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https://www.readbyqxmd.com/read/28423571/predictive-analysis-of-long-non-coding-rna-expression-profiles-in-diffuse-large-b-cell-lymphoma
#1
Danxia Zhu, Cheng Fang, Xiaodong Li, Yiting Geng, Ruiqi Li, Chen Wu, Jingting Jiang, Changping Wu
Long non-coding RNAs (lncRNAs) are implicated in many tumors. To find novel targets for study of diffuse large B-cell lymphoma (DLBCL), our team performed genome-wide analyses of lncRNA expression in 5 DLBCL cell lines using the 4*180K Agilent lncRNA Chip system, and in normal B cells. Five lncRNAs were validated by quantitative reverse transcription polymerase chain reaction. The differentially expressed lncRNAs and mRNAs were identified via false discovery rate and fold-change filtering. Potential targets correlated with DLBCL were recognized via gene ontology and pathway analysis...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28413614/the-pathlinker-app-connect-the-dots-in-protein-interaction-networks
#2
Daniel P Gil, Jeffrey N Law, T M Murali
PathLinker is a graph-theoretic algorithm for reconstructing the interactions in a signaling pathway of interest. It efficiently computes multiple short paths within a background protein interaction network from the receptors to transcription factors (TFs) in a pathway. We originally developed PathLinker to complement manual curation of signaling pathways, which is slow and painstaking. The method can be used in general to connect any set of sources to any set of targets in an interaction network. The app presented here makes the PathLinker functionality available to Cytoscape users...
2017: F1000Research
https://www.readbyqxmd.com/read/28413470/identification-of-genes-associated-with-the-effect-of-inflammation-on-the-neurotransmission-of-vascular-smooth-muscle-cell
#3
Shujie Gan, Shenlong Qiu, Yiwen Feng, Yanping Zhang, Qin Qian, Zhong Wan, Jingdong Tang
Vascular smooth muscle cell (VSMC) accumulation and hypertrophy are common in vascular disorders, and inflammation has a crucial role in the development of these diseases. To investigate the effect of inflammation on the neurotransmission of VSMC, bioinformatic analysis was performed, following next generation sequencing. Genes of lipopolysaccharide (LPS)-treated A7r5 cells and phosphate-buffered saline (PBS)-treated A7r5 cells were sequenced via next generation sequencing, and each assay was repeated three times...
April 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28411543/the-disorder-metabolic-profiling-in-kidney-and-spleen-of-mice-induced-by-mycotoxins-deoxynivalenol-through-gas-chromatography-mass-spectrometry
#4
Jian Ji, Pei Zhu, Fangchao Cui, Fuwei Pi, Yinzhi Zhang, Xiulan Sun
Gas chromatography mass spectrometry (GC-MS) based metabolomics strategy was implemented for the metabolites detection in kidney and spleen samples of mice, which were treated with 2 mg kg(-1) deoxynivalenol (DON), through intragastric administration for three weeks, for studying the toxicity of DON on the metabolic profiling in kidney and spleen. The spectrum was deconvoluted, aligned and identified with MS DIAL, equipped with Fiehn library. And the data matrix was processed with univariate analysis and multivariate analysis for selection of metabolites with VIP >1, t-test p value < 0...
March 31, 2017: Chemosphere
https://www.readbyqxmd.com/read/28395271/differential-circrna-expression-profiles-during-the-bmp2-induced-osteogenic-differentiation-of-mc3t3-e1-cells
#5
Dong-Yang Qian, Guang-Bin Yan, Bo Bai, Yi Chen, Shu-Jiang Zhang, Yong-Chang Yao, Hong Xia
OBJECTIVE: Recent studies have indicated that circular RNAs (circRNAs) might play important roles in various diseases. However, little is known about the functions of circRNAs in the skeletal system, and the role of circRNAs in the mechanism by which bone morphogenetic protein 2 (BMP2) promotes bone differentiation remains unknown. Here, we performed RNA-seq to analyze differential expression of circRNA during different osteoblast differentiation stages and investigated the relevant mechanisms...
