Special Issue on “Gene Regulatory Network”

The journal Genomics Proteomics & Bioinformatics (GPB) is now inviting submissions for a special issue (to be published around summer 2013) on the topic of "Gene Regulatory Network". The Gene Regulatory Network (GRN) is a collection of DNA sequences which interact with each other and other cellular components, thereby governing the     

Call for Papers Special Issue on"Gene Regulatory Network"

The journal Genomics Proteomics & Bioinformatics (GPB) is now inviting submissions for a special issue (to be published around April 2013) on the topic of ’’Gene Regulatory Network’’. The Gene Regulatory Network (GRN) is a collection of DNA sequences which interact with each other and other cellular components, thereby governing the rates at which genes in the network are transcribed to change the genomic activity. GRNs are evolutionally-conserved and play critical roles in various biological processes and attract     

Special Issue on “Gene Regulatory Network”

The journal Genomics Proteomics & Bioinformatics (GPB) is now inviting submissions for a special issue (to be published around Dec 2012) on the topic of "Gene Regulatory Network". The Gene Regulatory Network (GRN) is a collection of DNA sequences which interact with each other and other cellular components, thereby governing the rates at which genes in the network are transcribed to change the genomic activity. GRNs are evolutionally-conserved and play critical roles in various biological processes and attract more and more research interest.     

Special Issue on "Gene Regulatory Network"

The journal Genomics Proteomics & Bioinformatics(GPB) is now inviting submissions for a special issue(to be published around April 2013) on the topic of "Gene Regulatory Network".     

Special Issue on “Gene Regulatory Network”

The journal Genomics Proteomics & Bioinformatics (GPB) is now inviting submissions for a special issue (to be published around April 2013) on the topic of ’’Gene Regulatory Network’’.     

WocEA: The visualization of functional enrichment results in word clouds

正The integration,analysis and visualization of the big omics data are critical for addressing a broad spectrum of biological questions.One of the most frequently conducted procedures is enrichment analysis,which statistically tests whether individual functional annotations of Gene Ontology (GO)or Kyoto Encyclopedia of Genes     

NORMA: The Network Makeup Artist——A Web Tool for Network Annotation Visualization

The Network Makeup Artist(NORMA) is a web tool for interactive network annotation visualization and topological analysis, able to handle multiple networks and annotations simultaneously. Precalculated annotations(e.g., Gene Ontology, Pathway enrichment, community detection,or clustering results) can be uploaded and visualized in a network, either as colored pie-chart nodes or as color-filled areas in a 2D/3D Venn-diagram-like style. In the case where no annotation exists,algorithms for automated...     

基因组常用术语解释(下)

蛋白组 (Proteome) :一个特定基因组产生的全部蛋白质 (The full complement of proteins produced by aparticular genome)。蛋白组学 (Proteomics) :研究基因组编码的全部蛋白质的科学 (The study of the full set of proteins en-coded by a genome)。假基因 (Pseudogene) :类似于基因但却没有功能的 DNA序列 ,或许是曾经具有功能的基因积累突变后残留所致 (A sequence of DNA similar to a gene butnonfunctional;probably the remnantof a once- func-tional gene that accumulated mutations)。调控区 (Regulatory region) :控…     

Comparisons of graph-structure clustering methods for gene expression data

Although many numerical clustering algorithms have been applied to gene expression dataanalysis,the essential step is still biological interpretation by manual inspection.The correlation betweengenetic co-regulation and affiliation to a common biological process is what biologists expect.Here,weintroduce some clustering algorithms that are based on graph structure constituted by biological knowledge.After applying a widely used dataset,we compared the result clusters of two of these algorithms in terms ofthe homogeneity of clusters and coherence of annotation and matching ratio.The results show that theclusters of knowledge-guided analysis are the kernel parts of the clusters of Gene Ontology (GO)-Clustersoftware,which contains the genes that are most expression correlative and most consistent with biologicalfunctions.Moreover,knowledge-guided analysis seems much more applicable than GO-Cluster in a largerdataset.     

