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https://www.readbyqxmd.com/read/28623007/gene-networks-in-neurodegenerative-disorders
#1
REVIEW
Daniela Recabarren, Marcelo Alarcón
Three neurodegenerative diseases [Amyotrophic Lateral Sclerosis (ALS), Parkinson's disease (PD) and Alzheimer's disease (AD)] have many characteristics like pathological mechanisms and genes. In this sense some researchers postulate that these diseases share the same alterations and that one alteration in a specific protein triggers one of these diseases. Analyses of gene expression may shed more light on how to discover pathways, pathologic mechanisms associated with the disease, biomarkers and potential therapeutic targets...
June 13, 2017: Life Sciences
https://www.readbyqxmd.com/read/28619054/hgpec-a-cytoscape-app-for-prediction-of-novel-disease-gene-and-disease-disease-associations-and-evidence-collection-based-on-a-random-walk-on-heterogeneous-network
#2
Duc-Hau Le, Van-Huy Pham
BACKGROUND: Finding gene-disease and disease-disease associations play important roles in the biomedical area and many prioritization methods have been proposed for this goal. Among them, approaches based on a heterogeneous network of genes and diseases are considered state-of-the-art ones, which achieve high prediction performance and can be used for diseases with/without known molecular basis. RESULTS: Here, we developed a Cytoscape app, namely HGPEC, based on a random walk with restart algorithm on a heterogeneous network of genes and diseases...
June 15, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28603669/combining-multi-dimensional-data-to-identify-key-genes-and-pathways-in-gastric-cancer
#3
Wu Ren, Wei Li, Daguang Wang, Shuofeng Hu, Jian Suo, Xiaomin Ying
Gastric cancer is an aggressive cancer that is often diagnosed late. Early detection and treatment require a better understanding of the molecular pathology of the disease. The present study combined data on gene expression and regulatory levels (microRNA, methylation, copy number) with the aim of identifying key genes and pathways for gastric cancer. Data used in this study was retrieved from The Cancer Genomic Atlas. Differential analyses between gastric cancer and normal tissues were carried out using Limma...
2017: PeerJ
https://www.readbyqxmd.com/read/28599476/identification-of-gene-markers-associated-with-metastasis-in-clear-cell-renal-cell-carcinoma
#4
Hailing Yang, Pengfei Huo, Guozhang Hu, Bo Wei, Dalian Kong, Hongjun Li
The present study aimed to screen potential target genes for the early diagnosis and treatment of early metastatic clear cell renal cell carcinoma (ccRCC) using the microarray data of early metastatic and non-metastatic ccRCC samples. The DNA microarray dataset GSE47352 was downloaded from Gene Expression Omnibus and included 4 early metastatic and 5 non-metastatic ccRCC samples. Differentially expressed genes (DEGs) were screened using the limma package. Then, pheatmap package was used to conduct two-way clustering for the DEGs...
June 2017: Oncology Letters
https://www.readbyqxmd.com/read/28598087/-bioinformatic-analysis-of-differentially-expressed-genes-involved-in-the-post-hypoxic-ischemic-brain-damage-of-newborn-rats
#5
Jing Shi, Jun Tang, De-Zhi Mu
OBJECTIVES: To analyze the differentially expressed genes (DEGs) in cerebral cortices of rats which were seven weeks after neonatal hypoxic ischemic brain damage (HIBD) and elucidate the biological significance of the DEGs. METHODS: The gene expression profile of GSE37777, including 4 HI samples subjected to HIBD and 4 normal controls, was downloaded from the Gene Expression Omnibus database (GEO). DEGs were screened using the R package in HIBD groups compared with normal controls...
September 2016: Sichuan da Xue Xue Bao. Yi Xue Ban, Journal of Sichuan University. Medical Science Edition
https://www.readbyqxmd.com/read/28594854/identification-of-key-micrornas-and-genes-in-preeclampsia-by-bioinformatics-analysis
#6
Shouling Luo, Nannan Cao, Yao Tang, Weirong Gu
Preeclampsia is a leading cause of perinatal maternal-foetal mortality and morbidity. The aim of this study is to identify the key microRNAs and genes in preeclampsia and uncover their potential functions. We downloaded the miRNA expression profile of GSE84260 and the gene expression profile of GSE73374 from the Gene Expression Omnibus database. Differentially expressed miRNAs and genes were identified and compared to miRNA-target information from MiRWalk 2.0, and a total of 65 differentially expressed miRNAs (DEMIs), including 32 up-regulated miRNAs and 33 down-regulated miRNAs, and 91 differentially expressed genes (DEGs), including 83 up-regulated genes and 8 down-regulated genes, were identified...
2017: PloS One
https://www.readbyqxmd.com/read/28588707/identification-of-potential-target-genes-associated-with-the-effect-of-propranolol-on-angiosarcoma-via-microarray-analysis
#7
Shiyong Zhou, Pengfei Liu, Wenhua Jiang, Huilai Zhang
The purpose of the present study was to explore the effect of propranolol on angiosarcoma, and the potential target genes involved in the processes of proliferation and differentiation of angiosarcoma tumor cells. The mRNA expression profile (GSE42534) was downloaded from the Gene Expressed Omnibus database, including three samples without propranolol treatment (control), three samples with propranolol treatment for 4 h and three samples with propranolol treatment for 24 h. The differentially expressed genes (DEGs) in angiosarcoma tumor cells with or without propranolol treatment were obtained via the limma package of R and designated DEGs-4 h and DEGs-24 h...
