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https://www.readbyqxmd.com/read/29793188/prioritization-of-reproductive-toxicants-in-unconventional-oil-and-gas-operations-using-a-multi-country-regulatory-data-driven-hazard-assessment
#1
Salmaan H Inayat-Hussain, Masao Fukumura, A Muiz Aziz, Chai Meng Jin, Low Wei Jin, Rolando Garcia-Milian, Vasilis Vasiliou, Nicole C Deziel
BACKGROUND: Recent trends have witnessed the global growth of unconventional oil and gas (UOG) production. Epidemiologic studies have suggested associations between proximity to UOG operations with increased adverse birth outcomes and cancer, though specific potential etiologic agents have not yet been identified. To perform effective risk assessment of chemicals used in UOG production, the first step of hazard identification followed by prioritization specifically for reproductive toxicity, carcinogenicity and mutagenicity is crucial in an evidence-based risk assessment approach...
May 21, 2018: Environment International
https://www.readbyqxmd.com/read/29783871/eclerize-a-customized-force-directed-graph-drawing-algorithm-for-biological-graphs-with-ec-attributes
#2
Hasan Fehmi Danaci, Rengul Cetin-Atalay, Volkan Atalay
Visualizing large-scale data produced by the high throughput experiments as a biological graph leads to better understanding and analysis. This study describes a customized force-directed layout algorithm, EClerize, for biological graphs that represent pathways in which the nodes are associated with Enzyme Commission (EC) attributes. The nodes with the same EC class numbers are treated as members of the same cluster. Positions of nodes are then determined based on both the biological similarity and the connection structure...
March 26, 2018: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/29782863/analysis-of-mulberry-leaf-components-in-the-treatment-of-diabetes-using-network-pharmacology
#3
Qi Ge, Liang Chen, Min Tang, Shu Zhang, Lu Gao, Shangshang Ma, Lanlan Liu, Ming Kong, Qin Yao, Keping Chen, Fan Feng
Mulberry leaves are one of the most commonly used medicinal and herbaceous traditional Chinese medicines that are currently considered for the treatment of diabetes mellitus and its complications. The alkaloids, flavonoids, and polysaccharides in mulberry leaves impart regulatory effects on blood sugar levels. To identify the hypoglycemia-related active components in mulberry leaves and their targets, the present study conducted gas chromatography-mass spectrometer (GC/MS), which identified 202 components of mulberry leaf, of which 22 components may have significant curative effects on diabetes mellitus and its complications and chronic inflammation...
May 18, 2018: European Journal of Pharmacology
https://www.readbyqxmd.com/read/29769539/integrated-analysis-of-hepatic-mrna-and-mirna-profiles-identified-molecular-networks-and-potential-biomarkers-of-nafld
#4
Mingzhe Zhu, Qianlei Wang, Wenjun Zhou, Tao Liu, Lili Yang, Peiyong Zheng, Li Zhang, Guang Ji
To enhance our understanding of molecular mechanisms and mine novel biomarkers of non-alcoholic fatty liver disease (NAFLD), RNA sequencing was performed to gain hepatic expression profiles of mRNAs and miRNAs in NAFLD and normal rats. Using DESeq with thresholds of a two-fold change and a false discovery rate (FDR) less than 0.05, 336 mRNAs and 21 miRNAs were identified as differentially expressed. Among those, 17 miRNAs (e.g., miR-144-3p, miR-99a-3p, miR-200b-3p, miR-200b-5p, miR-200c-3p, etc.) might serve as novel biomarkers of NAFLD...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29760609/identification-of-potential-crucial-genes-and-construction-of-microrna-mrna-negative-regulatory-networks-in-osteosarcoma
#5
Yue Pan, Lingyun Lu, Junquan Chen, Yong Zhong, Zhehao Dai
Background: This study aimed to identify potential crucial genes and construction of microRNA-mRNA negative regulatory networks in osteosarcoma by comprehensive bioinformatics analysis. Methods: Data of gene expression profiles (GSE28424) and miRNA expression profiles (GSE28423) were downloaded from GEO database. The differentially expressed genes (DEGs) and miRNAs (DEMIs) were obtained by R Bioconductor packages. Functional and enrichment analyses of selected genes were performed using DAVID database...
