Non-biased distribution of tomato genes with no counterparts in Arabidopsis thaliana in expression patterns during fruit maturation

Yano, Kentarô; Tsugane, Taneaki; Watanabe, Masao; Maeda, Fumi; Aoki, Koh; Shibata, Daisuke

doi:10.5511/plantbiotechnology.23.199

Cited by 9 publications

(6 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…From fruit and leaf Micro-Tom cDNA libraries containing 37,972 cDNA clones, Yano et al (2006b) selected 10,905 cDNA clones as being representative of non-redundant sequences for constructing cDNA arrays. The current version of MiBASE contains BLAST annotations for each probe and the expression data for samples from leaves and fruit.…”

Section: Gene Expression Datamentioning

confidence: 99%

Genomic Databases for Tomato

Yano

Aoki

Shibata

2007

Plant Biotechnology

Self Cite

View full text Add to dashboard Cite

Section: Gene Expression Datamentioning

confidence: 99%

Genomic Databases for Tomato

Yano

Aoki

Shibata

2007

Plant Biotechnology

Self Cite

View full text Add to dashboard Cite

“…This database is a part of the tomato genome project, and contains basic microarray information including SGN-supported probe sequences and annotation information as well as microarray data for fruit development [ 11 , 34 - 36 ]. Several other databases, including ArrayExpress [ 37 ] and MiBASE [ 33 , 38 , 39 ], also have open gene expression data obtained from microarray experiments. These databases will continue to be updated with additional expression results.…”

Section: Current State Of Tomato Genomicsmentioning

confidence: 99%

Comprehensive Resources for Tomato Functional Genomics Based on the Miniature Model Tomato Micro-Tom

Matsukura

Aoki²,

Fukuda³

et al. 2008

View full text Add to dashboard Cite

Tomato (Solanum lycopersicum L., Solanaceae) is an excellent model plant for genomic research of solanaceous plants, as well as for studying the development, ripening, and metabolism of fruit. In 2003, the International Solanaceae Project (SOL, www.sgn.cornell.edu) was initiated by members from more than 30 countries, and the tomato genome-sequencing project is currently underway. Genome sequence of tomato obtained by this project will provide a firm foundation for forthcoming genomic studies such as the comparative analysis of genes conserved among the Solanaceae species and the elucidation of the functions of unknown tomato genes. To exploit the wealth of the genome sequence information, there is an urgent need for novel resources and analytical tools for tomato functional genomics. Here, we present an overview of the development of genetic and genomic resources of tomato in the last decade, with a special focus on the activities of Japan SOL and the National Bio-Resource Project in the development of functional genomic resources of a model cultivar, Micro-Tom.

show abstract

“…For example, the tomato unigene database MiBASE provides information about unigenes obtained by assembling ESTs in tomato and a wild relative as well as information about SNPs, simple sequence repeats (SSRs), GO terms, metabolic pathway names, and gene expression data (Yamamoto et al 2005, Yano et al 2006a, Yano et al 2006b). …”

Section: Expressed Sequence Tags and Unigenesmentioning

confidence: 99%

Omics databases in plant science: key to systems biology

Suwabe

Yano

2008

Plant Biotechnology

Self Cite

View full text Add to dashboard Cite

This wealth of comprehensive online resources and web databases allows us to extract new essential biological information beyond what is gleaned from the dataset obtained from a single study. The large-scale data collected from web databases can be used to detect patterns such as consensus sequences of expressed sequence tags (ESTs) (e.g., Lazo et al. 2004;Lee et al. 2005;Lopez et al. 2004), global patterns of gene expression (Obayashi et al. 2007) and orthologous DNA and protein sequences among different genomes (Tatusov et al. 2003). To handle such large amounts of data effectively and efficiently, many new bioinformatics tools are under development. Here, we review the current state of web databases and bioinformatics tools available for plant research. The websites mentioned in this article are summarized in Table 1. Abstract Recently, high-throughput technologies for comprehensive genomic, transcriptomic and proteomic analyses have been developed. Large-scale 'omics data' obtained from such experimental methods have rapidly accumulated and been stored into web databases. In addition, the number of web databases for molecular biology has rapidly increased, since most new projects construct and maintain new web databases for their own large-scale omics data. This wealth of comprehensive online resources and web databases allow us to extract essential new biological information beyond a dataset obtained from an individual study. For effective and efficient handling of such large sets of data, various kinds of bioinformatics tools are being developed. Here, we review the current state of web databases and bioinformatics tools for plant biosciences and systems biology. Collections of databases, tools, and experimental materials

show abstract

Non-biased distribution of tomato genes with no counterparts in Arabidopsis thaliana in expression patterns during fruit maturation

Cited by 9 publications

References 17 publications

Genomic Databases for Tomato

Genomic Databases for Tomato

Comprehensive Resources for Tomato Functional Genomics Based on the Miniature Model Tomato Micro-Tom

Omics databases in plant science: key to systems biology

Contact Info

Product

Resources

About