Transcriptomics

Dataset Information

21

Expression data from various tomato plant tissues


ABSTRACT: Gene-to-gene coexpression analysis is a powerful approach to infer function of uncharacterized genes. To perform non-targeted coexpression analysis of tomato genes, we collected a developmental gene expression dataset using various tissues of tomato plant. Expression data are collected from 24 different tissue types including root, hypocotyl, cotyledon, leaf at different stages, and fruit tissues at 4 different ripening stages from 4 different Solanum lycopersicum cultivars. Fruits were separated to the flesh and the peel. These two tissue types indeed showed remarkably different gene expression profiles. We also collected data from 4 different ripening stages (mature green, yellow, orange, and red) to detail the changes during ripening. By using this gene expression dataset, we calculated pair-wise Pearson’s correlation coefficients, and performed network-based coexpression analysis. The analysis generated a number of coexpression modules, some of which showed an enrichment of genes associated with specific functional categories. This result will be useful in inferring functions of uncharacterized tomato genes, and in prioritizing genes for further experimental analysis. We used Affymetrix GeneChip Tomato genome Arrays to detail the global gene expression change using 24 different tomato tissue types (67 hybridizations). We collected gene expression data from 24 different tomato tissue types using 67 hybridizations. Root, hypocotyl, cotyledon, and leaf were sampled from 3-week-old or 5-week–old plant of Solanum lycopersicum cultivar Micro-Tom. Fruit tissues were sampled from S. lycopersicum cultivars Micro-Tom, Anthocyanin fruit (Aft, LA1996), Line27859, and Momotaro 8 (Takii, Japan). From Micro-Tom fruit, the peel and the flesh were separately sampled from 4 different ripening stages: mature green (MG, approximately 30 day after anthesis), yellow (Y, approximately 35 days after anthesis), orange (O, approximately 38-40 days after anthesis), and red (R, approximately 45-48 days after anthesis). From fruits of Aft and Line27859, the peel and the flesh were sampled at mature green (MG, approximately 40 days after anthesis) and red (R, approximately 50-55 days after anthesis) stages. From Momotaro 8, the peel and the flesh were sampled at red (R, 50- approximately 50-55 days after anthesis) stages. For each tissue type, 2-4 biological replicates were made in RNA preparation.

ORGANISM(S): Solanum lycopersicum  

SUBMITTER: Chiaki Konishi   Shuji Inai  Taneaki Tsugane  Daisuke Shibata  Soichi Ozaki  Kunihiro Suda  Takashi Fujii  Yoshiyuki Ogata  Atsushi Kurabayashi  Naoki Yamamoto  Koh Aoki  Tatsuya Suzuki 

PROVIDER: E-GEOD-19326 | ArrayExpress | 2010-02-21

SECONDARY ACCESSION(S): GSE19326PRJNA120423

REPOSITORIES: GEO, ArrayExpress

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Publications

Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module.

Ozaki Soichi S   Ogata Yoshiyuki Y   Suda Kunihiro K   Kurabayashi Atsushi A   Suzuki Tatsuya T   Yamamoto Naoki N   Iijima Yoko Y   Tsugane Taneaki T   Fujii Takashi T   Konishi Chiaki C   Inai Shuji S   Bunsupa Somnuk S   Yamazaki Mami M   Shibata Daisuke D   Aoki Koh K  

DNA research : an international journal for rapid publication of reports on genes and genomes 20100203 2


Gene-to-gene coexpression analysis is a powerful approach to infer the function of uncharacterized genes. Here, we report comprehensive identification of coexpression gene modules of tomato (Solanum lycopersicum) and experimental verification of coordinated expression of module member genes. On the basis of the gene-to-gene correlation coefficient calculated from 67 microarray hybridization data points, we performed a network-based analysis. This facilitated the identification of 199 coexpressio  ...[more]

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