Cloning and characterization of nanos gene in silkworm Bombyx mori

Gene nanos is a maternal posterior group gene required for normal development of abdominal segments and the germ line in Drosophila. Expression of nanos-related genes is associated with the germ line in a broad variety of other taxa. In this study, the 5＇-RACE method and the in silico cloning method are used to isolate the new nanos-like gene of Bombyx mor/and the gene obtained is analyzed with bioinformatics tools. The putative protein is expressed in Escherichia coli and the antiserum has been produced in New Zealand white rabbits. The result shows that the nanos cDNA is 1,913 bp in full length and contains a 954 bp open reading frame. The deduced protein has 317 amino acid residues, with a predicted molecular weight of 35 kDa, isoelectric point of 5.38, and contains a conserved nanos RNA binding domain. The conserved region of the deduced protein shares 73% homology with the nanos protein conserved region of Honeybee （Apis mellifera）. This gene has been registered in the GenBank under the accession number EF647589. One encoding sequence of the nanos fragment has been successfully expressed in E. coli. Western blotting analysis indicates that homemade antiserum can specifically detect nanos protein expressed in prokaryotic cells.     

Dawn of ocular gene therapy:implications for molecular diagnosis in retinal disease

Personalized medicine aims to utilize genomic information about patients to tailor treatment.Gene replacement therapy for rare genetic disorders is perhaps the most extreme form of personalized medicine,in that the patients’ genome wholly determines their treatment regimen.Gene therapy for retinal disorders is poised to become a clinical reality.The eye is an optimal site for gene therapy due to the relative ease of precise vector delivery,immune system isolation,and availability for monitoring of any potential damage or side effects.Due to these advantages,clinical trials for gene therapy of retinal diseases are currently underway.A necessary precursor to such gene therapies is accurate molecular diagnosis of the mutation(s) underlying disease.In this review,we discuss the application of Next Generation Sequencing(NGS) to obtain such a diagnosis and identify disease causing genes,using retinal disorders as a case study.After reviewing ocular gene therapy,we discuss the application of NGS to the identification of novel Mendelian disease genes.We then compare current,array based mutation detection methods against next NGS-based methods in three retinal diseases:Leber’s Congenital Amaurosis,Retinitis Pigmentosa,and Stargardt’s disease.We conclude that next-generation sequencing based diagnosis offers several advantages over array based methods,including a higher rate of successful diagnosis and the ability to more deeply and efficiently assay a broad spectrum of mutations.However,the relative difficulty of interpreting sequence results and the development of standardized,reliable bioinformatic tools remain outstanding concerns.In this review,recent advances NGS based molecular diagnoses are discussed,as well as their implications for the development of personalized medicine.     

A new distributed feature selection technique for classifying gene expression data

Classification of gene expression data is a pivotal research area that plays a substantial role in diagnosis and prediction of diseases. Generally, feature selection is one of the extensively used techniques in data mining approaches, especially in classification. Gene expression data are usually composed of dozens of samples characterized by thousands of genes. This increases the dimensionality coupled with the existence of irrelevant and redundant features. Accordingly, the selection of informative genes (features) becomes difficult, which badly affects the gene classification accuracy. In this paper, we consider the feature selection for classifying gene expression microarray datasets. The goal is to detect the most possibly cancer-related genes in a distributed manner, which helps in effectively classifying the samples. Initially, the available huge amount of considered features are subdivided and distributed among several processors. Then, a new filter selection method based on a fuzzy inference system is applied to each subset of the dataset. Finally, all the resulted features are ranked, then a wrapper-based selection method is applied. Experimental results showed that our proposed feature selection technique performs better than other techniques since it produces lower time latency and improves classification performance.     

Regulated genes in mesenchymal stem cells and gastric cancer

AIM: To investigate the genes regulated in mesenchymal stem cells(MSCs) and diffuse-type gastric cancer(GC),gene expression was analyzed. METHODS: Gene expression of MSCs and diffuse-type GC cells were analyzed by microarray. Genes related to stem cells, cancer and the epithelial-mesenchymal transition(EMT) were extracted from human gene lists using Gene Ontology and reference information. Gene panels were generated, and messenger RNA gene expression in MSCs and diffuse-type GC cells was analyzed. Cluster analysis was performed using the NCSS software.RESULTS: The gene expression of regulator of G-protein signaling 1(RGS1) was up-regulated in diffuse-type GC cells compared with MSCs. A panel of stem-cell related genes and genes involved in cancer or the EMT were examined. Stem-cell related genes, such as growth arrest-specific 6, musashi RNA-binding protein 2 and hairy and enhancer of split 1(Drosophila), NOTCH family genes and Notch ligands, such as delta-like 1(Drosophila) and Jagged 2, were regulated.CONCLUSION: Expression of RGS1 is up-regulated, and genes related to stem cells and NOTCH signaling are altered in diffuse-type GC compared with MSCs.     