April 7, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28391457/fishing-for-contaminants-identification-of-three-mechanism-specific-transcriptome-signatures-using-danio-rerio-embryos
#6
Jonas Hausen, Jens C Otte, Jessica Legradi, Lixin Yang, Uwe Strähle, Martina Fenske, Markus Hecker, Song Tang, Monika Hammers-Wirtz, Henner Hollert, Steffen H Keiter, Richard Ottermanns
In ecotoxicology, transcriptomics is an effective way to detect gene expression changes in response to environmental pollutants. Such changes can be used to identify contaminants or contaminant classes and can be applied as early warning signals for pollution. To do so, it is important to distinguish contaminant-specific transcriptomic changes from genetic alterations due to general stress. Here we present a first step in the identification of contaminant class-specific transcriptome signatures. Embryos of zebrafish (Danio rerio) were exposed to three substances (methylmercury, chlorpyrifos and Aroclor 1254, each from 24 to 48 hpf exposed) representing sediment typical contaminant classes...
April 8, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28380454/comparative-study-of-joint-bioinformatics-analysis-of-underlying-potential-of-neurimmir-mir-212-3p-mir-132-3p-being-involved-in-epilepsy-and-its-emerging-role-in-human-cancer
#7
Lu Xia, Daojiang Li, Changwei Lin, Shuchun Ou, Xiaorong Li, Songqing Pan
Considering the critical roles of miR-132/212 participated in central nervous system, many researches started to explored the contributions of miR-132/212 to epilepsy and achieve something worthwhile. Further illuminates all the genes targeted by miR-132/212 may be a valuable means for us to completely understand the working mechanism playing in epilepsy, by which it can influence diverse biological process. This study attempts to establish macrocontrol regulation system and knowledge that miR-212-3p/132-3p effected the epilepsy, for this literature search, miRbase, Vienna RNAfold webserver, Human miRNA tissue atlas, DIANA-TarBase, miRtarbase, STRING, TargetScanhuman, Cytoscape plugin ClueGO + Cluepedia+STRING, DAVID Bioinformatics Resources, Starbase, GeneCards suite and GEO database are comprehensive employed, miR-132-3p/212-3p and its target gene were found have highly expressed in brain and lots of molecular function and metabolic pathways associated with epilepsy may be intervened by it...
March 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/28377683/interinstitutional-collaboration-for-end-user-bioinformatics-training-cytoscape-as-a-case-study
#8
Marci D Brandenburg, Rolando Garcia-Milian
BACKGROUND: This case study describes the value of and need for interinstitutional collaboration to train biomedical researchers in data visualization, using Cytoscape network analysis software as an example. To provide training on Cytoscape software to Yale University biomedical researchers, a collaboration was formed between the Yale Harvey Cushing/John Hay Whitney Medical Library's (CWML's) biomedical sciences research support librarian and the University of Michigan (U-M) Taubman Health Sciences Library's bioinformationist, who has expertise in Cytoscape software...
April 2017: Journal of the Medical Library Association: JMLA
https://www.readbyqxmd.com/read/28374912/a-computational-approach-to-identify-a-potential-alternative-drug-with-its-positive-impact-towards-pmp22
#9
Ashish Kumar Agrahari, George Priya Doss C
Mutations in the peripheral myelin protein 22 (PMP22) leads to Charcot Marie Tooth type 1A (CMT1A, a subtype of CMT1) disease which is the most common inherited neuropathy of peripheral nervous system. In the present study, we used series of in silico prediction methods to screen and identify the most deleterious non-synonymous SNPs (nsSNPs) in PMP22 gene. Out of 48 nsSNPs, five nsSNPs (L16P, L19P, T23R, W28R & L147R) associated with PMP22 were predicted to be highly deleterious and destabilizing the protein...
April 4, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28368806/analysis-of-organization-of-the-interactome-using-dominating-sets-a-case-study-on-cell-cycle-interaction-networks
#10
Huiru Zheng, Chaoyang Wang, Haiying Wang
In this study, a minimum dominating set based approach was developed and implemented as a Cytoscape plugin to identify critical and redundant proteins in a protein interaction network. We focused on the investigation of the properties associated with critical proteins in the context of the analysis of interaction networks specific to cell cycle in both yeast and human. A total of 132 yeast genes and 129 human proteins have been identified as critical nodes while 950 in yeast and 980 in human have been categorized as redundant nodes...
