA and SIMCA classification. Journal of Chemometrics. 2006, 20: 341-351. 10.1002/cem.1006.
Article
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics. 2000, 25: 25-9. 10.1038/75556.
Article
PubMed
CAS
PubMed Central
Google Scholar
PopGenIE: Populus Genome Integrative Explorer. [http://www.popgenie.db.umu.se/]
Sterky F, Bhalerao RR, Unneberg P, Segerman B, Nilsson P, Brunner AM, Charbonnel-Campaa L, Lindvall JJ, Tandre K, Strauss SH, Sundberg B, Gustafsson P, Uhlen M, Bhalerao RP, Nilsson O, Sandberg G, Karlsson J, Lundeberg J, Jansson S: A Populus EST resource for plant functional genomics. Proceedings of the National Academy of Sciences, USA. 2004, 101 (38): 13951-13956. 10.1073/pnas.0401641101.
Article
Google Scholar
Lindow M, Jacobsen A, Nygaard S, Mang Y, Krogh A: Intragenomic Matching Reveals a Huge Potential for miRNA-Mediated Regulation in Plants. PLoS Computational Biology. 2007, 3 (11): e238-10.1371/journal.pcbi.0030238.
Article
PubMed
PubMed Central
Google Scholar
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ: miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 2006, D140-D144. 10.1093/nar/gkj112. 34 Database
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU: A gene expression map of Arabidopsis thaliana development. Nature Genetics. 2005, 37 (5): 501-6. 10.1038/ng1543.
Article
PubMed
CAS
Google Scholar
Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, de Peer YV, Rokhsar D: The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006, 313 (5793): 1596-1604. 10.1126/science.1128691.
Article
PubMed
CAS
Google Scholar
Plant Genome Duplication Database. [http://chibba.agtec.uga.edu/duplication/]
Zhao W, Su H, Song J, Zhao X, Zhang X: Ectopic expression of TaYAB1, a member of YABBY gene family in wheat, causes the partial abaxialization of the adaxial epidermises of leaves and arrests the development of shoot apical meristem in Arabidopsis. Plant Science. 2006, 170 (2): 364-371. 10.1016/j.plantsci.2005.09.008.
Article
CAS
Google Scholar
Sawa S, Watanabe K, Goto K, Kanaya E, Morita E, Okada K: FILAMENTOUS FLOWER, a meristem and organ identity gene of Arabidopsis, encodes a protein with a zinc finger and HMG-related domains. Genes & Development. 1999, 13 (9): 1079-1088. 10.1101/gad.13.9.1079.
Article
CAS
Google Scholar
Siegfried KR, Eshed Y, Baum SF, Otsuga D, Drews GN, Bowman JL: Members of the YABBY gene family specify abaxial cell fate in Arabidopsis. Development. 1999, 126 (18): 4117-28.
PubMed
CAS
Google Scholar
Luquez V, Hall D, Albrectsen B, Karlsson J, Ingvarsson P, Jansson S: Natural phenological variation in aspen (Populus tremula): the SwAsp collection. Tree Genetics & Genomes. 2007, 4: 279-292. 10.1007/s11295-007-0108-y.
Article
Google Scholar
Taylor G, Street NR, Tricker PJ, Sjodin A, Graham L, Skogstrom O, Calfapietra C, Scarascia-Mugnozza G, Jansson S: The transcriptome of Populus in elevated CO2. New Phytologist. 2005, 167: 143-154. 10.1111/j.1469-8137.2005.01450.x.
Article
PubMed
CAS
Google Scholar
Kono A, Umeda-Hara C, Lee J, Ito M, Uchimiya H, Umeda M: Arabidopsis D-Type Cyclin CYCD4;1 Is a Novel Cyclin Partner of B2-Type Cyclin-Dependent Kinase. Plant Physiology. 2003, 132 (3): 1315-1321. 10.1104/pp.103.020644.
