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"geo database" or "gene expression omnibus"

Jinggang Cui, Wei Li, Guohua Liu, Xiaojun Chen, Xiaolai Gao, Huiling Lu, Dang Lin
More and more circular RNAs (circRNAs) revealed to play a critical role in the initiation and progression of cancer, however, the effects of circRNAs on non-small cell lung cancer (NSCLC) remain largely undetermined. In the present study, we screened the dysregulated circRNAs in paired NSCLC and normal samples from GEO database and identified circ_0043278 was to be significantly up-regulated in NSCLC and demonstrated it promotes NSCLC progression in vitro and in vivo. Then, we revealed the expression of miR-520f, a downstream factor of circ_0043278, was significantly down-regulated in NSCLC and acted as a tumor inhibitor...
December 2019: Artificial Cells, Nanomedicine, and Biotechnology
Yaoyao Bian, Lili Yang, Min Zhao, Zhengjun Li, Yuying Xu, Guilian Zhou, Wenlin Li, Li Zeng
Introduction: Post-traumatic stress disorder (PTSD) is characterized by impaired fear extinction, excessive anxiety, and depression. However, the potential pathogenesis and cause of PTSD are not fully understood. Hence, the purpose of this study was to identify key genes and pathway involved in PTSD and reveal underlying molecular mechanisms by using bioinformatics analysis. Methods: The mRNA microarray expression profile dataset was retrieved and downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were screened using GEO2R...
2019: Frontiers in Psychology
Kai Wu, Xiaotao Yin, Yipeng Jin, Fangfang Liu, Jiangping Gao
Background: Methylation plays a key role in the aetiology and pathogenesis of prostate cancer (PCa). This study aimed to identify aberrantly methylated differentially expressed genes (DEGs) and pathways in PCa and explore the underlying mechanisms of tumourigenesis. Methods: Expression profile (GSE29079) and methylation profile (GSE76938) datasets were obtained from the Gene Expression Omnibus (GEO). We used R 3.4.4 software to assess aberrantly methylated DEGs...
2019: Cancer Cell International
Huan-Ming Hsu, Chi-Ming Chu, Yu-Jia Chang, Jyh-Cherng Yu, Chien-Ting Chen, Chen-En Jian, Chia-Yi Lee, Yueh-Tao Chiang, Chi-Wen Chang, Yu-Tien Chang
Gene co-expression network analysis (GCNA) can detect alterations in regulatory activities in case/control comparisons. We propose a framework to detect novel genes and networks for predicting breast cancer recurrence. Thirty-four prognosis candidate genes were selected based on a literature review. Four Gene Expression Omnibus Series (GSE) microarray datasets (n = 920) were used to create gene co-expression networks based on these candidates. We applied the framework to four comparison groups according to node (+/-) and recurrence (+/-)...
March 14, 2019: Scientific Reports
Shan Yu, Xuepeng Jiang, Juan Li, Chao Li, Mian Guo, Fei Ye, Maomao Zhang, Yufei Jiao, Baoliang Guo
Integrated studies of accumulated data can be performed to obtain more reliable information and more feasible measures for investigating the potential diagnostic and prognostic biomarkers of breast cancer and exploring related molecular mechanisms. Our study aimed to explore the GATA family members involved in breast cancer by integrating data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and other online databases. We performed an integrated analysis of published studies from GEO and analyzed clinical data from TCGA and GTEx to evaluate the clinical significance and prognosis values of the GATA family in breast cancer...
March 14, 2019: Scientific Reports
Shulong Zhang, Quan Wang, Qi Han, Huazhong Han, Pinxiang Lu
The molecular mechanism of the occurrence and development of papillary thyroid carcinoma (PTC) has been widely explored, but has not been completely elucidated. This study aimed to identify and analyze genes associated with PTC by bioinformatics methods. Two independent datasets were downloaded from GEO database. The differentially expressed genes (DEGs) between PTC tissues and matched non-cancerous tissues were identified using GEO2R tool. The common DEGs in the two datasets were screened out by VennDiagram package, and analyzed by the following tools: KOBAS, DAVID, STRING, UALCAN and GEPIA...
March 14, 2019: Bioscience Reports
Gang Liu, Yahong Wang, Lawei Yang, Baoan Zou, Shenglan Gao, Zeqing Song, Ziying Lin
Tetraspanin 1(TSPAN1) as a clinically relevant gene target in cancer has been studied, but there is no direct in vivo or vitro evidence for pulmonary fibrosis (PF). Using reanalysing Gene Expression Omnibus data, here, we show for the first time that TSPAN1 was markedly down-regulated in lung tissue of patient with idiopathic PF (IPF) and verified the reduced protein expression of TSPAN1 in lung tissue samples of patient with IPF and bleomycin-induced PF mice. The expression of TSPAN1 was decreased and associated with transforming growth factor-β1 (TGF-β1 )-induced molecular characteristics of epithelial-to-mesenchymal transition (EMT) in alveolar epithelial cells (AECs)...
