tomatomics  The Tomato Integrated Database

Microarray Data Search from Keyword
To construct gene expression networks in tomato, we identified gene sets showing similar expression patterns. From the GEO, we collected 50 sample data sets of a microarray platform ‘Affymetrix Gene Chip Tomato Genome Array’ (Solanum lycopersicum, GPL4741). The data sets were normalized by RMA method in R/BioConductor. Then, Pearson’s correlation coefficients and MRs (Mutual Ranks) for each gene (probe) pair were calculated by statistical language R. Based on the correlation coefficients and MRs, gene expression networks were constructed. From the page of Gene Expression Data, the metabolic information in the database KaPPA-View 4 is accessible.
Input keyword(s). Put a phrase in each line.
And select "OR search" or "AND search".
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Number of matched probe pairs  >=
*Probe annotations are used in this keyword search.


K. Hamada, K. Hongo, K. Suwabe, A. Shimizu, T. Nagayama, R. Abe, S. Kikuchi, N. Yamamoto, T. Fujii, K. Yokoyama, H. Tsuchida, K. Sano, T. Mochizuki, N. Oki, Y. Horiuchi, M. Fujita, M. Watanabe, M. Matsuoka, N. Kurata and K. Yano (2011) OryzaExpress: An integrated database of gene expression networks and omics annotations in rice. Plant Cell Physiol. 52: 220-229.