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https://www.readbyqxmd.com/read/28545060/signet-a-signaling-network-data-simulator-to-enable-signaling-network-inference
#1
Elizabeth A Coker, Costas Mitsopoulos, Paul Workman, Bissan Al-Lazikani
Network models are widely used to describe complex signaling systems. Cellular wiring varies in different cellular contexts and numerous inference techniques have been developed to infer the structure of a network from experimental data of the network's behavior. To objectively identify which inference strategy is best suited to a specific network, a gold standard network and dataset are required. However, suitable datasets for benchmarking are difficult to find. Numerous tools exist that can simulate data for transcriptional networks, but these are of limited use for the study of signaling networks...
2017: PloS One
https://www.readbyqxmd.com/read/28536832/proteomic-profiling-reveals-crucial-retinal-protein-alterations-in-the-early-phase-of-an-experimental-glaucoma-model
#2
Fabian Anders, Julia Teister, Sebstian Funke, Norbert Pfeiffer, Franz Grus, Thanos Solon, Verena Prokosch
PURPOSE: Clinical glaucoma is difficult to assess in terms of molecular pathophysiology, prompting studies in experimental models of glaucoma. The purpose of this study was to investigate quantitative changes in retinal protein expression at the onset of experimental glaucoma in rats. Analyzing the proteome provides a suitable tool to decipher the pathophysiological processes in glaucomatous degeneration. METHODS: Thermic cauterization of episcleral veins was utilized to elevate the intraocular pressure in Sprague Dawley rats...
May 24, 2017: Graefe's Archive for Clinical and Experimental Ophthalmology
https://www.readbyqxmd.com/read/28521404/silencing-tak1-alters-gene-expression-signatures-in-bladder-cancer-cells
#3
Jimin Chen, Nan Zhang, Jiaming Wen, Zhewei Zhang
The aim of the present study was to identify the differentially expressed genes (DEGs) that are induced by the silencing of transforming growth factor-β-activated kinase 1 (TAK1) in bladder cancer cells and to analyze the potential biological effects. Dataset GSE52452 from mutant fibroblast growth factor receptor 3 (FGFR3) bladder cancer cells transfected with control siRNA or TAK1-specific siRNA was downloaded from Gene Expression Omnibus. The DEGs between the two groups were identified using Limma package following data pre-processing by Affy in Bioconductor...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28515914/analysis-of-the-function-of-microrna-375-in-humans-using-bioinformatics
#4
Xiaohua Chen, Baoxia Li, Rongcheng Luo, Sina Cai, Cao Zhang, Xiaolong Cao
MicroRNA-375 (miR-375) is expressed at low levels in many types of solid tumor, particularly in gastrointestinal tumors. It is considered to be important in the development of cancer and certain diseases. Thus, more detailed knowledge is required on the particular functions of miR-375. miRs function by regulating target genes. Therefore, in the current study, miRWalk (which includes the data from 10 prediction software programs) was used to predict the target genes of miR-375. The genes, which were co-predicted using five different software programs were further analyzed using Database for Annotation, Visualization and Integrated Discovery online software [including gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis]...
May 2017: Biomedical Reports
https://www.readbyqxmd.com/read/28501630/identification-of-potential-crucial-genes-associated-with-steroid-induced-necrosis-of-femoral-head-based-on-gene-expression-profile
#5
Zhe Lin, Yongsheng Lin
The aim of this study was to explore potential crucial genes associated with the steroid-induced necrosis of femoral head (SINFH) and provided valid biological information for further investigation of SINFH. Gene expression profile of GSE26316, generated from 3 SINFH rat samples and 3 normal rat samples were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified using LIMMA package. After functional enrichment analyses of DEGs, protein-protein interaction (PPI) network and sub-PPI network analyses were conducted based on the STRING database and cytoscape...