March 14, 2019: Journal of Cellular and Molecular Medicine
Lianmin Zhang, Hailong Wang, Changli Wang
BACKGROUND: Tobacco use is responsible for approximately 80-90% of non-small cell lung cancer cases. A large evidence base has shown that the ERBB pathway is associated with the occurrence of lung cancer. However, the mechanisms of how smoking activates the ERBB pathway have yet to be explained. We hypothesized that microRNAs may induce ERBB pathway activity during the process of lung cancer carcinogenesis. METHODS: We analyzed microRNA array data from the Gene Expression Omnibus and the Kyoto Encyclopedia of Genes and Genomes to determine any associations between genes and smoking in three groups of patients with NSCLC: smokers, former smokers, and non-smokers...
March 13, 2019: Thoracic Cancer
Siqi Dong, Hongjun Huo, Yu Mao, Xin Li, Lixin Dong
Osteosarcoma is the most common primary solid malignancy of the bone, and its high mortality usually correlates with early metastasis. In this study, we developed a risk score model to help predict metastasis at the time of diagnosis. We downloaded and mined four expression profile datasets associated with osteosarcoma metastasis from the Gene Expression Omnibus. After data normalization, we performed LASSO logistic regression analysis together with 10-fold cross validation using the GSE21257 dataset. A combination of eight genes ( RAB1 , CLEC3B , FCGBP , RNASE3 , MDL1 , ALOX5AP , VMO1 and ALPK3 ) were identified as being associated with osteosarcoma metastasis...
March 2019: FEBS Open Bio
Xiao-Lan Zhong, Xiao-Ming Liao, Fei Shen, Hai-Jian Yu, Wen-Sheng Yan, Yun-Fang Zhang, Jia-Jun Ye, Zhi-Ping Lv
Dengue fever (DF) and dengue hemorrhagic fever (DHF) are recurrent diseases that are widespread in the tropics. Here, we identified candidate genes associated with these diseases by performing integrated analyses of DF (GSE51808) and DHF (GSE18090) microarray datasets in the Gene Expression Omnibus (GEO). In all, we identified 7635 differentially expressed genes (DEGs) in DF and 8147 DEGs in DHF as compared to healthy controls ( P  < 0.05). In addition, we discovered 215 differentially expressed long non-coding RNAs (DElncRNAs) in DF and 225 DElncRNAs in DHF...
March 2019: FEBS Open Bio
Yang Xu, Rongxin Geng, Fan'en Yuan, Qian Sun, Baohui Liu, Qianxue Chen
Gliomas are a very diverse group of brain tumors that are most commonly primary tumor and difficult to cure in central nervous system. It's necessary to distinguish low-grade tumors from high-grade tumors by understanding the molecular basis of different grades of glioma, which is an important step in defining new biomarkers and therapeutic strategies. We have chosen the gene expression profile GSE52009 from gene expression omnibus (GEO) database to detect important differential genes. GSE52009 contains 120 samples, including 60 WHO II samples and 24 WHO IV samples that were selected in our analysis...
2019: PeerJ
Lu-Mei Chi, Li-Ping Wang, Dan Jiao
Objectives: This study aims to determine differentially expressed genes (DEGs) and long noncoding RNAs (lncRNAs) associated with Parkinson's disease (PD) using a microarray. Methods: We downloaded the microarray data GSE6613 from the Gene Expression Omnibus, which included 105 samples. We selected 72 samples comprising 22 healthy control blood samples and 50 PD blood samples for further analysis. Later, we used Limma to screen DEGs and differentially expressed lncRNAs (DElncRNAs) and estimated their functions by the Gene Ontology (GO)...
2019: Parkinson's Disease
Kaiyuan Jiang, Hongmei Liu, Dongyi Xie, Qiang Xiao
Gastric cancer (GC) is one of the most common malignancies worldwide. To the best of our knowledge, no biomarkers have been widely accepted for the early diagnosis and prognostic prediction of GC. This study aimed to identify potential novel prognostic biomarkers for GC. The dataset GSE29272, which originates from the public database Gene Expression Omnibus, was employed in the present study. The online tool GEO2R was used to calculate the differentially expressed genes (DEGs) in GSE29272 between tumour tissues and adjacent tissues...
