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https://www.readbyqxmd.com/read/27907142/ibisa_tools-a-computational-toolkit-for-ion-binding-state-analysis-in-molecular-dynamics-trajectories-of-ion-channels
#1
Kota Kasahara, Kengo Kinoshita
Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD) method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering...
2016: PloS One
https://www.readbyqxmd.com/read/27900679/bioinformatic-profiling-identifies-a-glucose-related-risk-signature-for-the-malignancy-of-glioma-and-the-survival-of-patients
#2
Shihong Zhao, Jinquan Cai, Jianlong Li, Guiqiu Bao, Di Li, Yongli Li, Xiuwei Zhai, Chuanlu Jiang, Lihua Fan
The aim of this study is to investigate the glucose metabolic status and its prognostic value in glioma. The Chinese Glioma Genome Atlas (CGGA), The Cancer Genome Atlas (TCGA), and GSE16011 datasets were used to develop the glucose-related signature. A cohort of 305 glioma samples with whole genome microarray expression data from the Chinese Glioma Genome Atlas database was included for discovery. TCGA and GSE16011 datasets were used for validation. Gene Set Enrichment Analysis (GSEA) and Cytoscape were used to explore the bioinformatic implication...
November 29, 2016: Molecular Neurobiology
https://www.readbyqxmd.com/read/27899966/analysis-of-the-molecular-mechanism-of-osteosarcoma-using-a-bioinformatics-approach
#3
Jianxun Yang, Ning Wang
The aim of this study was to explore the underlying molecular mechanism related to the process and progression of osteosarcoma (OS). The differentially expressed genes (DEGs) were downloaded from the Gene Expression Omnibus database. The pathway and gene ontology (GO) enrichment analysis, as well as transcription factor, tumor-associated gene and tumor suppressor gene analyses were performed to investigate the functions of DEGs. Next, the protein-protein interaction (PPI) network was constructed and module analysis was further assessed by cluster analysis with the overlapping neighborhood expansion (Cluster ONE) cytoscape plug-in...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27896985/a-new-relevance-estimator-for-the-compilation-and-visualization-of-disease-patterns-and-potential-drug-targets
#4
Modest VON Korff, Tobias Fink, Thomas Sander
A new computational method is presented to extract disease patterns from heterogeneous and text-based data. For this study, 22 million PubMed records were mined for co-occurrences of gene name synonyms and disease MeSH terms. The resulting publication counts were transferred into a matrix Mdata. In this matrix, a disease was represented by a row and a gene by a column. Each field in the matrix represented the publication count for a co-occurring disease-gene pair. A second matrix with identical dimensions Mrelevance was derived from Mdata...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27895852/protein-protein-interaction-network-of-celiac-disease
#5
Mona Zamanian Azodi, Hassan Peyvandi, Mohammad Rostami-Nejad, Akram Safaei, Kamran Rostami, Reza Vafaee, Mohammadhossein Heidari, Mostafa Hosseini, Mohammad Reza Zali
AIM: The aim of this study is to investigate the Protein-Protein Interaction Network of Celiac Disease. BACKGROUND: Celiac disease (CD) is an autoimmune disease with susceptibility of individuals to gluten of wheat, rye and barley. Understanding the molecular mechanisms and involved pathway may lead to the development of drug target discovery. The protein interaction network is one of the supportive fields to discover the pathogenesis biomarkers for celiac disease...
2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/27895744/identification-of-targets-of-mirna-221-and-mirna-222-in-fulvestrant-resistant-breast-cancer
#6
Pengfei Liu, Manna Sun, Wenhua Jiang, Jinkun Zhao, Chunyong Liang, Huilai Zhang
The present study aimed to identify the differentially expressed genes (DEGs) regulated by microRNA (miRNA)-221 and miRNA-222 that are associated with the resistance of breast cancer to fulvestrant. The GSE19777 transcription profile was downloaded from the Gene Expression Omnibus database, and includes data from three samples of antisense miRNA-221-transfected fulvestrant-resistant MCF7-FR breast cancer cells, three samples of antisense miRNA-222-transfected fulvestrant-resistant MCF7-FR cells and three samples of control inhibitor (green fluorescent protein)-treated fulvestrant-resistant MCF7-FR cells...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27895742/comparative-analysis-of-gene-expression-profiles-of-gastric-cardia-adenocarcinoma-and-gastric-non-cardia-adenocarcinoma
#7
Bin Song, Juan Du, Neng Deng, Ji-Chen Ren, Zhen-Bo Shu
In the present study, gene expression profiles were analyzed to identify the molecular mechanisms underlying gastric cardia adenocarcinoma (GCA) and gastric non-cardia adenocarcinoma (GNCA). A gene expression dataset (accession number GSE29272) was downloaded from Gene Expression Omnibus, and consisted of 62 GCA samples and 62 normal controls, as well as 72 GNCA samples and 72 normal controls. The two groups of differentially-expressed genes (DEGs) were compared to obtain common and unique DEGs. A differential analysis was performed using the Linear Models for Microarray Data package in R...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27855613/hoxb7-and-hsa-mir-222-as-the-potential-therapeutic-candidates-for-metastatic-colorectal-cancer
#8
Maryam Iman, Seyede Samaneh Mostafavi, Seyed Shahriar Arab, Sadegh Azimzadeh, Mansour Poorebrahim
BACKGROUND: Recent studies have shown that the high mortality of patients with colorectal cancer (CRC) is related to its ability to spread the surrounding tissues, thus there is a need for designing and developing new drugs. OBJECTIVE: Here, we proposed a combinational therapy strategy, an inhibitory peptide in combination with miRNA targeting, for modulating CRC metastasis. In this study, some of the recent patents were also reviewed. METHODS: After data analysis with GEO2R and gene annotation using DAVID server, regulatory interactions of differentially expressed genes (DEGs) were obtained from STRING, GeneMANIA, KEGG and TRED databases...
