MYB proteins are a superfamily of transcription factors (TF) that play regulatory roles in developmental processes and resistance mechanism in plants. We identified 130 and 109 genes in the MYB superfamily from an analysis of the complete Arabidopsis and rice genome sequence. Although microarray based transcriptome analysis approach allows the investigation of the biological networks of MYB TF in DNA level, the underling mechanisms related to their functional role is not fully understood. In this work, we performed meta-analysis of public microarray data that analyzed with Arabidopsis and rice using co-expression analysis. A phylogenetic comparison of the members of this superfamily were performed with Sorghum bicolour to suggested that MYB super family underwent a rapid expansion their evolutionary times. We identified conserved expression pairs which play important role in transcription. Our comprehensive analysis of this huge transcription factor of Arabidopsis and rice may shed further light on the possible biological roles of the MYB TF in various plants.

Rapid extension of genomic database leads to the remarkable advance of functional genomics. This study proposes a novel methodology of functional analysis using 5-methyltrytophan (5 MT) mutant together with their 2-DE analysis and public microarray database. A total of 24 proteins was changed in 5 MT mutant and four remarkably different expressed proteins were identified. Among them, three spots were converted to Affymetrix probe. A total of 155 microarray samples from Gene Expression Omnibus (GEO) in NCBI was retrieved and followed by constructing gene co-expression networks over a broad range of biological issues through Self-Organising Tree Algorithm. Three co-expressing gene clusters were retrieved and each functional categorization with differential expression pattern was exhibited from 5 MT resistance mutant rice. It was indicated new co-expression networks in the mutant. This study suggests that on investigating possibility which correspond 2-DE to microarray database with their full potential.

Most gene functions of biochemical pathways were still unexplored, especially interactions of constituent genes. We attempted to uncover interaction network of biochemical pathways via a survey of co-expression clusters, which we have constructed from the NCBI GEO database, and then to define key genes of networks with expression correlations between members. Top 20 pathways with high numbers of individual genes were retrieved from 178 pathways. One pathway, ‘removal of superoxide radicals’ was excluded for further study, evidencing somewhat low degree (16%, 13 out of 79 genes) of mapped probes. We employed expression correlations of random pairs of 1,000 randomly selected genes for determining a cut off r-value for gene networks. Numbers of interactions with a significant expression correlation values between members might evidence that “hub genes” play key roles among a given pathway genes. For example most interactive pathway, ‘tRNA charging pathway’, that is composed of 60 probes corresponding to genes showed 264 positive significant interactions between members of 47 genes while 5 negative interactions between members of 7 genes., evidencing ‘Os10g26050’ (methionyl-tRNA synthetase) gene with highest interactions is suggestive of a hub gene. These findings might provide some clues on evolutionary fate of co-expression genes including each of biochemical pathways, e.g. convergent evolution

The genetic diversity was evaluated using RAPD and ISSR among natural populations and Korean wheat cultivars (Triticum aestivum). Understanding the genetic diversity of putative parental and wild stocks would be useful in wheat breeding programs. Ninety three populations were evaluated with fifty RAPD and three ISSR primers. A total of 185 RAPD and ISSR polymorphism were produced. These markers were considered to estimate the genetic distance among accessions. The genetic similarity ranged from 0.41 to 0.86. The dendrogram were constructed by using the UPGMA clustering algorithm based on genetic similarity. The genetic diversity within and among accession was assessed through Principal Component Analysis (PCA) for statistics analysis. In cluster analysis, four groups were clustered and 17 accessions were not clustered. The PCA was corresponded well to the result. This study provides basic information about the genetic relationships for breeding purposes.