TOMATOMICS

tomatomics  The Tomato Integrated Database

Microarray Data Search from Name
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 "KTU4 name(s)" and/or "Affymetrix probe ID(s)".
Put a name/ID in each line.
Upload a file : 
Number of matched probe pairs  >=

Reference
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/span>
 
Example

[KTU4 name]
KTU4-H00090
KTU4-H01821
KTU4-B12977
KTU4-B16946
KTU4-E29829
KTU4-E46987

[Affymetrix probe ID]
Les.1008.1.A1_at
Les.3309.1.S1_at