Article
PubMed
CAS
PubMed Central
Google Scholar
Eshed Y, Izhaki A, Baum S, Floyd S, Bowman J: Asymmetric leaf development and blade expansion in Arabidopsis are mediated by KANADI and YABBY activities. Development. 2004, 131 (12): 2997-3006. 10.1242/dev.01186.
Article
PubMed
CAS
Google Scholar
Bowman J: The YABBY gene family and abaxial cell fate. Current Opinion in Plant Biology. 2000, 3: 17-22. 10.1016/S1369-5266(99)00035-7.
Article
PubMed
CAS
Google Scholar
Golz J, Hudson A: Plant development: YABBYs claw to the fore. Current Biology. 1999, 9 (22): R861-R863. 10.1016/S0960-9822(00)80047-0.
Article
PubMed
CAS
Google Scholar
Iwakawa , Hidekazu , Iwasaki , Mayumi , Kojima , Shoko , Ueno , Yoshihisa , Soma , Teppei , Tanaka , Hirokazu , Semiarti , Endang , Machida , Yasunori , Machida , Chiyoko : Expression of the ASYMMETRIC LEAVES2 gene in the adaxial domain of Arabidopsis leaves represses cell proliferation in this domain and is critical for the development of properly expanded leaves. Plant Journal. 2007, 51 (2): 173-184. 10.1111/j.1365-313X.2007.03132.x.
Article
PubMed
CAS
Google Scholar
Kim JH, Choi D, Kende H: The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis. The Plant Journal. 2003, 36: 94-104. 10.1046/j.1365-313X.2003.01862.x.
Article
PubMed
CAS
Google Scholar
Byrne M, Barley R, Curtis M, Arroyo J, Dunham M, Hudson A, Martienssen R: Asymmetric leaves1 mediates leaf patterning and stem cell function in Arabidopsis. Nature. 2000, 408 (6815): 967-971. 10.1038/35050091.
Article
PubMed
CAS
Google Scholar
Theodoris G, Inada N, Freeling M: Conservation and molecular dissection of ROUGH SHEATH2 and ASYMMETRIC LEAVES1 function in leaf development. Proceedings of the National Academy of Sciences, USA. 2003, 100 (11): 6837-6842. 10.1073/pnas.1132113100.
Article
CAS
Google Scholar
Eckardt N: The Role of PHANTASTICA in Leaf Development. Plant Cell. 2004, 16 (5): 1073-1075. 10.1105/tpc.060510.
Article
PubMed Central
Google Scholar
Xu L, Xu Y, Dong A, Sun Y, Pi L, Xu Y, Huang H: Novel as1 and as2 defects in leaf adaxial-abaxial polarity reveal the requirement for ASYMMETRIC LEAVES1 and 2 and ERECTA functions in specifying leaf adaxial identity. Development. 2003, 130 (17): 4097-4107. 10.1242/dev.00622.
Article
PubMed
CAS
Google Scholar
Qi Y, Sun Y, Xu L, Xu Y, Huang H: ERECTA is required for protection against heat-stress in the AS1/AS2 pathway to regulate adaxial-abaxial leaf polarity in Arabidopsis. Planta. 2004, 219 (2): 270-276. 10.1007/s00425-004-1248-z.
Article
PubMed
CAS
Google Scholar
Hibara K, Takada S, Tasaka M: CUC1 gene activates the expression of SAM-related genes to induce adventitious shoot formation. Plant Journal. 2003, 36 (5): 687-696. 10.1046/j.1365-313X.2003.01911.x.
Article
PubMed
CAS
Google Scholar
Hertzberg M, Aspeborg H, Schrader J, Andersson A, Erlandsson R, Blomqvist K, Bhalerao R, Uhlen M, Teeri TT, Lundeberg J, Sundberg B, Nilsson P, Sandberg G: A transcriptional roadmap to wood formation. Proceedings of the National Academy of Sciences, USA. 2001, 98 (25): 14732-14737. 10.1073/pnas.261293398.
