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dc.contributor.authorKudo, Toru
dc.contributor.authorKobayashi, Masaaki
dc.contributor.authorTerashima, Shin
dc.contributor.authorKatayama, Minami
dc.contributor.authorOzaki, Soichi
dc.contributor.authorKanno, Maasa
dc.contributor.authorSaito, Misa
dc.contributor.authorYokoyama, Koji
dc.contributor.authorOhyanagi, Hajime
dc.contributor.authorAoki, Koh
dc.contributor.authorKubo, Yasutaka
dc.contributor.authorYano, Kentaro
dc.date.accessioned2017-01-25T08:57:41Z
dc.date.available2017-01-25T08:57:41Z
dc.date.issued2017-01-22
dc.identifier.citationKudo T, Kobayashi M, Terashima S, Katayama M, Ozaki S, et al. (2017) TOMATOMICS: A Web Database for Integrated Omics Information in Tomato. Plant and Cell Physiology: pcw207. Available: http://dx.doi.org/10.1093/pcp/pcw207.
dc.identifier.issn0032-0781
dc.identifier.issn1471-9053
dc.identifier.doi10.1093/pcp/pcw207
dc.identifier.urihttp://hdl.handle.net/10754/622730
dc.description.abstractSolanum lycopersicum (tomato) is an important agronomic crop and a major model fruit-producing plant. To facilitate basic and applied research, comprehensive experimental resources and omics information on tomato are available following their development. Mutant lines and cDNA clones from a dwarf cultivar, Micro-Tom, are two of these genetic resources. Large-scale sequencing data for ESTs and full-length cDNAs from Micro-Tom continue to be gathered. In conjunction with information on the reference genome sequence of another cultivar, Heinz 1706, the Micro-Tom experimental resources have facilitated comprehensive functional analyses. To enhance the efficiency of acquiring omics information for tomato biology, we have integrated the information on the Micro-Tom experimental resources and the Heinz 1706 genome sequence. We have also inferred gene structure by comparison of sequences between the genome of Heinz 1706 and the transcriptome, which are comprised of Micro-Tom full-length cDNAs and Heinz 1706 RNA-seq data stored in the KaFTom and Sequence Read Archive databases. In order to provide large-scale omics information with streamlined connectivity we have developed and maintain a web database TOMATOMICS (http://bioinf.mind.meiji.ac.jp/tomatomics/). In TOMATOMICS, access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes is available through search functions and the genome browser, which has an intuitive graphical interface.
dc.description.sponsorshipThis work was supported in part by Grants-in-Aid for Scientific Research (No. 24113518 and No. 26113716 to K.Y.) from the Ministry of Education, Culture, Sports, Science, and Technology of Japan (MEXT) and for Scientific Research (B) (No. 16H04873 to Y.K.) from the Japan Society for Promotion of Science (JSPS). Support was also provided by the MEXT-Supported Program for the Strategic Research Foundation at Private Universities (2014–2018), Research Project Grant (A) by Institute of Science and Technology, Meiji University and by Research Funding for the Computational Software Supporting 70 Program from Meiji University to K.Y.
dc.publisherOxford University Press (OUP)
dc.relation.urlhttps://academic.oup.com/pcp/article/doi/10.1093/pcp/pcw207/2849735/TOMATOMICS-A-Web-Database-for-Integrated-Omics
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectGenome
dc.subjectDatabase
dc.subjectTranscriptome
dc.subjectMicro-tom
dc.subjectSolanum Lycopersicum (Tomato)
dc.titleTOMATOMICS: A Web Database for Integrated Omics Information in Tomato
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.identifier.journalPlant and Cell Physiology
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionBioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan.
dc.contributor.institutionGraduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, 599-8531 Japan.
dc.contributor.institutionGraduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530 Japan.
dc.contributor.institutionBioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan. kyano@isc.meiji.ac.jp.
kaust.personOhyanagi, Hajime
refterms.dateFOA2018-06-13T14:46:50Z


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This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Except where otherwise noted, this item's license is described as This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.