May 10, 2017: Gene
https://www.readbyqxmd.com/read/28500349/quantitative-succinyl-proteome-profiling-of-camellia-sinensis-cv-anji-baicha-during-periodic-albinism
#6
Yan-Xia Xu, Chen-Jia Shen, Jian-Qiang Ma, Wei Chen, Juan Mao, Yan-Yan Zhou, Liang Chen
Lysine succinylation is a novel dynamic and evolutionarily conserved post-translational modification (PTM) that regulates various biological processes. 'Anji Baicha' is an albino tea variety that exhibits temperature-based variability of leaf colour and amino acid concentrations. However, the mechanism underlying albinism in 'Anji Baicha' has not been investigated at the level of succinylation. Here, we identify 3530 lysine succinylation sites mapped to 2132 proteins in 'Anji Baicha', representing the first extensive data on the lysine succinylome in the tea plant...
May 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28499430/genome-wide-dna-methylation-analysis-in-lung-fibroblasts-co-cultured-with-silica-exposed-alveolar-macrophages
#7
Juan Li, Wu Yao, Lin Zhang, Lei Bao, Huiting Chen, Di Wang, Zhongzheng Yue, Yiping Li, Miao Zhang, Changfu Hao
BACKGROUND: Exposure to crystalline silica is considered to increase the risk of lung fibrosis. The primary effector cell, the myofibroblast, plays an important role in the deposition of extracellular matrix (ECM). DNA methylation change is considered to have a potential effect on myofibroblast differentiation. Therefore, the present study was designed to investigate the genome-wide DNA methylation profiles of lung fibroblasts co-cultured with alveolar macrophages exposed to crystalline silica in vitro...
May 12, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28498422/garlic-extract-in-bladder-cancer-prevention-evidence-from-t24-bladder-cancer-cell-xenograft-model-tissue-microarray-and-gene-network-analysis
#8
Won Tae Kim, Sung-Pil Seo, Young Joon Byun, Ho-Won Kang, Yong-June Kim, Sang-Cheol Lee, Pildu Jeong, Yoonhee Seo, Soo Young Choe, Dong-Joon Kim, Seon-Kyu Kim, Sung-Kwon Moon, Yung-Hyun Choi, Geun Taek Lee, Isaac Yi Kim, Seok Joong Yun, Wun-Jae Kim
There is a growing interest in the use of naturally occurring agents in cancer prevention. This study investigated the garlic extract affects in bladder cancer (BC) prevention. The effect of garlic extract in cancer prevention was evaluated using the T24 BC BALB/C-nude mouse xenograft model. Microarray analysis of tissues was performed to identify differences in gene expression between garlic extract intake and control diet, and gene network analysis was performed to assess candidate mechanisms of action. Furthermore, we investigated the expression value of selected genes in the data of 165 BC patients...
May 11, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28484645/gene-expression-profiling-of-the-optic-nerve-head-of-patients-with-primary-open-angle-glaucoma
#9
Xinrong Wang, Ke Gong, Haiyan Li, Congyi Wang, Chaoyi Qu, Hui Li
Background. The pressure-induced axonal injury of the vulnerable ONH has led many researchers to view glaucoma from the perspective of the genetic basis of the angle of the ONH. However, genetic studies on POAG from this perspective are limited. Methods. Microarray dataset GSE45570 of the ONH of healthy individuals and POAG patients were downloaded from the Gene Expression Omnibus. After screening for the DEGs using the limma package, enrichment analysis was performed using DAVID. The DEG interaction network was constructed using cancer spider at BioProfiling...
2017: Journal of Ophthalmology
https://www.readbyqxmd.com/read/28476771/signature-of-microbial-dysbiosis-in-periodontitis
#10
Vincent Meuric, Sandrine Le Gall-David, Emile Boyer, Luis Acuña-Amador, Bénédicte Martin, Shao Bing Fong, Frederique Barloy-Hubler, Martine Bonnaure-Mallet
Periodontitis is driven by a disproportionate host inflammatory immune response induced by an imbalance in the composition of oral bacteria. It instigates microbial dysbiosis along with failed resolution of the chronic destructive inflammation.The objective of this study is to identify microbial signatures for health and chronic periodontitis at the genus level and to propose a model of dysbiosis including the calculation of bacterial ratios. DESIGN AND METHODS: Published sequencing data obtained from several different studies (196 sub-gingival samples from patients with chronic periodontitis and 422 sub-gingival samples from healthy subjects) were pooled and submitted to a new microbiota analysis using the same VAMPS (Visualization and Analysis of Microbial Population Structures) analysis pipeline to identify microbiota specific to health and disease...
