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https://www.readbyqxmd.com/read/28343001/comprehensive-functional-analysis-of-large-lists-of-genes-and-proteins
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
https://www.readbyqxmd.com/read/28281877/comprehensive-analysis-of-interaction-networks-of-telomerase-reverse-transcriptase-with-multiple-bioinformatic-approach-deep-mining-the-potential-functions-of-telomere-and-telomerase
#8
Chunyu Hou, Fei Wang, Xuewen Liu, Guangming Chang, Feng Wang, Xin Geng
Telomerase reverse transcriptase (TERT)is the protein component of telomerase complex. Evidence has accumulated showing that the non-telomeric functions of TERT are independent of telomere elongation. However, the mechanisms governing the interaction between TERT and its target genes are not revealed clear. The biological functions of TERT are not fully elucidated and have thus far been underestimated. To further explore these functions, we investigated TERT interaction networks using multiple bioinformatic databases, including BioGRID, STRING, DAVID, GeneCards, GeneMANIA, PANTHER, miRWalk, mirTarBase, miRNet, miRDB and TargetScan...
March 6, 2017: Rejuvenation Research
https://www.readbyqxmd.com/read/28274758/gfd-net-a-novel-semantic-similarity-methodology-for-the-analysis-of-gene-networks
#9
Juan J Díaz-Montaña, Norberto Díaz-Díaz, Francisco Gómez-Vela
Since the popularization of biological network inference methods, it has become crucial to create methods to validate the resulting models. Here we present GFD-Net, the first methodology that applies the concept of semantic similarity to gene network analysis. GFD-Net combines the concept of semantic similarity with the use of gene network topology to analyze the functional dissimilarity of gene networks based on Gene Ontology (GO). The main innovation of GFD-Net lies in the way that semantic similarity is used to analyze gene networks taking into account the network topology...
March 5, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28268236/design-network-analysis-and-in-silico-modeling-of-biologically-significant-4-substituted-benzyl-2-amino-6-hydroxypyrimidine-5-carboxamide-nanoparticles
#10
Theivendren Panneerselvam, Vellaichamy Sivakumar, Subramanian Arumugam, Kunjiappan Selvaraj, Murugan Indhumathy
The synthesized 4-(4-hydroxy benzyl)-2-amino-6-hydroxy pyrimidine-5-carboxamide was chosen to perform in silico modeling with identified drug target AGT, TNF, F2 and BCL2L1. The identified human proteins are vital in the pain management and also an important target for the study of wound healing activity. The enzymes were identified by using BioGRID, string database and network analysis through Cytoscape software. The wound healing activity was evaluated by excision wound model. The observed results revealed that, the pyrimidine nanoparticles showed significant wound healing activity compared to standard and synthesized compound...
March 7, 2017: Drug Research
https://www.readbyqxmd.com/read/28260111/molecular-characterization-of-metastatic-osteosarcoma-differentially-expressed-genes-transcription-factors-and-micrornas
#11
Lisong Heng, Zhen Jia, Jie Bai, Kun Zhang, Yangjun Zhu, Jianbing Ma, Jun Zhang, Honghao Duan
The present study aimed to understand the molecular mechanisms underlying osteosarcoma metastasis. Microarray dataset GSE49003 was downloaded from the Gene Expression Omnibus database and used for analysis. Raw expression data were preprocessed using the preprocessCore, impute and aggregate packages in R. Differentially expressed genes (DEGs) between metastatic and non‑metastatic osteosarcoma cell lines were screened using the limma package following exclusion of DEGs with a higher significance in intra‑groups compared with inter‑groups using the genefilter package...