March 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28365935/selecting-key-genes-associated-with-ovarian-cancer-based-on-differential-expression-network
#11
Xuemei Lu, Jianfang Wang, Xinfang Shan, Yun Li
PURPOSE: The purpose in this study was to select key genes related to ovarian cancer. METHODS: The gene expression profiles of E-GEOD-6008, E-GEOD-26712, E-GEOD-27651, E-GEOD-14001 were obtained from ArrayExpress database (http://www.ebi.ac.uk/arrayexpress/). Following data recruitment and preprocessing, differentially expressed genes (DEGs) were characterized using Significance Analysis of Microarrays (SAM). Then, a differential expression network (DEN) was constructed using Cytoscape 2...
January 2017: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
https://www.readbyqxmd.com/read/28356939/identification-of-genes-associated-with-tongue-cancer-in-patients-with-a-history-of-tobacco-and-or-alcohol-use
#12
Yin Zhao, Dongna Fu, Chengbi Xu, Jingpu Yang, Zonggui Wang
The present study aimed to identify genes associated with tongue cancer in patients with a history of tobacco and/or alcohol use. Microarray dataset GSE42023, including 10 tissue samples of tongue cancer from patients with a history of tobacco and/or alcohol use (habit group) and 11 tissue samples of non-habit-associated tongue cancer (non-habit group), were downloaded from the Gene Expression Omnibus database. Differentially-expressed genes (DEGs) between the habit and non-habit groups were identified using the Linear Models for Microarray Data software package...
February 2017: Oncology Letters
https://www.readbyqxmd.com/read/28349685/ptmoracle-a-cytoscape-app-for-covisualizing-and-coanalyzing-post-translational-modifications-in-protein-interaction-networks
#13
Aidan P Tay, Chi Nam Ignatius Pang, Daniel L Winter, Marc R Wilkins
Post-translational modifications of proteins (PTMs) act as key regulators of protein activity and of protein-protein interactions (PPIs). To date, it has been difficult to comprehensively explore functional links between PTMs and PPIs. To address this, we developed PTMOracle, a Cytoscape app for coanalyzing PTMs within PPI networks. PTMOracle also allows extensive data to be integrated and coanalyzed with PPI networks, allowing the role of domains, motifs, and disordered regions to be considered. For proteins of interest, or a whole proteome, PTMOracle can generate network visualizations to reveal complex PTM-associated relationships...
April 6, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28343001/comprehensive-functional-analysis-of-large-lists-of-genes-and-proteins
#14
Bernhard Mlecnik, Jérôme Galon, Gabriela Bindea
The interpretation of high dimensional datasets resulting from genomic and proteomic experiments in a timely and efficient manner is challenging. ClueGO software is a Cytoscape App that extracts representative functional biological information for large lists of genes or proteins. The functional enrichment analysis is based on the latest publicly available data from multiple annotation and ontology resources that can be automatically accessed through ClueGO. Predefined settings for the selection of the terms are provided to facilitate the analysis...
March 22, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28337225/bufei-huoxue-capsule-attenuates-pm2-5-induced-pulmonary-inflammation-in-mice
#15
Yue Jing, Hongchun Zhang, Zhe Cai, Yukun Zhao, Ye Wu, Xuan Zheng, Ying Liu, Yuying Qin, Mingjie Gu, Jin Jin
Atmospheric fine particulate matter 2.5 (PM 2.5) may carry many toxic substances on its surface and this may pose a public health threat. Epidemiological research indicates that cumulative ambient PM2.5 is correlated to morbidity and mortality due to pulmonary and cardiovascular diseases and cancer. Mitigating the toxic effects of PM2.5 is therefore highly desired. Bufei Huoxue (BFHX) capsules have been used in China to treat pulmonary heart disease (cor pulmonale). Thus, we assessed the effects of BFHX capsules on PM2...
