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Phylo rice transcription factor database: a resource for phylogenomics based systematic analysis of rice transcription factor for functional studies
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.