2018: Hereditas
https://www.readbyqxmd.com/read/29755572/introducing-potential-key-proteins-and-pathways-in-human-laryngeal-cancer-a-system-biology-approach
#6
Hassan Peyvandi, Ali Asghar Peyvandi, Akram Safaei, Mona Zamanian Azodi, Mostafa Rezaei-Tavirani
The most common malignant neoplasm of the head and neck region is laryngeal cancer which presents a significant international health problem. The present study aims to screen potential proteins related to laryngeal cancer by network analysis to further understanding disease pathogenesis and biomarker discovery. Differentially expressed proteins were extracted from literatures of laryngeal cancer that compare proteome profiling of patient›s tissue with healthy controls. The PPI network analyzed for up and down regulated proteins with Cytoscape Version 3...
2018: Iranian Journal of Pharmaceutical Research: IJPR
https://www.readbyqxmd.com/read/29753646/network-visualization-and-analysis-of-spatially-aware-gene-expression-data-with-insitunet
#7
John Salamon, Xiaoyan Qian, Mats Nilsson, David John Lynn
In situ sequencing methods generate spatially resolved RNA localization and expression data at an almost single-cell resolution. Few methods, however, currently exist to analyze and visualize the complex data that is produced, which can encode the localization and expression of a million or more individual transcripts in a tissue section. Here, we present InsituNet, an application that converts in situ sequencing data into interactive network-based visualizations, where each unique transcript is a node in the network and edges represent the spatial co-expression relationships between transcripts...
April 27, 2018: Cell Systems
https://www.readbyqxmd.com/read/29749511/bioinformatics-analysis-of-microarray-data-to-reveal-the-pathogenesis-of-brain-ischemia
#8
Jiaxuan He, Ya Gao, Gang Wu, Xiaoming Lei, Yong Zhang, Weikang Pan, Hui Yu
Brain ischemia leads to energy depletion, mitochondrial dysfunction and neuronal cell death. The present study was designed to identify key genes and pathways associated with brain ischemia. The gene expression profile GSE52001, including 3 normal brain samples and 3 cerebral ischemia samples, was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified using the limma package. Then functional and pathway enrichment analyses were performed by the MATHT tool...
May 9, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29745857/identification-of-novel-drug-targets-for-diamond-blackfan-anemia-based-on-rps19-gene-mutation-using-protein-protein-interaction-network
#9
Abbas Khan, Arif Ali, Muhammad Junaid, Chang Liu, Aman Chandra Kaushik, William C S Cho, Dong-Qing Wei
BACKGROUND: Diamond-Blackfan anemia (DBA) is a congenital erythroid aplasia that usually presents in infancy. In order to explore the molecular mechanisms of wild and mutated samples from DBA patients were exposed to bioinformatics investigation. Biological network of differentially expressed genes was constructed. This study aimed to identify novel therapeutic signatures in DBA and uncovered their mechanisms. The gene expression dataset of GSE14335 was used, which consists of 6 normal and 4 diseased cases...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29744300/gene-expression-profiles-and-pathway-enrichment-analysis-of-human-osteosarcoma-cells-exposed-to-sorafenib
#10
Zhehao Dai, Haoyu Tang, Yue Pan, Junquan Chen, Yongping Li, Jun Zhu
Sorafenib is an inhibitor of a variety of tyrosine kinase receptors used to treat various cancers including hepatocellular, renal cell and thyroid carcinoma. It has been shown to change various targets associated with osteosarcoma, but the detailed mechanism remains unclear. In order to identify key genes, enriched pathways and important modules during the exposure of human osteosarcoma cells to sorafenib, data for gene expression profiles (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53155) were downloaded from the GEO database...