June 2017: Oncology Letters
https://www.readbyqxmd.com/read/28586059/identification-of-critical-genes-in-nucleus-pulposus-cells-isolated-from-degenerated-intervertebral-discs-using-bioinformatics-analysis
#8
Zhuangchen Zhu, Guang Chen, Wei Jiao, Defeng Wang, Yan Cao, Qingfu Zhang, Junqin Wang
Intervertebral disc (IVD) degeneration is a pathological process, which may lead to lower back pain. The present study aimed to investigate the pathogenesis of IVD degeneration. GSE42611 was downloaded from Gene Expression Omnibus, including 4 nucleus pulposus samples isolated from degenerated IVDs and 4 nucleus pulposus samples separated from normal IVDs. The differentially expressed genes (DEGs) between the degenerated and normal samples were screened using the limma package in R. Functional and pathway enrichment analyses were conducted separately for the upregulated and downregulated genes, using Database for Annotation, Visualization and Integrated Discovery software...
July 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28580409/data-from-proteome-analysis-of-lasiodiplodia-theobromae-botryosphaeriaceae
#9
Carla C Uranga, Majid Ghassemian, Rufina Hernández-Martínez
Trunk disease fungi are a global problem affecting many economically important fruiting trees. The Botryosphaeriaceae are a family of trunk disease fungi that require detailed biochemical characterization in order to gain insight into their pathogenicity. The application of a modified Folch extraction to protein extraction from the Botryosphaeriaceae Lasiodiplodia theobromae generated an unprecedented data set of protein identifications from fragmentation analysis and de novo peptide sequencing of its proteome...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28574823/integrated-transcriptomic-analysis-of-distance-related-field-cancerization-in-rectal-cancer-patients
#10
Honglin Guo, Weigen Zeng, Lin Feng, Xuexin Yu, Ping Li, Kaitai Zhang, Zhixiang Zhou, Shujun Cheng
Field cancerization (FC) occurs in various epithelial carcinomas, including colorectal cancer, which indicates that the molecular events in carcinogenesis might occur in normal tissues extending from tumors. However, the transcriptomic characteristics of FC in colorectal cancer (CRC) remain largely unexplored. To investigate the changes in gene expression associated with proximity to the tumor, we analyzed the global gene expression profiles of cancer tissues and histologically normal tissues taken at various distances from the tumor (1 cm, 5 cm and the proximal end of the resected sample) from 32 rectal cancer patients...
May 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28565775/identification-of-key-genes-and-pathways-for-peri-implantitis-through-the-analysis-of-gene-expression-data
#11
Huang Zhang, Xiong Zhang, Jie Huang, Xusheng Fan
The present study attempted to identify potential key genes and pathways of peri-implantitis, and to investigate the possible mechanisms associated with it. An array data of GSE57631 was downloaded, including six samples of peri-implantitis tissue and two samples of normal tissue from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in the peri-implantitis samples compared with normal ones were analyzed with the limma package. Moreover, Gene Ontology annotation and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses for DEGs were performed by DAVID...
May 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28560417/atheroprotective-effects-of-statins-in-patients-with-unstable-angina-by-regulating-the-blood-borne-microrna-network
#12
Sufang Li, Chengfu Cao, Hong Chen, Junxian Song, Chongyou Lee, Jing Zhang, Feng Zhang, Qiang Geng, Zheng Li, Jingjin Li
Experimental studies have demonstrated several effects of statins in acute coronary syndrome (ACS) that may extend their clinical benefit beyond the lipid profile modification itself. However, the precise underlying mechanism remains to be elucidated. microRNAs (miRNAs) serve significant roles in the pathophysiology of atherosclerotic plaque progression. The present study investigated the protective role of statins in patients with unstable angina (UA) by regulating the circulating miRNA network. miRNA array results demonstrated that there were 21 differentially expressed miRNAs in non‑statin‑treated patients with UA (n=8) compared with non‑coronary artery disease controls (n=8), and 33 differentially expressed miRNAs in statin‑treated patients with UA (n=8) compared with non‑statin patients...
July 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28552713/mass-spectrometric-detection-combined-with-bioinformatic-analysis-identified-possible-protein-markers-and-key-pathways-associated-with-bladder-cancer
#13
Ziyu Wu, Sugui Wang, Fujin Jiang, Qiang Li, Chao Wang, Huanqiang Wang, Wei Zhang, Peng Xue, Shoulin Wang
We aimed to find possible protein markers and key pathways related to bladder cancer. In total, we extracted three bladder cancer tissues and three paracancerous tissues from Jiangsu Provincial People's Hospital Urology Department, and performed mass spectrometric detection with Q Exactive. Subsequently, we screened the differentially expressed proteins in the disease group and the normal group using the LIMMA package, and performed functional enrichment analyses using DAVID. Further, we constructed protein-protein interaction (PPI) networks with Cytoscape software, and analyzed modules with ClusterONE...
May 25, 2017: Gene
https://www.readbyqxmd.com/read/28545060/signet-a-signaling-network-data-simulator-to-enable-signaling-network-inference
#14
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
#15
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...
July 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
#16
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
#17
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
#18
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
#19
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
#20
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
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