Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module.
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 coexpression modules. A gene ontology annotation search revealed that 75 out of the 199 modules are enriched with genes associated with common functional categories. To verify the coexpression relationships between module member genes, we focused on one module enriched with genes associated with the flavonoid biosynthetic pathway. A non-enzyme, non-transcription factor gene encoding a zinc finger protein in this module was overexpressed in S. lycopersicum cultivar Micro-Tom, and expression levels of flavonoid pathway genes were investigated. Flavonoid pathway genes included in the module were up-regulated in the plant overexpressing the zinc finger gene. This result demonstrates that coexpression modules, at least the ones identified in this study, represent actual transcriptional coordination between genes, and can facilitate the inference of tomato gene function.
Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan.
Soichi
S
Ozaki
Yoshiyuki
Y
Ogata
Kunihiro
K
Suda
Atsushi
A
Kurabayashi
Tatsuya
T
Suzuki
Naoki
N
Yamamoto
Yoko
Y
Iijima
Taneaki
T
Tsugane
Takashi
T
Fujii
Chiaki
C
Konishi
Shuji
S
Inai
Somnuk
S
Bunsupa
Mami
M
Yamazaki
Daisuke
D
Shibata
Koh
K
Aoki
D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D018745:Genome, Plant; D023281:Genomics; D018551:Solanum lycopersicum / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics
D010940:Plant Proteins