May 5, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28476618/identification-of-repaglinide-as-a-therapeutic-drug-for-glioblastoma-multiforme
#11
Zui Xuan Xiao, Ruo Qiao Chen, Dian Xing Hu, Xiao Qiang Xie, Shang Bin Yu, Xiao Qian Chen
Glioblastoma multiforme (GBM) is a highly aggressive brain tumor with a median survival time of only 14 months after treatment. It is urgent to find new therapeutic drugs that increase survival time of GBM patients. To achieve this goal, we screened differentially expressed genes between long-term and short-term survived GBM patients from Gene Expression Omnibus database and found gene expression signature for the long-term survived GBM patients. The signaling networks of all those differentially expressed genes converged to protein binding, extracellular matrix and tissue development as revealed in BiNGO and Cytoscape...
June 17, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28476119/parameter-identifiability-analysis-and-visualization-in-large-scale-kinetic-models-of-biosystems
#12
Attila Gábor, Alejandro F Villaverde, Julio R Banga
BACKGROUND: Kinetic models of biochemical systems usually consist of ordinary differential equations that have many unknown parameters. Some of these parameters are often practically unidentifiable, that is, their values cannot be uniquely determined from the available data. Possible causes are lack of influence on the measured outputs, interdependence among parameters, and poor data quality. Uncorrelated parameters can be seen as the key tuning knobs of a predictive model. Therefore, before attempting to perform parameter estimation (model calibration) it is important to characterize the subset(s) of identifiable parameters and their interplay...
May 5, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28472919/webgivi-a-web-based-gene-enrichment-analysis-and-visualization-tool
#13
Liang Sun, Yongnan Zhu, A S M Ashique Mahmood, Catalina O Tudor, Jia Ren, K Vijay-Shanker, Jian Chen, Carl J Schmidt
BACKGROUND: A major challenge of high throughput transcriptome studies is presenting the data to researchers in an interpretable format. In many cases, the outputs of such studies are gene lists which are then examined for enriched biological concepts. One approach to help the researcher interpret large gene datasets is to associate genes and informative terms (iTerm) that are obtained from the biomedical literature using the eGIFT text-mining system. However, examining large lists of iTerm and gene pairs is a daunting task...
May 4, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28470264/reconstruction-and-analysis-of-the-lncrna-mirna-mrna-network-based-on-competitive-endogenous-rna-reveal-functional-lncrnas-in-rheumatoid-arthritis
#14
Hui Jiang, Rong Ma, Shubiao Zou, Yongzhong Wang, Zhuqing Li, Weiping Li
Rheumatoid arthritis (RA) is an autoimmune disease with an unknown etiology, occurring in approximately 1.0% of general population. More and more studies have suggested that long non-coding RNAs (lncRNAs) could play important roles in various biological processes and be associated with the pathogenesis of different kinds of diseases including RA. Although a large number of lncRNAs have been found, our knowledge of their function and physiological/pathological significance is still in its infancy. In order to reveal functional lncRNAs and identify the key lncRNAs in RA, we reconstructed a global triple network based on the competitive endogenous RNA (ceRNA) theory using the data from National Center for Biotechnology Information Gene Expression Omnibus and our previous paper...
May 4, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28466792/orthoscape-a-cytoscape-application-for-grouping-and-visualization-kegg-based-gene-networks-by-taxonomy-and-homology-principles
#15
Zakhar Sergeevich Mustafin, Sergey Alexandrovich Lashin, Yury Georgievich Matushkin, Konstantin Vladimirovich Gunbin, Dmitry Arkadievich Afonnikov
BACKGROUND: There are many available software tools for visualization and analysis of biological networks. Among them, Cytoscape ( http://cytoscape.org/ ) is one of the most comprehensive packages, with many plugins and applications which extends its functionality by providing analysis of protein-protein interaction, gene regulatory and gene co-expression networks, metabolic, signaling, neural as well as ecological-type networks including food webs, communities networks etc. Nevertheless, only three plugins tagged 'network evolution' found in Cytoscape official app store and in literature...