March 3, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28259920/identification-of-the-key-genes-implicated-in-the-transformation-of-olp-to-oscc-using-rna-sequencing
#12
Qiaozhen Yang, Bin Guo, Hongying Sun, Jie Zhang, Shangfeng Liu, Saiyin Hexige, Xuedi Yu, Xiaxia Wang
Oral lichen planus (OLP) is a chronic inflammatory disease that may transform to oral squamous cell carcinoma (OSCC), while its carcinogenesis mechanisms are not entirely clear. This study was designed to identify the important genes involved in the malignant transformation of OLP to OSCC. After RNA-sequencing, the differently expressed genes (DEGs) in OLP vs. normal and OSCC vs. normal groups, respectively, were identified by limma package in R language, and then clustering analysis were conducted by Pheatmap package in R language...
March 2, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28238728/an-integrative-transcriptomic-analysis-reveals-bisphenol-a-exposure-induced-dysregulation-of-microrna-expression-in-human-endometrial-cells
#13
Wei-Chun Chou, Pei-Hsuan Lee, Yan-Yan Tan, Ho-Chen Lin, Chung-Wei Yang, Kuan-Hsueh Chen, Chun-Yu Chuang
Bisphenol A (BPA) are commonly used in the manufacture of polycarbonate plastics. Higher BPA exposure levels have been found in patients with endometrial hyperplasia that is one of risk factors of endometrial cancer (EC). Aberrant microRNAs (miRNAs) regulation has been observed in the development of cancer. Thus, this study investigated whether BPA exposure can disrupt miRNA regulation and its gene expression regarding to EC carcinogenic progress. Microarray experiments of miRNA and mRNA were performed in human endometrial cancer RL95-2 cells with treatment of low-to-moderate (10, 10(3) and 10(5)nM) BPA to explore the aberrant genes corresponding to human EC progression...
February 24, 2017: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/28237528/identification-of-potential-therapeutic-target-genes-key-mirnas-and-mechanisms-in-oral-lichen-planus-by-bioinformatics-analysis
#14
Cuihua Gong, Shangtong Sun, Bing Liu, Jing Wang, Xiaodong Chen
The study aimed to identify the potential target genes and key miRNAs as well as to explore the underlying mechanisms in the pathogenesis of oral lichen planus (OLP) by bioinformatics analysis. The microarray data of GSE38617 were downloaded from Gene Expression Omnibus (GEO) database. A total of 7 OLP and 7 normal samples were used to identify the differentially expressed genes (DEGs) and miRNAs. The DEGs were then performed functional enrichment analyses. Furthermore, DEG-miRNA network and miRNA-function network were constructed by Cytoscape software...
February 12, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28224024/topological-and-functional-analysis-of-nonalcoholic-steatohepatitis-through-protein-interaction-mapping
#15
Hamid Asadzadeh-Aghdaee, Vahid Mansouri, Ali Asghar Peyvandi, Fathollah Moztarzadeh, Farshad Okhovatian, Farhad Lahmi, Reza Vafaee, Mohammad Reza Zali
AIM: The corresponding proteins are important for network mapping since the interaction analysis can provide a new interpretation about disease underlying mechanisms as the aim of this study. BACKGROUD: Nonalcoholic steatohepatitis (NASH) is one of the main causes of liver disease in the world. It has been known with many susceptible proteins that play essential role in its pathogenesis. METHODS: In this paper, protein-protein interaction (PPI) network analysis of fatty liver disease retrieved from STRING db by the application of Cytoscape Software...
December 2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28224023/evaluation-of-liver-cirrhosis-and-hepatocellular-carcinoma-using-protein-protein-interaction-networks
#16
Mohammad Javad Ehsani Ardakani, Akram Safaei, Afsaneh Arefi Oskouie, Hesam Haghparast, Mehrdad Haghazali, Hamid Mohaghegh Shalmani, Hassan Peyvandi, Nosratollah Naderi, Mohammad Reza Zali
AIM: In the current study, we analysised only the articles that investigate serum proteome profile of cirrhosis patients or HCC patients versus healthy controls. BACKGROUND: Increased understanding of cancer biology has enabled identification of molecular events that lead to the discovery of numerous potential biomarkers in diseases. Protein-protein interaction networks is one of aspect that could elevate the understanding level of molecular events and protein connections that lead to the identification of genes and proteins associated with diseases...
