Tomato functional genomics database: A comprehensive resource and analysis package for tomato functional genomics

Nucleic Acids Research

Volumn 39, Issue SUPPL. 1, 2011, Pages

  Fei, Zhangjun ^a,b   Joung, Je Gun ^a   Tang, Xuemei ^a   Zheng, Yi ^a   Huang, Mingyun ^a   Lee, Je Min ^a   McQuinn, Ryan ^a   Tieman, Denise M ^c   Alba, Rob ^a   Klee, Harry J ^c   Giovannoni, James J ^a,b  

^a United States Department of Agriculture Agricultural Research Service and Boyce Thompson Institute for Plant Research   (United States)

^b ROBERT W HOLLEY CENTER FOR AGRICULTURE AND HEALTH   (United States)

^c UNIVERSITY OF FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RNA;

ARTICLE; DATA ANALYSIS; DATA BASE; DATA MINING; FUNCTIONAL GENOMICS; GENE EXPRESSION; METABOLITE; MICROARRAY ANALYSIS; NONHUMAN; PRIORITY JOURNAL; RNA SEQUENCE; TOMATO; TOMATO FUNCTIONAL GENOMICS DATABASE;

DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENOME, PLANT; GENOMICS; LYCOPERSICON ESCULENTUM; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, SMALL UNTRANSLATED;

LYCOPERSICON ESCULENTUM;

EID: 78651325241     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq991     Document Type: Article

References (29)

