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We present a shape-space approach for analyzing genetic influences on the shapes of the sulcal folding patterns on the cortex. Sulci are represented as continuously parameterized functions in a shape space, and shape differences between sulci are obtained via geodesics between them. The resulting statistical shape analysis framework is used not only to construct populations averages, but also used...
In extraction of information from the biomedical literature, name disambiguation of domain-specific entities, such as proteins, is one of the most important issues. The entity ambiguity with the highest dimension is the species to which an entity is associated with. Furthermore, one of the bottlenecks in inter-species gene name normalization is species disambiguation. To enhance the performance of...
The regulation of gene expression is a dynamic process, hence it is of vital interest to identify and characterize these dynamic processes. Since genes work in a cascade of networks, gene regulatory network (GRN) reconstruction is a crucial process for thorough understanding of the underlying biological interactions. We present here a technique based on partial correlations to infer the GRN. Our proposed...
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...
Codon usage bias in UL53 gene of DEV was analyzed in this paper, the results indicated that it had strong bias towards to the synonymous codons with A or T at the third codon position. The codon usage bias of DEV UL53 gene and 26 reference herpesviruses were analyzed by EMBOSS program and RSCU. In addition, Phylogenetic tree indicated DEV was evolutionarily closer to CaHV-2, CaHV-3, MeHV-1. The ENC-GC...
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...
Previous studies have suggested that some graph properties of protein interaction networks might be related with gene morbidity. In particular, it has been suggested that when a polymorphism affects a gene, it is more likely to produce a disease if the node degree in the interaction network is higher than for other genes. However, these results do not take into account the possible bias introduced...
Expressions of Notchl and Cyclin D1 were analysed by immunohistochemical method in the specimens of normal mammary tissue, usual hyperplasia, atypical hyperplasia, cancer in situ, and invasive cancer tissue, which were obtained from the patients operated due to some kind of breast disease. We observed an evidently decreased Notchl and increased cyclin D1 expression respectively from normal tissue...
It is generally believed that semantic similarity between GO terms is critical in resolving semantic heterogeneousness when integrating heterogeneous biological databases. In this paper, we propose an approach to determine the semantic similarity of two GO terms based on both the locations of these terms in the GO graph and their semantic relations with their ancestor terms. First, we collect all...
Research of gene regulatory network is critically important for diagnosis and therapy of tumor. We propose a method on construction of gene regulatory network and selection of feature genes on cancer. Firstly we selected 277 genes whose expressions differ greatly between tumor tissues and normal tissues ,then collected multiple group feature genes using Peano Count Tree; Secondly we picked the gene...
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....
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