May 2018: FEBS Open Bio
https://www.readbyqxmd.com/read/29741786/reconstruction-and-analysis-of-the-aberrant-lncrna-mirna-mrna-network-based-on-competitive-endogenous-rna-in-cesc
#11
Jukun Song, Aizhu Ye, Enli Jiang, Xinhai Yin, Zhu Chen, Guohui Bai, Yu Zhou, Jianguo Liu
A growing body of studies has demonstrated that long non-coding RNA (lncRNA) are regarded as the primary section of the ceRNA network. This is thought to be the case owing to its regulation of protein-coding gene expression by functioning as miRNA sponges. However, functional roles and regulatory mechanisms of lncRNA-mediated ceRNA in cervical squamous cell carcinoma (CESC), as well as their use for potential prediction of CESC prognosis, remains unknown. The aberrant expression profiles of mRNA, lncRNA, and miRNA of 306 cervical squamous cancer tissues and three adjacent cervical tissues were obtained from the TCGA database...
May 9, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29739919/identification-of-core-genes-and-key-pathways-via-integrated-analysis-of-gene-expression-and-dna-methylation-profiles-in-bladder-cancer
#12
Yongzhen Zhang, Liang Fang, Yuanwei Zang, Zhonghua Xu
BACKGROUND Bladder cancer (BC) is the most common urological malignant tumor. In BC, aberrant DNA methylation is believed to be associated with carcinogenesis. Therefore, the identification of key genes and pathways could help determine the potential molecular mechanisms of BC development. MATERIAL AND METHODS Microarray data on gene expression and gene methylation were downloaded from the Gene Expression Omnibus (GEO) database. Abnormal methylated/expressed genes were analyzed by GEO2R and statistical software R...
May 9, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/29739047/identification-of-differentially-expressed-micrornas-involved-in-the-pathogenesis-of-colorectal-cancer
#13
Haiyi Feng, Ming Xu, Yunpeng Zhang, Bo Han, Jue Wang, Peng Sun
BACKGROUND: The ability to diagnose or treat colorectal cancer (CRC) at an early stage could lead to the improved survival. The purpose of this study was to identify differentially expressed microRNAs (miRNAs) involved in the pathogenesis of CRC. These miRNAs may serve as the biomarkers or potential therapeutic targets for CRC early detection or treatment. METHODS: The GSE39814 miRNA expression profile dataset was downloaded from the NCBI GEO database. MiRNAs were extracted from the exosome fractions of three normal fetal colon-derived cells and HCT116 and SW480 cell lines...
May 1, 2018: Clinical Laboratory
https://www.readbyqxmd.com/read/29728040/-exploration-on-mechanism-of-anti-influenza-virus-activity-of-genus-paeonia-based-on-network-pharmacology
#14
Ya-Qi Cai, Ya-Ting Bao, Hong-Jin Wang, Xiao-Dong Ren, Lin-Fang Huang, Jie He, Tian-Tian Liu, Rui Zeng
This paper aimed to investigate the anti-influenza virus activity of the genus Paeonia, screen potential anti-influenza virus compounds and predict targets of anti-influenza virus to explore the mechanism of anti-influenza virus activity. First of all, a total of 301 compounds of the genus Paeonia were summarized from the literatures in recent ten years. The candidate active ingredients from the genus Paeonia were identified by database such as PubChem and Chemical Book. The ligands were constructed by ChemDraw, Avogadro and Discovery Studio Visualizer...
April 2018: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29725417/identification-and-functional-analysis-of-a-core-gene-module-associated-with-hepatitis-c-virus-induced-human-hepatocellular-carcinoma-progression
#15
Gaobo Bai, Wenling Zheng, Wenli Ma
Hepatitis C virus (HCV)-induced human hepatocellular carcinoma (HCC) progression may be due to a complex multi-step processes. The developmental mechanism of these processes is worth investigating for the prevention, diagnosis and therapy of HCC. The aim of the present study was to investigate the molecular mechanism underlying the progression of HCV-induced hepatocarcinogenesis. First, the dynamic gene module, consisting of key genes associated with progression between the normal stage and HCC, was identified using the Weighted Gene Co-expression Network Analysis tool from R language...