Article
CAS
Google Scholar
Moreau C, Aksenov N, Lorenzo MG, Segerman B, Funk C, Nilsson P, Jansson S, Tuominen H: A genomic approach to investigate developmental cell death in woody tissues of Populus trees. Genome Biology. 2005, 6 (4): R34-10.1186/gb-2005-6-4-r34.
Article
PubMed
PubMed Central
Google Scholar
Wilson DL, Buckley MJ, Helliwell CA, Wilson IW: New normalization methods for cDNA microarray data. Bioinformatics. 2003, 19 (11): 1325-1332. 10.1093/bioinformatics/btg146.
Article
PubMed
CAS
Google Scholar
Andersson A, Keskitalo J, Sjodin A, Bhalerao R, Sterky F, Wissel K, Tandre K, Aspeborg H, Moyle R, Ohmiya Y, Bhalerao R, Brunner A, Gustafsson P, Karlsson J, Lundeberg J, Nilsson O, Sandberg G, Strauss S, Sundberg B, Uhlen M, Jansson S, Nilsson P: A transcriptional timetable of autumn senescence. Genome Biology. 2004, 5 (4): R24-10.1186/gb-2004-5-4-r24.
Article
PubMed
PubMed Central
Google Scholar
Ramirez-Carvajal GA, Morse AM, Davis JM: Transcript profiles of the cytokinin response regulator gene family in Populus imply diverse roles in plant development. New Phytologist. 2007, 177: 77-89.
PubMed
Google Scholar
Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R: NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucleic Acids Research. 2007, D760-D765. 10.1093/nar/gkl887. 35 Database
Groover A, Mansfield S, DiFazio S, Dupper G, Fontana J, Millar R, Wang Y: The Populus homeobox gene ARBORKNOX1 reveals overlapping mechanisms regulating the shoot apical meristem and the vascular cambium. Plant Molecular Biology. 2006, 61 (6): 917-932. 10.1007/s11103-006-0059-y.
Article
PubMed
CAS
Google Scholar
Segerman B, Jansson S, Karlsson J: Characterization of genes with tissue-specific differential expression patterns in Populus. Tree Genetics & Genomes. 2007, 3 (4): 351-362. 10.1007/s11295-006-0077-6.
Article
Google Scholar
Riano-Pachon DM, Ruzicic S, Dreyer I, Mueller-Roeber B: PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics. 2007, 8: 42-10.1186/1471-2105-8-42.
Article
PubMed
PubMed Central
Google Scholar
Zhu QH, Guo AY, Gao G, Zhong YF, Xu M, Huang M, Luo J: DPTF: a database of poplar transcription factors. Bioinformatics. 2007, 23 (10): 1307-1308. 10.1093/bioinformatics/btm113.
Article
PubMed
CAS
Google Scholar
Wold S: Cross Validatory Estimation of the Number of Components in Factor and Principal Components Models. Technometrics. 1978, 20: 397-406. 10.2307/1267639.
Article
Google Scholar
Shao J: Linear-Model Selection by Cross-Validation. Journal of The American Statistical Association. 1993, 88 (422): 486-494. 10.2307/2290328.
Article
Google Scholar
Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL: Hierarchical Organization of Modularity in Metabolic Networks. Science. 2002, 297 (5586): 1551-1555. 10.1126/science.1073374.
Article
PubMed
CAS
Google Scholar
Maere S, Heymans K, Kuiper M: BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics. 2005, 21 (16): 3448-3449. 10.1093/bioinformatics/bti551.
Article
PubMed
CAS
Google Scholar
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research. 2003, 13 (11): 2498-2504. 10.1101/gr.1239303.
Article
PubMed
CAS
PubMed Central
Google Scholar
Huala E, Dickerman AW, Garcia-Hernandez M, Weems D, Reiser L, LaFond F, Hanley D, Kiphart D, Zhuang M, Huang W, Mueller LA, Bhattacharyya D, Bhaya D, Sobral BW, Beavis W, Meinke DW, Town CD, Somerville C, Rhee SY: The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Research. 2001, 29: 102-5. 10.1093/nar/29.1.102.
Article
PubMed
CAS
PubMed Central
Google Scholar