2016: Recent Patents on Anti-cancer Drug Discovery
https://www.readbyqxmd.com/read/27853520/dot-app-a-graphviz-cytoscape-conversion-plug-in
#9
Braxton Fitts, Ziran Zhang, Massoud Maher, Barry Demchak
dot-app is a Cytoscape 3 app that allows Cytoscape to import and export Graphviz (*.dot, *.gv) files, also known as DOT files due to the *.dot extension and their conformance to the DOT language syntax. The DOT format was originally created in the early 2000s to represent graph topologies, layouts and formatting. DOT-encoded files are produced and consumed by a number of open-source graph applications, including GraphViz, Gephi, neato, smyrna, and others. While DOT-based graph applications are popular, they emphasize general graph layout and styling over the topological and semantic analysis functions available in domain-focused applications such as Cytoscape...
2016: F1000Research
https://www.readbyqxmd.com/read/27853512/contextual-hub-analysis-tool-chat-a-cytoscape-app-for-identifying-contextually-relevant-hubs-in-biological-networks
#10
Tanja Muetze, Ivan H Goenawan, Heather L Wiencko, Manuel Bernal-Llinares, Kenneth Bryan, David J Lynn
: Highly connected nodes (hubs) in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we report a Cytoscape app, the Contextual Hub Analysis Tool (CHAT), which enables users to easily construct and visualize a network of interactions from a gene list of interest, integrate contextual information, such as gene expression data, and identify hub nodes that are more highly connected to contextual nodes (e...
2016: F1000Research
https://www.readbyqxmd.com/read/27853510/conet-app-inference-of-biological-association-networks-using-cytoscape
#11
Karoline Faust, Jeroen Raes
Here we present the Cytoscape app version of our association network inference tool CoNet. Though CoNet was developed with microbial community data from sequencing experiments in mind, it is designed to be generic and can detect associations in any data set where biological entities (such as genes, metabolites or species) have been observed repeatedly. The CoNet app supports Cytoscape 2.x and 3.x and offers a variety of network inference approaches, which can also be combined. Here we briefly describe its main features and illustrate its use on microbial count data obtained by 16S rDNA sequencing of arctic soil samples...
2016: F1000Research
https://www.readbyqxmd.com/read/27846294/identification-and-verification-of-potential-therapeutic-target-genes-in-berberine-treated-zucker-diabetic-fatty-rats-through-bioinformatics-analysis
#12
Yang Sheng Wu, Yi-Tao Chen, Yu-Ting Bao, Zhe-Ming Li, Xiao-Jie Zhou, Jia-Na He, Shi-Jie Dai, Chang Yu Li
BACKGROUND: Berberine is used to treat diabetes and dyslipidemia. However, the effect of berberine on specific diabetes treatment targets is unknown. In the current study, we investigated the effect of berberine on the random plasma glucose, glycated hemoglobin (HbA1C), AST, ALT, BUN and CREA levels of Zucker diabetic fatty (ZDF) rats, and we identified and verified the importance of potential therapeutic target genes to provide molecular information for further investigation of the mechanisms underlying the anti-diabetic effects of berberine...
2016: PloS One
https://www.readbyqxmd.com/read/27835046/identifying-mirna-regulatory-mechanisms-in-preeclampsia-by-systems-biology-approaches
#13
Orsolya Biró, Bálint Nagy, János Rigó
BACKGROUND: Preeclampsia (PE) is the major cause of maternal and fetal morbidity and mortality, affecting 3-8% of all pregnancies around the globe. miRNAs are small, noncoding RNA molecules, which negatively regulate gene expression. Abnormally expressed miRNAs contribute to pregnancy complications such as PE. The aim of our study was to find possible regulatory mechanisms by system biology approaches, which are connected to the pathogenesis of PE. METHODS: We integrated publicly available miRNA and gene expression profiles and created a network from the significant miRNA-mRNA pairs with the help of MAGIA and Cytoscape softwares...