1. Mueller, L., Lankhorst, R.K., Tanksley, S.D., Giovannoni, J.J., White, R., Vrebalov, J., Fei, Z., van Eck, J., Buels, R., Mills, A.A. et al. (2009) A snapshot of the emerging tomato genome sequence. Plant Genome, 2, 78-92.
2. Aoki, K., Yano, K., Suzuki, A., Kawamura, S., Sakurai, N., Suda, K., Kurabayashi, A., Suzuki, T., Tsugane, T., Watanabe, M. et al. (2010) Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics. BMC Genomics, 11, 210.
3. Carrari, F., Baxter, C., Usadel, B., Urbanczyk-Wochniak, E., Zanor, M.I., Nunes-Nesi, A., Nikiforova, V., Centero, D., Ratzka, A., Pauly, M. et al. (2006) Integrated analysis of metabolite and transcript levels reveals the metabolic shifts that underlie tomato fruit development and highlight regulatory aspects of metabolic network behavior. Plant Physiol., 142, 1380-1396.
4. Schauer, N., Semel, Y., Roessner, U., Gur, A., Balbo, I., Carrari, F., Pleban, T., Perez-Melis, A., Bruedigam, C., Kopka, J. et al. (2006) Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nat Biotechnol., 24, 447-454.
5. Tieman, D.M., Zeigler, M., Schmelz, E.A., Taylor, M.G., Bliss, P., Kirst, M. and Klee, H.J. (2006) Identification of loci affecting flavour volatile emissions in tomato fruits. J. Exp. Bot., 54, 887-896.
6. Mathieu, S., Dal Cin, V., Fei, Z., Li, H., Bliss, P., Taylor, M., Klee, H. and Tieman, D. (2009) Flavor compounds in tomato fruits: Identification of loci and potential pathways affecting volatile composition. J. Exp. Bot., 60, 325-337.
7. Pilcher, R.L., Moxon, S., Pakseresht, N., Moulton, V., Manning, K., Seymour, G. and Dalmay, T. (2007) Identification of novel small RNAs in tomato (Solanum lycopersicum). Planta, 226, 709-717.
8. Itaya, A., Bundschuh, R., Archual, A.J., Joung, J.G., Fei, Z., Dai, X., Zhao, P.X., Tang, Y., Nelson, R.S. and Ding, B. (2008) Small RNAs in tomato fruit and leaf development. Biochim Biophys Acta., 1779, 99-107.
9. Moxon, S., Jing, R., Szittya, G., Schwach, F., Pilcher, R.L.R., Moulton, V. and Dalmay, T. (2008) Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res., 18, 1602-1609.
10. Fei, Z., Tang, X., Alba, R. and Giovannoni, J. (2006) Tomato Expression Database (TED): A suite of data presentation and analysis tools. Nucleic Acids Res., 34, D766-D770.
11. Mueller, L.A., Solow, T.H., Taylor, N., Skwarecki, B., Buels, R., Binns, J., Lin, C., Wright, M.H., Ahrens, R., Wang, Y. et al. (2005) The SOL Genomics Network: A comparative resource for Solanaceae biology and beyond. Plant Physiol., 138, 1310-1317.
12. Camon, E., Magrane, M., Barrell, D., Lee, V., Dimmer, E., Maslen, J., Binns, D., Harte, N., Lopez, R. and Apweiler, R. (2004) The Gene Ontology Annotation (GOA) Database: Sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res., 32, D262-D266. (Pubitemid 38081652)
13. Barrett, T., Troup, D.B., Wilhite, S.E., Ledoux, P., Rudnev, D., Evangelista, C., Kim, I.F., Soboleva, A., Tomashevsky, M., Marshall, K.A. et al. (2009) NCBI GEO: Archive for high-throughput functional genomic data. Nucleic Acids Res., 37, D885-D890.
14. Parkinson, H., Kapushesky, M., Kolesnikov, N., Rustici, G., Shojatalab, M., Abeygunawardena, N., Berube, H., Dylag, M., Emam, I., Farne, A. et al. (2009) ArrayExpress update-from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res., 37, D868-D872.
15. Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C.A., Causton, H.C. et al. (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet., 29, 365-371.
16. 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.
17. Grant, G.R., Liu, J. and Stoeckert, C.J. Jr (2005) A practical false discovery rate approach to identifying patterns of differential expression in microarray data. Bioinformatics, 11, 2684-2690.
18. Wu, Z., Irizarry, R.A., Gentleman, R., Martinez Murillo, F. and Spencer, F. (2004) A model based background adjustment for oligonucleotide expression arrays. J. Am. Stat. Assoc., 99, 909-917.
19. Smyth, G.K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol., 3, 1-29.
20. Joung, J.G., Corbett, A.M., Fellman, S.M., Tieman, D.M., Klee, H.J., Giovannoni, J.J. and Fei, Z. (2009) Plant MetGenMAP: An integrative analysis system for plant systems biology. Plant Physiol., 151, 1758-1768.
21. Boyle, E.I., Weng, S., Gollub, J., Jin, H., Botstein, D., Cherry, J.M. and Sherlock, G. (2004) GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics, 20, 3710-3715.
22. Fiehn, O., Kopka, J., Dörmann, P., Altmann, T., Trethewey, R.N. and Willmitzer, L. (2000) Metabolite profiling for plant functional genomics. Nat. Biotechnol., 18, 1157-1161.
23. Eshed, Y. and Zamir, D. (1994) A genomic library of Lycopersicon pennellii in L.esculentum: A tool for fine mapping of genes. Euphytica, 79, 175-179.
24. Monforte, A. and Tanksley, S. (2000) Development of a set of near isogenic and backcross recombinant inbred lines containing most of the Lycopersicon hirsutum genome in a L. esculentum genetic background: A tool for gene mapping and gene discovery. Genome, 43, 803-813.
25. Vaucheret, H. (2006) Post-transcriptional small RNA pathways in plants: Mechanisms and regulations. Genes Dev., 20, 759-771.
26. Hofacker, I.L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res., 31, 3429-3431.
27. Rajagopalan, R., Vaucheret, H., Trejo, J. and Bartel, D.P. (2006) A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev., 20, 3407-3425.
28. Griffiths-Jones, S., Saini, H.K., van Dongen, S. and Enright, A.J. (2008) miRBase: Tools for microRNA genomics. Nucleic Acids Res., 36, D154-D158.
29. Jones-Rhoades, M.W. and Bartel, D.P. (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell, 14, 787-799.