2017: Evidence-based Complementary and Alternative Medicine: ECAM
https://www.readbyqxmd.com/read/28336332/how-to-use-and-integrate-bioinformatics-tools-to-compare-proteomic-data-from-distinct-conditions-a-tutorial-using-the-pathological-similarities-between-aortic-valve-stenosis-and-coronary-artery-disease-as-a-case-study
#16
Fábio Trindade, Rita Ferreira, Beatriz Magalhães, Adelino Leite-Moreira, Inês Falcão-Pires, Rui Vitorino
Nowadays we are surrounded by a plethora of bioinformatics tools, powerful enough to deal with the large amounts of data arising from proteomic studies, but whose application is sometimes hard to find. Therefore, we used a specific clinical problem - to discriminate pathophysiology and potential biomarkers between two similar cardiovascular diseases, aortic valve stenosis (AVS) and coronary artery disease (CAD) - to make a step-by-step guide through four bioinformatics tools: STRING, DisGeNET, Cytoscape and ClueGO...
March 20, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28331560/introducing-crucial-protein-panel-of-gastric-adenocarcinoma-disease
#17
Mostafa Rezaei-Tavirani, Majid Rezaei-Tavirani, Vahid Mansouri, Seyed Mohammad Mahdavi, Reza Valizadeh, Mohammad Rostami-Nejad, Mohammad Reza Zali
AIM: Since interactome analysis of diseases can provide candidate biomarker panel related to the diseases, in this research, protein-protein interaction (PPI) network analysis is used to introduce the involved crucial proteins in Gastric adenocarcinoma (GA). BACKGROUND: Gastric adenocarcinoma (GA) is the most common type of stomach cancer. There is no efficient diagnostic molecular method for GA. METHOD: Applying Cytoscape software 3.4.0 and String Database, the PPI network was constructed for 200 genes...
2017: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28318762/gene-expression-profiling-reveals-genes-and-transcription-factors-associated-with-dilated-and-ischemic-cardiomyopathies
#18
Aiqing Qiao, Zhenying Zhao, Hui Zhang, Zhenyu Sun, Xiao Cui
AIMS: Dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM) can cause heart failure, and this study aims to identify genes and transcription factors (TFs) associated with DCM and ICM. METHODS: Gene expression dataset GSE42955 was generated from GEO database, and it contained 12 DCM, 12 ICM, and 5 control samples. Differentially expressed genes (DEGs) were identified between DCM (or ICM) and controls. Gene functions were investigated, and their associations were analyzed using Enrichmentmap plugin in Cytoscape...
December 29, 2016: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28302149/identification-and-interaction-analysis-of-key-genes-and-micrornas-in-hepatocellular-carcinoma-by-bioinformatics-analysis
#19
Tong Mou, Di Zhu, Xufu Wei, Tingting Li, Daofeng Zheng, Junliang Pu, Zhen Guo, Zhongjun Wu
BACKGROUND: Hepatocellular carcinoma (HCC) is the most common liver malignancy worldwide. However, present studies of its multiple gene interaction and cellular pathways still could not explain the initiation and development of HCC perfectly. To find the key genes and miRNAs as well as their potential molecular mechanisms in HCC, microarray data GSE22058, GSE25097, and GSE57958 were analyzed. METHODS: The microarray datasets GSE22058, GSE25097, and GSE57958, including mRNA and miRNA profiles, were downloaded from the GEO database and were analyzed using GEO2R...
March 16, 2017: World Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28289583/microarray-technology-reveals-potentially-novel-genes-and-pathways-involved-in-non-functioning-pituitary-adenomas
#20
X Qiao, H Wang, X Wang, B Zhao, J Liu
Microarray data of non-functioning pituitary adenomas (NFPAs) were analyzed to disclose novel genes and pathways involved in NFPA tumorigenesis. Raw microarray data were downloaded from Gene Expression Omnibus. Data pre-treatment and differential analysis were conducted using packages in R. Functional and pathway enrichment analyses were performed using package GOs-tats. A protein-protein interaction (PPI) network was constructed using server STRING and Cytoscape. Known genes involved in pituitary adenomas (PAs), were obtained from the Comparative Toxicogenomics Database...
December 1, 2016: Balkan Journal of Medical Genetics: BJMG
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