January 27, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28465213/metabolomic-changes-and-metabolic-responses-to-expression-of-heterologous-biosynthetic-genes-for-lycopene-production-in-yarrowia-lipolytica
#16
Chen Zhao, Qi Gao, Jun Chen, Liujing Wei, Tadayuki Imanaka, Qiang Hua
The metabolomic studies were conducted for both the engineered lycopene-producing Yarrowia lipolytica strain and the control strain. The changes in metabolome profiling and main pathway abundance of Y. lipolytica with the introduction of heterologous crt genes were investigated by multiple analytical and statistical methods More importantly, the metabolome data were transformed into pathway abundances visualized by a pathway relationship network using Cytoscape software. This network provided a simple way to present the statistical results of pathway abundance and interpret the effects of the crt genes in a metabolic view, and the results highlighted the up-regulation of eight pathways and the down-regulation of three pathways in the lycopene fast production phase...
April 29, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28454467/investigation-of-differentially-expressed-micrornas-and-genes-in-cervical-cancer-using-an-integrated-bioinformatics-analysis
#17
Zhanzhan Xu, Yu Zhou, Fang Shi, Yexuan Cao, Thi Lan Anh Dinh, Jing Wan, Min Zhao
Cervical cancer is one of the most common types of cancer among women worldwide. In order to identify the microRNAs (miRNAs/miRs) and mRNAs associated with the carcinogenesis of cervical cancer, and to investigate the molecular mechanisms of cervical cancer, an miRNA microarray, GSE30656, and 3 mRNA microarrays, GSE63514, GSE39001 and GSE9750, for cervical cancer were retrieved from Gene Expression Omnibus. These datasets were analyzed in order to obtain differentially-expressed genes (DEGs) and miRNAs using the GEO2R tool...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454442/identification-of-target-genes-of-cediranib-in-alveolar-soft-part-sarcoma-using-a-gene-microarray
#18
Wenhua Jiang, Pengfei Liu, Xiaodong Li, Ping Wang
The aim of the present study was to identify the target genes of cediranib and the associated signaling pathways in alveolar soft part sarcoma (ASPS). A microarray dataset (GSE32569) was obtained from the Gene Expression Omnibus database. The R software package was used for data normalization and screening of differentially expressed genes (DEGs). The Database for Annotation, Visualization and Integrated Discovery was used to perform Gene Ontology analysis. Gene Set Enrichment Analysis was performed to obtain the up- and downregulated pathways in ASPS...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28453679/biopaxviz-a-cytoscape-application-for-the-visual-exploration-of-metabolic-pathway-evolution
#19
Fotis E Psomopoulos, Dimitrios M Vitsios, Shakuntala Baichoo, Christos A Ouzounis
Summary: BioPAXViz is a Cytoscape (version 3) application, providing a comprehensive framework for metabolic pathway visualization. Beyond the basic parsing, viewing and browsing roles, the main novel function that BioPAXViz provides is a visual comparative analysis of metabolic pathway topologies across pre-computed pathway phylogenomic profiles given a species phylogeny. Furthermore, BioPAXViz supports the display of hierarchical trees that allow efficient navigation through sets of variants of a single reference pathway...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453502/identification-of-key-genes-affecting-results-of-hyperthermia-in-osteosarcoma-based-on-integrative-chip-seq-targetscan-analysis
#20
Yuxia Shi, Fan Yang, Shuqing Wei, Gang Xu
BACKGROUND The purpose of this study was to research the effects of hyperthermia on osteosarcoma (OS) by integrating the Chromatin Immunoprecipitation with the generation sequencing (ChIP-Seq) and TargetScan analysis of heat shock transcription factor 1 (HSF1). MATERIAL AND METHODS The HSF1 ChIP-seq dataset of GSE60984 was downloaded from the Gene Expressed Omnibus (GEO) database. The HSF1-binding sites were screened by MACS2 in OS cells after 10 and 20 min of hyperthermia, and they were annotated using the ChIPseeker package...
April 28, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
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