November 11, 2016: Hypertension in Pregnancy
https://www.readbyqxmd.com/read/27834916/systematic-analysis-of-protein-interaction-network-associated-with-azoospermia
#14
Soudabeh Sabetian, Mohd Shahir Shamsir
Non-obstructive azoospermia is a severe infertility factor. Currently, the etiology of this condition remains elusive with several possible molecular pathway disruptions identified in the post-meiotic spermatozoa. In the presented study, in order to identify all possible candidate genes associated with azoospermia and to map their relationship, we present the first protein-protein interaction network related to azoospermia and analyze the complex effects of the related genes systematically. Using Online Mendelian Inheritance in Man, the Human Protein Reference Database and Cytoscape, we created a novel network consisting of 209 protein nodes and 737 interactions...
November 10, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27831650/critical-genes-of-hepatocellular-carcinoma-revealed-by-network-and-module-analysis-of-rna-seq-data
#15
M-R Yang, Y Zhang, X-X Wu, W Chen
OBJECTIVE: RNA-seq data of hepatocellular carcinoma (HCC) was analyzed to identify critical genes related to the pathogenesis and prognosis. MATERIALS AND METHODS: Three RNA-seq datasets of HCC (GSE69164, GSE63863 and GSE55758) were downloaded from Gene Expression Omnibus (GEO), while another dataset including 54 HCC cases with survival time was obtained from The Cancer Genome Atlas (TCGA). Differentially expressed genes (DEGs) were identified by significant analysis of microarrays (SAM) method using package samr of R...
October 2016: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/27830058/autoannotate-a-cytoscape-app-for-summarizing-networks-with-semantic-annotations
#16
Mike Kucera, Ruth Isserlin, Arkady Arkhangorodsky, Gary D Bader
Networks often contain regions of tightly connected nodes, or clusters, that highlight their shared relationships. An effective way to create a visual summary of a network is to identify clusters and annotate them with an enclosing shape and a summarizing label. Cytoscape provides the ability to annotate a network with shapes and labels, however these annotations must be created manually one at a time, which can be a laborious process. AutoAnnotate is a Cytoscape 3 App that automates the process of identifying clusters and visually annotating them...
2016: F1000Research
https://www.readbyqxmd.com/read/27829444/potential-molecular-characteristics-in-situ-in-response-to-repetitive-uvb-irradiation
#17
Wenqi Chen, Jinhai Zhang
BACKGROUND: To identify molecular characteristics in situ in response to repetitive UVB (ultraviolet-B) irradiation. METHODS: Microarray data from the Gene Expression Omnibus were re-analyzed to identify DEGs (differentially expressed genes) between UVB-irradiated and non-irradiated skin biopsies. Enrichment and annotation analyses were performed respectively using DAVID, and TSGene and TAG databases. PPIs (protein-protein interactions) were analyzed using STRING, and miRNAs (microRNAs) and TFs (transcription factors) were predicted separately by miRNA-related databases and ENCODE...
November 10, 2016: Diagnostic Pathology
https://www.readbyqxmd.com/read/27826930/visualization-and-analysis-of-mirna-targets-interactions-networks
#18
Luis E León, Sebastián D Calligaris
MicroRNAs are a class of small, noncoding RNA molecules of 21-25 nucleotides in length that regulate the gene expression by base-pairing with the target mRNAs, mainly leading to down-regulation or repression of the target genes. MicroRNAs are involved in diverse regulatory pathways in normal and pathological conditions. In this context, it is highly important to identify the targets of specific microRNA in order to understand the mechanism of its regulation and consequently its involvement in disease. However, the microRNA target identification is experimentally laborious and time-consuming...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27814735/gene-expression-profiles-and-protein-protein-interaction-networks-in-amyotrophic-lateral-sclerosis-patients-with-c9orf72-mutation
#19
Meena Kumari Kotni, Mingzhu Zhao, Dong-Qing Wei
BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that involves the death of neurons. ALS is associated with many gene mutations as previously studied. In order to explore the molecular mechanisms underlying ALS with C9orf72 mutation, gene expression profiles of ALS fibroblasts and control fibroblasts were subjected to bioinformatics analysis. Genes with critical functional roles can be detected by a measure of node centrality in biological networks. In gene co-expression networks, highly connected genes called as candidate hubs have been associated with key disease-related pathways...
November 5, 2016: Orphanet Journal of Rare Diseases
https://www.readbyqxmd.com/read/27802793/identification-of-crucial-mirnas-and-the-targets-in-renal-cortex-of-hypertensive-patients-by-expression-profiles
#20
Guohua Wang, Lan Wu, Zhi Chen, Jinghui Sun
BACKGROUNDS: Defect in kidney is one major reason of hypertension. The study aimed ao uncovering the regulatory mechanisms of miRNAs and the targets in hypertensive kidney. METHODS: Gene expression profile of GSE28345 and miRNA expression profile of GSE28283 were downloaded from GEO database. After data preprocessing, differently expressed genes (DEGs) and miRNAs (DE-miRs) were identified using limma package. Then targets of miRNAs were predicted according to information in relevant databases...
November 2, 2016: Renal Failure
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