TOMATOMICS: An Integrated Database for Omics Information in Tomato

Large-scale omics information provides new insights to various biological characteristics such as gene functions, mechanisms for regulations of gene expressions and metabolic processes. We have maintained web-databases MiBASE, KaFTom and TOMATOMICS to provide information on ESTs, cDNAs, Unigenes, gene expression profiles, metabolic pathways and so on in tomato. The TOMATOMICS has been constructed to store comprehensive omics information, including genome sequences. To advance a comprehensive view of transcriptome, we constructed a new non-redundant sequence set, Kazusa Tomato Unigene ver. 4 (KTU4), with ESTs and HTCs. For each unigene, functional annotations including metabolic pathways and detections of SNPs and SSRs were executed. Information on genome structural annotations and SNPs between ‘Heniz 1706’ and Micro-Tom are accessible through the genome browser in TOMATOMICS. With publicly available sequence data in SRA, tomato gene expression networks have been constructed. The networks are also graphically shown in the TOMATOMICS. TOMATOMICS is directly linked to the clone request web-page. Micro-Tom cDNA clones (including full-length cDNA clones) are available from the National BioResource Project (NBRP) Tomato. Information of T-DNA insertion allele of mutants in TOMATOMA, a web-database of mutant resources, is also accessible from the GBrowse in TOMATOMICS. This work is partially supported by Resarch Funding for Computational Software Supporting Program in Meiji University.

URL     TOMATOMICS: http://bioinf.mind.meiji.ac.jp/tomatomics/

           MiBASE: http://www.pgb.kazusa.or.jp/mibase/

           KaFTom: http://www.pgb.kazusa.or.jp/kaftom/

           NBRP Tomato: http://tomato.nbrp.jp/indexEn.html