Rice gene functional annotation is greatly hindered due to functional redundancy. Based on OGRO database information, function of only 1022 genes were characterized previously where estimated expressed genes is approximately 50000. TFs protein class consist of 80 families and function of only 211 were reported. To address this issue, we developed web resource using MySQL, PHP and related frame work. Database integrates expression pattern and diverse data in phylogenomic contest. Since TFs plays diverse role in plants, meta-expression analysis would provide putative function of remaining genes. Using this approach and in-house database, we have identified featured expression groups: 228 belongs to anatomy, 224 to abiotic stress, 202 to biotic stress and hormone responsive group includes 267 genes. Out of 315 known genes through loss of functional studies, 294 genes have no closely related family members. Among 12 pairs with probes in database, 6 genes have PCC value with more than 0.5 among closely related genes. These data suggest that TFs showing more than 0.5 PCC value among closely relating family members more likely have functional dominancy. This study will provide useful functional information for whole rice TFs and suggest promising functional genomic studies.

Water-deficiency is one of the most serious challenges which restrict crop production. Root is the primary tissues exposed to water limitation in soil. Although a number of transcriptome data under water limitation have been produced in rice, but most of them have analyzed the effect of leaf or shoot. Thus, understanding of relating molecular mechanism is still limited. To get global view of the effect on water deficiency in rice root, we carried out RNA-Seq experiment. To do this, we compared the RNA-Seq transcriptome data of 3 day samples under water deficiency with those of unstressed rice roots with unstressed control. As a result, we identified 1,098 genes upregulated in water stress condition for 3 days. Gene ontology (GO) enrichment analysis revealed that 18 GO terms are overrepresented. Of them, valyl-tRNA aminoacylation, transcription from RNA polymerase II promoter, glycine catabolic process, and L-phenylalanine catabolic process are more significant, indicating that transcription of new transcripts, control of translation fidelity, and reuse of primary and secondary metabolites can be activated during water stress.

E3 ubiquitin ligase plays a central role in determining specificity of the ubiquitination system by selecting appropriate candidate proteins. Compared with other eukaryotic species there are significantly more U-box protein-encoding genes in plant genome. The rice genome contain 77 U-box-type E3 encoding genes. The 77 members of the rice plant U-box (PUB) E3 family can be placed into 8 major groups based on their domain organizations. In this study, we generate and analyze phylogenomic data integrating anatomical expression patterns consisting of anatomical and stress responsive expression patterns base on 1150 affymetrix arrays to the phylogenic tree of rice plant U-box E3 family. We further developed functional gene network meditated by E3 ligases and refined the components in network by integrating gene expression patterns in response to drought stresses. We expect that our analysis will be a useful platform to facilitate the functional identification for each of U-box E3 family.

E3 ubiquitin ligase plays a central role in determining specificity of the ubiquitination system by selecting appropriate candidate proteins. Compared with other eukaryotic species there are significantly more U-box protein-encoding genes in plant genome. The rice genome contain 77 U-box-type E3 encoding genes. The 77 members of the rice plant U-box (PUB) E3 family can be placed into 8 major groups based on their domain organizations. In this study, we generate and analyze phylogenomic data integrating anatomical expression patterns consisting of anatomical and stress responsive expression patterns base on 1150 affymetrix arrays to the phylogenic tree of rice plant U-box E3 family. Then, we highlighted 8 genes in subfamilies II (5) and VII (3) of E3 ligases showing significant upregulation in water stress conditions such as drought and high concentration of salt stress. We further developed functional gene network meditated by E3 ligases and refined the components in network by integrating gene expression patterns in response to drought and salt stresses. We expect that our analysis will be a useful platform to facilitate the functional identification for each of U-box E3 family.