基因芯片技术检测拉美夫定相关的HBV变异

In order to study the feasibility of gene chips technology in the detection of HBV mutation associated with lamivudine, we detected the mutation of HBV in peripheral blood of 30 patients treated with lamivudine for at least half a year by gene chips. The result was compared with that from direct sequencing. Both results are highly coincident. The rate reaches 100% while detecting single strain of virus infection, and 85% in multi-strains virus infection. Gene chip technology is quite valuable and practical in future clinic.     

Comparison of Algorithms for an Electronic Nose in Identifying Liquors

When the electronic nose is used to identify different varieties of distilled liquors, the pattern recognition algorithm is chosen on the basis of the experience, which lacks the guiding principle. In this research, the different brands of distilled spirits were identified using the pattern recognition algorithms （principal component analysis and the artificial neural network）. The recognition rates of different algorithms were compared. The recognition rate of the Back Propagation Neural Network （BPNN） is the highest. Owing to the slow convergence speed of the BPNN, it tends easily to get into a local minimum. A chaotic BPNN was tried in order to overcome the disadvantage of the BPNN. The convergence speed of the chaotic BPNN is 75.5 times faster than that of the BPNN.     

Mining functional gene modules linked with rheumatoid arthritis using a SNP-SNP network

The identification of functional gene modules that are derived from integration of information from different types of networks is a powerful strategy for interpreting the etiology of complex diseases such as rheumatoid arthritis (RA). Genetic variants are known to increase the risk of developing RA. Here, a novel method, the construction of a genetic network, was used to mine functional gene modules linked with RA. A polymorphism interaction analy-sis (PIA) algorithm was used to obtain cooperating single nucleotide polymorphisms (SNPs) that contribute to RA disease. The acquired SNP pairs were used to construct a SNP-SNP network. Sub-networks defined by hub SNPs were then extracted and turned into gene modules by mapping SNPs to genes using dbSNP database. We per-formed Gene Ontology (GO) analysis on each gene module, and some GO terms enriched in the gene modules can be used to investigate clustered gene function for better understanding RA pathogenesis. This method was applied to the Genetic Analysis Workshop 15 (GAW 15) RA dataset. The results show that genes involved in func-tional gene modules, such as CD160 (rs744877) and RUNX1 (rs2051179), are especially relevant to RA, which is supported by previous reports. Furthermore, the 43 SNPs involved in the identified gene modules were found to be the best classifiers when used as variables for sample classification.     

A novel ubiquitin carboxyl terminal hydrolase is involved in toad oocyte maturation

p28, a 28kD protein from toad (Bufo bufo gargarizans) oocytes, was identified by using p13sucl-agarose affinity chromatography. Sequence homology analysis of the full-length cDNA of p28 (Gene Bank accession number: AF 314091) indicated that it encodes a protein containing 224 amino-acids with about 55% identities and more than 70% positives to human, rat or mouse UCH-L1, and contains homological functional domains of UCH family. Anti-p28 monoclonal antibody, on injecting into the oocytes, could inhibit the progesterone-induced resumption of meiotic division in a dose-dependent manner. The recombinant protein p28 showed similar SDS/PAGE behaviors to the native one, and promoted ubiquitin ethyl ester hydrolysis, a classical catalytic reaction for ubiquitin carboxyl terminal hydrolases (UCHs). The results in this paper reveal that a novel protein, p28, exists in the toad oocytes, is a UCH L1 homolog, was engaged in the process of progesterone-induced oocyte maturation possibly through an involvement in prot     

Molecular and <Emphasis Type="Italic">in vitro</Emphasis> characterization of field isolates of bovine herpesvirus-1

Bovine Herpesvirus-1 (BoHV-1) is distributed worldwide and is a major pathogen in cattle,being the causal agent of a variety of clinical syndromes.The aim of this study was to isolate and to characteri...