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Since diseases might be related with each other, systematically assessing their relationships could provide us novel insight into their mechanisms. One of the most important methods to study diseases' relationships is to calculate their phenotype similarity scores based on the text and clinical synopsis parts of their records in the OMIM database. However, as demonstrated in this paper, the similarity...
We determined the nucleotide sequence of a portion of the duck enteritis virus (DEV) strain CHv which was suspected to be the UL10 gene(GenBank accession no EU195100.), encoding glycoprotein M(gM). The UL10 gene was cloned and sequenced, which was composed of 1230 nucleotides encoding 409 amino acids, with a predicted molecular mass of 45.752 kDa. We calculated the codon usage bias in the newly identified...
Glycoprotein K encoded by the DEV-UL53 gene is one of the DEV envelope glycoproteins. Like most members of the alphaherpesvirinae, the genes in the UL region of its genome are well conserved, which means that the major DEV envelope glycoprotein K possessing similar functions of envelope glycoprotein K of alphaherpesvirinae plays an essential role in viral replication and cell fusion. Glycoprotein...
Bidirectional gene pairs have received considerable attention because this unique genomic organization is so prevalent in vertebrate genome that it covers more than 10% of the whole genes in human. To study the character of these adjacent head-to-head gene pairs and to improve the understanding of the difference between bi- and unidirectional genes, we identified all the bidirectional gene pair members...
Mitochondria are a vital organelle of eukaryotic cells. Many diseases are caused by the mitochondrial gene mutation , therefore, there is an urgent requirement to explore the proteins of mitochondrion. In this paper we have created a list of 1086 human mitochondrial genes by combining 13 datasets from publications or genomic experiments. Then we created a functional linkage network among mitochondrial...
Alpha-fetoprotein (AFP) is a major serum protein (Mr, =70,000) synthesized during fetal life. Reappearance of AFP in adult serum often signals pathological conditions, particularly hepatocarcinomas and teratocarcinomas. To obtain monoclonal antibodies against AFP for further study of the structure and biological function of AFP, a novel method for making hybridoma cell lines producing monoclonal antibodies...
Due to involvement in changing of chromatin structure, histone modifications are very important in regulation for gene expression. Some attempts have been done to resolve the relationship among histone modifications and gene expression. In this study, four types of Bayeasian network methods, Maximum weight spanning tree (MWST), K2, Markov Chain Monte Carlo (MCMC) and greedy-search(GS), are used to...
Alignment analysis indicated that the nucleotide sequences of Liver X receptors α (LXRα) of Landes goose are highly conserved to other species including chicken, human, rat, mouse and cattle, and the homologies are 95.2%, 76.3%, 74.5%, 74.3% and 74.9%, respectively. Furthermore, molecular phylogeny analyses have shown that LXRα were divided into two main evolution branches, one was the mammals branch,...
Though the functional relationship analysis for gene products is useful, a convenient and user- friendly tool to measure the functional similarity for genome-wide gene products in multiple species is still not available. We computed the functional similarity of gene products in genome wide in human, mouse and rat based on our algorithm. Database and web services were built based on the precomputed...
Myogenesis in skeletal muscle is a cascade of developmental events, whose initiation involves the MRFs family of the myogenic regulatory factors. Comparing the characterization of MRFs family members and their deduced proteins is necessary to know the reasons of their different role in muscle development. In order to investigate the reasons why MRFs members have different roles in duck myogenesis,...
In order to predict and compare the identities and differences of HLA-A*0201 restricted cytotoxic T lymphocyte (CTL) epitopes among the influenza A virus ( H1N1), avian influenza virus (H5N1) and human influenza virus (H3N2). The SYFPEITHI, a T-cell epitope prediction tool, was adopted to predict the HLA-A*0201-restricted CTL epitopes in the three influenza viruses; DNAMAN was used to analyze the...
The UL27 open reading frame of the Duck Plague virus encodes glycoprotein B, the molecular characteristic of this gene was analyzed with bioinformatics software. The results indicated that this gene encodes an estimated 1000 putative proteins, contains the conserved domain of the Herpesvirus UL27-like protein. Similarity comparisons of DPV CHv strain gB protein sequences with those of 20 known herpesviruses...
Duck enteritis virus (DEV) is an alphaherpesvirinae that causes an acute, contagious, and fatal disease. In this study, the DEV-ULS3 gene from Key Laboratory of Animal Disease and Human Health of Sichuan Province was cloned and sequenced. Nucleotide sequence analysis revealed a 1032 bp open reading frame (ORF) theoretically encoding a 343-amino acid polypeptide was homologous to UL53 gene of alphaherpesvirinaes...
The functional knowledge of cancer proteins and cancer pathways is currently limited and not detailed enough, remaining as a major hurdle to cancer studies. Particularly, many cancer proteins are only annotated to high-level general GO categories. Here, we apply an efficient algorithm, by constructing function-specific protein-protein interaction sub-networks, to find finer functions of the cancer...
This paper explores the fallout from the decision in S & Marper v UK (2008), where the European Court of Human Rights, in ruling the UK's DNA retention regime breached human rights, was `struck by the blanket and indiscriminate nature' of the power to retain DNA and stated that the UK Government required `weighty reasons' to justify the retention of DNA in cases of unconvicted individuals. Since...
The basic helix-loop-helix (bHLH) proteins make up of a complex multigene family of transcription factors that play the important roles in many biological processes. Although much effort has been made on their functional roles, their evolutionary origin and functional diversity remain to be clarified. In this study, we compared genomes and interactomes of bHLH gene families from model organisms such...
Many high-throughput DNA sequencing methods provide very short reads, typically of a few tens of base pairs. New algorithms and softwares are needed to analysis those short reads effectively. There are some software tools for aligning short reads to a reference genome. Here we introduce a new method, Umap, to align theses short reads faster and more exact. Applying Umap to simulated very short reads...
Sequencing by hybridization is a promising cost-effective technology for high-throughput DNA sequencing via microarray chips. However, due to the effects of spectrum errors rooted from experimental conditions, a fast and accurate reconstruction of original sequences has become a challenging problem. In the last decade, a variety of analyses and designs have been tried to overcome this problem, where...
Protein phosphorylation is a reversible post-translational modification commonly used by cell signaling networks to transmit information about the extracellular environment into intracellular organelles for the regulation of the activity and sorting of proteins within the cell. For this study we reconstructed a literature-based mammalian kinase-substrate network from several online resources. The...
The identification of significant disease-related genes and networks is an important issue in understanding underlying mechanisms of cells. We integrate phenotype networks, protein networks and efficiently utilize gene expression data to identify human disease networks. We use prostate cancer data as our test domain. In comparison with statistical methods such as t-test and Wilcoxon test, our method...
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