Improved Algorithms for the Identification of Yeast Proteins and Significant Transcription Factor and Motif Analysis

With the rapid development of MS technologiesy, the demands for a more sophisticated MS interpretation algorithm haves grown as well. We have developed a new protein fingerprinting method using a binomial distribution, (fBIND). With the fBIND, we improved the performance accuracy of protein fingerprinting up to the maximum 49% (more than MOWSE) and 2% than(at a previous binomial distribution approach studied by of Wool et al.) as compared to the established algorithms. Moreover, we also suggest a the statistical approach to define the significance of transcription factors and motifs in the identified proteins based on the Gene Ontology (GO).

Computational Analysis of Neighboring Genes on Arabidopsis thaliana Chromosomes 4 and 5: Their Genomic Association as Functional Subunits

The genes related to specific events or pathways in bacteria are frequently localized proximate to the genome of their neighbors, as with the structures known as operon, but eukaryotic genes seem to be independent of their neighbors, and are dispersed randomly throughout genomes. Although cases are rare, the findings from structures similar to prokaryotic operons in the nematode genome, and the clustering of housekeeping genes on human genome, lead us to assess the genomic association of genes as functional subunits. We evaluated the genomic association of neighboring genes on chromosomes 4 and 5 of Arabidopsis thaliana with and without respectively consideration of the scaffold/matrix-attached regions (S/MAR) loci. The observed number of functionally identical bigrams and trig rams were significantly higher than expected, and these results were verified statistically by calculating rho-values for weighted random distributions. The observed frequency of functionally identical big rams and trig rams were much higher in chromosome 4 than in chromosome 5, but the frequencies with, and without, consideration of the S/MAR in each chromosome were similar. In this study, a genomic association among functionally related neighboring genes in Arabidopsis thaliana was suggested.