May 2018: Oncology Letters
https://www.readbyqxmd.com/read/29706616/identification-of-potentially-functional-circrna-mirna-mrna-regulatory-network-in-hepatocellular-carcinoma-by-integrated-microarray-analysis
#16
Xiaoming Lin, Yuhan Chen
BACKGROUND Hepatocellular carcinoma (HCC) is the most common malignancy of the liver and recent studies have revealed that circular RNA (circRNA) plays an important role in the pathogenesis of HCC. Some circRNAs may act as a microRNA (miRNA) sponge to affect miRNA activities in the regulation of messenger RNA (mRNA) expression. However, the circRNA-miRNA-mRNA network in HCC remains largely unknown. MATERIAL AND METHODS The circRNA expression profiles (GSE94508 and GSE97332), miRNA and mRNA expression profile (GSE22058) were downloaded from Gene Expression Omnibus microarray data and then a circRNA-miRNA-mRNA regulatory network in HCC was constructed...
April 30, 2018: Medical Science Monitor Basic Research
https://www.readbyqxmd.com/read/29705125/systematically-analyses-of-the-common-dysregulated-networks-to-understand-the-common-pathologies-between-t2d-and-atherosclerosis
#17
Zijing Lin, Fan Yang, Lijie Sun, Jie Gao, Yan Cao, Hui Qiu, Xiaorong Zhan
BACKGROUND: Diabetic macroangiopathy, atherosclerosis secondary to diabetes mellitus, causes cerebro-cardiovascular diseases (CVD), which increase the risk of death in patients with DM and significantly reduce their quality of life. Therefore, mechanisms underlying the common shared pathologies between type 2 diabetes (T2D) and atherosclerosis are key to prevention and treatment of diabetic macroangiopathy. However, the common shared pathological links between T2D and atherosclerosis are not fully understood...
April 26, 2018: Gene
https://www.readbyqxmd.com/read/29703138/transcriptional-profiling-of-human-bronchial-epithelial-cell-beas-2b-exposed-to-diesel-and-biomass-ultrafine-particles
#18
Andrea Grilli, Rossella Bengalli, Eleonora Longhin, Laura Capasso, Maria Carla Proverbio, Mattia Forcato, Silvio Bicciato, Maurizio Gualtieri, Cristina Battaglia, Marina Camatini
BACKGROUND: Emissions from diesel vehicles and biomass burning are the principal sources of primary ultrafine particles (UFP). The exposure to UFP has been associated to cardiovascular and pulmonary diseases, including lung cancer. Although many aspects of the toxicology of ambient particulate matter (PM) have been unraveled, the molecular mechanisms activated in human cells by the exposure to UFP are still poorly understood. Here, we present an RNA-seq time-course experiment (five time point after single dose exposure) used to investigate the differential and temporal changes induced in the gene expression of human bronchial epithelial cells (BEAS-2B) by the exposure to UFP generated from diesel and biomass combustion...
April 27, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29693365/identification-of-key-candidate-genes-and-pathways-in-endometrial-cancer-by-integrated-bioinformatical-analysis
#19
Lihong Liu, Fangxu Chen, Aihui Xiu, Bo Du, Hao Ai, Wei Xie
Endometrial Cancer is the most common female genital tract malignancy, its pathogenesis is complex, not yet fully described. To identify key genes of Endometrial Cancer we downloaded the gene chip GSE17025 from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified through the GEO2R analysis tool. Functional and pathway enrichment analysis were performed for DEGs using DAVID database. The network of protein–protein-interaction (PPI) was established by STRING website and visualized by Cytoscape...
April 25, 2018: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/29693274/combining-multi-dimensional-data-to-identify-a-key-signature-gene-and-mirna-of-cisplatin-resistant-gastric-cancer
#20
Danyang Zhou, Xing Li, Hengyu Zhao, Banghao Sun, Anqi Liu, Xue Han, Zhongqi Cui, Lijie Yuan
Gastric cancer (GC) is one of the most lethal malignant tumors; the resistance of this type of tumor is the main source of GC treatment failure. In this study, we used bioinformatics analysis to verify differences in resistant GCs and identify an effective method for reversing drug resistance in GC. Microarray data [gene and microRNA (miRNA)] were analyzed using GEO2R software, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were applied to further enrich the genetic data...
April 25, 2018: Journal of Cellular Biochemistry
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