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Regulation of gene expression has been shown to involve not only binding of transcription factor in target gene promoters but also characterization of histone around which DNA is wrapped around. Some histone modification, for example di-methylated histone H3 at lysine 4 (H3K4me2), has been shown to be associated with gene activation. However, no clear pattern has been shown to predict human promoters...
Allelic DNA aberrations across our genome have been associated with normal human genetic heterogeneity as well as with a number of diseases and disorders. When copy-number variations (CNVs) occur in gene-coding regions, known relationships between genes may help us understand correlations between CNVs. However, a large number of these aberrations occur in non-coding, extragenic regions and their correlations...
In the study, we calculated the codon usage bias in the newly identified UL38 gene of Duck Enteritis Virus (DEV) and performed a correlation analysis of codon bias of DEV UL38 gene and its host animal. There was a strong bias in the DEV UL38 gene towards the synonymous codons with A and T at the third codon position. The amino acids codon usage bias in the DEV UL38 gene was compared with other 15...
Fractal dimension and Shannon entropy were used to analyze the nucleotide fluctuation of dim-light vision rhodopsin gene. The maximal absorption wavelengths of the studied gene sequences span a range of 480 nm to 526 nm. The di-nucleotide Shannon entropy correlates with (a) the mono-nucleotide Shannon entropy with R2 of 0.99; (b) the CG+GC content with R2 of 0.86 (N = 6). The absorption maximal wavelength...
Through the comparative studies of k-mer distribution in Saccharomyces cerevisiae (S.ce) and Schizosaccharomyces pombe (S.po) transcription factor binding site (TFBS) sequences we have discovered that the average distance between a pair of transcription regulatory 7-mer motifs is conservative in S.ce-S.po promoters. The distance conservation is a new kind of evolutionary conservation, not based on...
The existence of BLAST sequence comparison algorithm and microarray technology are among the reasons that make bioinformatics the domain with the most abundant large relational datasets. For example, by BLAST-ing the genes of the human genome (around 30,000 genes) we obtain a 30,000 by 30,000 distance matrix. This matrix can not be currently stored in the memory of a typical desktop PC. In the same...
Increasing variety of molecular networks emerge from high-throughput genome data. In eukaryote, transcription factor is a major regulator at transcription level. Examining relations between features of these networks and their biological significance attracts attention of many researchers. While abundant quantity of studies represented connections between protein networks and topological parameters,...
We investigate the possibility that microRNA could act as an oncogene or tumor suppressor gene. Experimentally verified microRNA targeted genes information are integrated with microRNA and mRNA expression data to study this hypothesis, in which the Pearson correlation coefficient is used to quantify these relations. Cancer related microRNA and genes information are retrieved by literature search....
This paper presents feature extraction and estimations of multifractal measures for deoxyribonucleic acid (DNA) sequences, and demonstrates the intriguing possibility of identifying biological functionality using information contained within the DNA sequence. We have developed a technique that seeks patterns or correlations in the DNA sequence at a higher level. The technique has three main steps:...
The choice of a reference material in two-colour microarray experiments is an important issue of the experimental design. We consider a number of cell lines derived from a variety of primary tissues in order to construct a reference material. The aim of the present study is to understand the correlation structure of the data and develop a common reference that would enable comparison of expression...
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