December 2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28224022/introduction-of-inflammatory-bowel-disease-biomarkers-panel-using-protein-protein-interaction-ppi-network-analysis
#17
Hamid Asadzadeh-Aghdaee, Shabnam Shahrokh, Mohsen Norouzinia, Mostafa Hosseini, Aliasghar Keramatinia, Mostafa Jamalan, Bijan Naghibzadeh, Ali Sadeghi, Somayeh Jahani Sherafat, Mohammad Reza Zali
AIM: In the present study, a protein-protein interaction network construction is conducted for IBD. BACKGROUND: Inflammatory bowel diseases as serious chronic gastrointestinal disorders attracted many molecular investigations. Diverse molecular information is present for IBD. However, these molecular findings are not highlighted based on interactome analysis. On the other hand, PPI network analysis is a powerful method for study of molecular interactions in the protein level that provide useful information for highlighting the desired key proteins...
December 2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28222782/identification-of-mirna-mrna-crosstalk-in-cd4-t-cells-during-hiv-1-infection-by-integrating-transcriptome-analyses
#18
Qibin Liao, Jin Wang, Zenglin Pei, Jianqing Xu, Xiaoyan Zhang
BACKGROUND: HIV-1-infected long-term nonprogressors (LTNPs) are characterized by infection with HIV-1 more than 7-10 years, but keeping high CD4(+) T cell counts and low viral load in the absence of antiretroviral treatment, while loss of CD4(+) T cells and high viral load were observed in the most of HIV-1-infected individuals with chronic progressors (CPs) However, the mechanisms of different clinical outcomes in HIV-1 infection needs to be further resolved. METHODS: To identify microRNAs (miRNAs) and their target genes related to distinct clinical outcomes in HIV-1 infection, we performed the integrative transcriptome analyses in two series GSE24022 and GSE6740 by GEO2R, R, TargetScan, miRDB, and Cytoscape softwares...
February 21, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28199418/analysis-of-long-noncoding-rna-and-mrna-using-rna-sequencing-during-the-differentiation-of-intramuscular-preadipocytes-in-chicken
#19
Tao Zhang, Xiangqian Zhang, Kunpeng Han, Genxi Zhang, Jinyu Wang, Kaizhou Xie, Qian Xue, Xiaomei Fan
Long noncoding RNAs (lncRNAs) regulate metabolic tissue development and function, including adipogenesis. However, little is known about the function and profile of lncRNAs in intramuscular preadipocyte differentiation in chicken. Here, we identified lncRNAs in chicken intramuscular preadipocytes at different differentiation stages using RNA sequencing. A total of 1,311,382,604 clean reads and 25,435 lncRNAs were obtained from 12 samples. In total, 7,433 differentially expressed genes (4,698 lncRNAs and 2,735 mRNAs) were identified by pairwise comparison...
2017: PloS One
https://www.readbyqxmd.com/read/28191039/elevated-transcriptional-levels-of-aldolase-a-aldoa-associates-with-cell-cycle-related-genes-in-patients-with-nsclc-and-several-solid-tumors
#20
Fan Zhang, Jie-Diao Lin, Xiao-Yu Zuo, Yi-Xuan Zhuang, Chao-Qun Hong, Guo-Jun Zhang, Xiao-Jiang Cui, Yu-Kun Cui
BACKGROUND: Aldolase A (ALDOA) is one of the glycolytic enzymes primarily found in the developing embryo and adult muscle. Recently, a new role of ALDOA in several cancers has been proposed. However, the underlying mechanism remains obscure and inconsistent. In this study, we tried to investigate ALDOA-associated (AA) genes using available microarray datasets to help elucidating the role of ALDOA in cancer. RESULTS: In the dataset of patients with non-small-cell lung cancer (NSCLC, E-GEOD-19188), 3448 differentially expressed genes (DEGs) including ALDOA were identified, in which 710 AA genes were found to be positively associated with ALDOA...
2017: BioData Mining
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