March 2019: Oncology Letters
Yiyun Tan, Lei Liu
Osteoporosis (OP) is a common metabolic bone disease with high incidence, and is recognized as a major public health problem worldwide. It is essential to clarify the pathogenesis of the disease for improving the diagnosis, prevention and treatment of OP. The aim of this study was to clarify the pivotal pathways and hub genes in OP using Gibbs sampling. The gene expression profile datasets were obtained from Gene Expression Omnibus (GEO) database. The pathways were enriched by Kyoto Encyclopedia of Genes and Genomes (KEGG) with genes intersection ≥5 based on gene expression profile data...
March 2019: Experimental and Therapeutic Medicine
Yanqiu Tong, Yang Song, Shixiong Deng
Background: Prostate cancer (PCa) is a malignancy cause of cancer deaths and frequently diagnosed in male. This study aimed to identify tumor suppressor genes, hub genes and their pathways by combined bioinformatics analysis. Methods: A combined analysis method was used for two types of microarray datasets (DNA methylation and gene expression profiles) from the Gene Expression Omnibus (GEO). Differentially methylated genes (DMGs) were identified by the R package minfi and differentially expressed genes (DEGs) were screened out via the R package limma...
2019: Cancer Cell International
Aditya Lahiri, Priyadharshini S Venkatasubramani, Aniruddha Datta
BACKGROUND: Plants are sessile organisms and are unable to relocate to favorable locations under extreme environmental conditions. Hence they have no choice but to acclimate and eventually adapt to the severe conditions to ensure their survival. As traditional methods of bolstering plant defense against stressful conditions come to their biological limit, we require newer methods that can allow us to strengthen plants' internal defense mechanism. These factors motivated us to look into the genetic networks of plants...
March 12, 2019: BMC Plant Biology
Guangyu Zhou, Xiaofei Zhang, Wanning Wang, Wenlong Zhang, Huaying Wang, Guangda Xin
BACKGROUND To identify noninvasive diagnostic biomarkers for membranous nephropathy (MN). MATERIAL AND METHODS The mRNA microarray datasets GSE73953 using peripheral blood mononuclear cells (PBMCs) of 8 membranous nephropathy patients and 2 control patients; and microRNAs (miRNA) microarray dataset GSE64306 using urine sediments of 4 membranous nephropathy patients and 6 control patients were downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were respectively identified from PBMCs and urine sediments of membranous nephropathy patients, followed with functional enrichment analysis, protein-protein interaction (PPI) analysis, and miRNA-target gene analysis...
March 13, 2019: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Zide Chen, Jiehua Chen, Xuan Huang, Yi Wu, Kuiyuan Huang, Weikang Xu, Linqing Xie, Xiaoyong Zhang, Hongyan Liu
Hepatitis B virus-associated (HBV(+)) hepatocellular carcinoma (HCC) accounts for a large proportion of liver cancer with poor clinical outcomes and treatment options. However, the underlying molecular mechanisms are still poorly understood. To explore potential key genes in the development of HBV(+)HCC, four series of data (GSE14520, GSE94660, GSE25599, and GSE55092) derived from Gene Expression Omnibus database were analyzed. Totally, 84 upregulated and 46 downregulated common differentially expressed genes (DEGs) were discovered...
March 13, 2019: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Fan Wu, Feng Gao, Siyi He, Yingbin Xiao
Chronic hypoxia can be observed in the heart under physiological or pathophysiological states, including embryonic development or cyanotic congenital heart disease. The aim of the present study was to examine gene expression profiles of chronically hypoxic myocardium and to explore the pathophysiological mechanisms by which the heart adapts to chronic hypoxia. Raw data from the next‑generation sequencing data set GSE36761 were downloaded from the Gene Expression Omnibus database. The data set comprised 30 specimens, including 8 healthy myocardia and 22 tetralogy of Fallot (TOF) congenital cardiac malformations; only 7 original data sets of healthy myocardia were obtained, and 5/22 TOFs were excluded...
March 1, 2019: Molecular Medicine Reports
Yiwen Feng, Wenzhao Hang, Zhenyu Sang, Shuangdi Li, Wei Xu, Yi Miao, Xiaowei Xi, Qian Huang
MicroRNAs (miRNAs) serve important roles in drug‑resistance; however, exosomal miRNAs associated with drug‑resistance in ovarian cancer (OC) have not been reported to date. The current study aimed to analyze the drug resistance‑associated exosomal miRNAs in original OC cells and their derived exosomes using microarray data downloaded from the Gene Expression Omnibus database (series GSE76449). The chemosensitive OC cell lines SKOV3_ip1, A2780_PAR and HEYA8, as well as the chemoresistant cell lines SKOV3_TR, A2780_CP20 and HEYA8_MDR, were investigated...
March 5, 2019: Molecular Medicine Reports
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