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"geo database" or "gene expression omnibus"

Zhiyu Dong, Junwen Wang, Tingting Zhan, Shuchang Xu
Purpose: Esophageal adenocarcinoma (EAC) is the most common type of esophageal cancer in Western countries. It is usually detected at an advanced stage and has a poor prognosis. The aim of this study was to identify key genes and miRNAs in EAC. Methods: The mRNA microarray data sets GSE1420, GSE26886, and GSE92396 and miRNA data set GSE16456 were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were obtained using R software...
2018: OncoTargets and Therapy
Dhayalan Pavithra, Kesavan Sabitha, Thangarajan Rajkumar
Gastric cancer is a common cancer in the world with higher incidence rates. Micro RNAs (miRNAs) are known to control biological processes and are also involved in the initiation and progression of numerous cancers. The aim of this study was to identify small molecule inhibitors using bioinformatics methods for over-expressed miRNAs that are known to play a major role in the genesis of gastric cancer. Our study included three datasets from Gene expression omnibus (GEO) database and we used bioinformatics tool to identify differentially expressed miRNAs in all the three datasets...
July 21, 2018: Computational Biology and Chemistry
Butian Zhang, Lili Yu, Ning Han, Zhenzhen Hu, Shuang Wang, Lei Ding, Jinlan Jiang
OBJECTIVE: The purpose of this study was to find out the important lncRNA-miRNA-mRNA axis and pathway in osteosarcoma (OS) through bioinformatics analysis and verify the biological functions of lncRNA/miRNA/mRNA in OS through in vitro and in vivo assays. METHODS: The differential expression mRNAs and lncRNAs were identified through microarray analysis, and the altered pathways were identified by GSEA. The Pearson Coefficient was used to analyze the correlations between mRNAs and lncRNAs...
August 8, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Dan-Dan Xiong, Yi-Wu Dang, Peng Lin, Dong-Yue Wen, Rong-Quan He, Dian-Zhong Luo, Zhen-Bo Feng, Gang Chen
BACKGROUND: Circular RNAs (circRNAs) have received increasing attention in human tumor research. However, there are still a large number of unknown circRNAs that need to be deciphered. The aim of this study is to unearth novel circRNAs as well as their action mechanisms in hepatocellular carcinoma (HCC). METHODS: A combinative strategy of big data mining, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and computational biology was employed to dig HCC-related circRNAs and to explore their potential action mechanisms...
August 9, 2018: Journal of Translational Medicine
Pichai Raman, Ravikanth Maddipati, Kian Huat Lim, Aydin Tozeren
Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer death in the US. Despite multiple large-scale genetic sequencing studies, identification of predictors of patient survival remains challenging. We performed a comprehensive assessment and integrative analysis of large-scale gene expression datasets, across multiple platforms, to enable discovery of a prognostic gene signature for patient survival in pancreatic cancer. PDAC RNA-Sequencing data from The Cancer Genome Atlas was stratified into Survival+ (>2-year survival) and Survival-(<1-year survival) cohorts (n = 47)...
2018: PloS One
Wenzong Lu, Gun Li
OBJECTIVE: The aim of this study was to identify potential key candidate genes and uncover their potential mechanisms in rheumatoid arthritis. MATERIALS AND METHODS: The gene expression profiles of GSE12021, GSE55457, GSE55584 and GSE55235 were downloaded from the gene expression omnibus database, including 45 rheumatoid arthritis and 29 normal samples. The differentially expressed genes between the two types of samples were identified with the Linear Models for Microarray Analysis package using R language...
April 2018: Acta Reumatológica Portuguesa
Silvija Cvitic, Boris Novakovic, Lavinia Gordon, Christine M Ulz, Magdalena Mühlberger, Francisca I Diaz-Perez, Jihoon E Joo, Vendula Svendova, Michael G Schimek, Slave Trajanoski, Richard Saffery, Gernot Desoye, Ursula Hiden
AIMS/HYPOTHESIS: An adverse intrauterine environment can result in permanent changes in the physiology of the offspring and predispose to diseases in adulthood. One such exposure, gestational diabetes mellitus (GDM), has been linked to development of metabolic disorders and cardiovascular disease in offspring. Epigenetic variation, including DNA methylation, is recognised as a leading mechanism underpinning fetal programming and we hypothesised that this plays a key role in fetoplacental endothelial dysfunction following exposure to GDM...
August 8, 2018: Diabetologia
Ma'en Obeidat, Anna Dvorkin-Gheva, Xuan Li, Yohan Bossé, Corry-Anke Brandsma, David C Nickle, Philip M Hansbro, Rosa Faner, Alvar Agusti, Peter D Paré, Martin R Stampfli, Don D Sin
Genome-wide mRNA profiling in lung tissue from human and animal models can provide novel insights into the pathogenesis of chronic obstructive pulmonary disease (COPD). While 6 months of smoke exposure are widely used, shorter durations were also reported. The overlap of short term and long-term smoke exposure in mice is currently not well understood, and their representation of the human condition is uncertain. Lung tissue gene expression profiles of six murine smoking experiments (n = 48) were obtained from the Gene Expression Omnibus (GEO) and analyzed to identify the murine smoking signature...
August 8, 2018: Scientific Reports
Maria Luisa Amaral, Galina A Erikson, Maxim N Shokhirev
BACKGROUND: Microarray experiments comprise more than half of all series in the Gene Expression Omnibus (GEO). However, downloading and analyzing raw or semi-processed microarray data from GEO is not intuitive and requires manual error-prone analysis and a bioinformatics background. This is due to a lack of standardization in array platform fabrication as well as the lack of a simple interactive tool for clustering, plotting, differential expression testing, and testing for functional enrichment...
August 8, 2018: BMC Bioinformatics
Yu-Ting Chen, Jian-Ni Yao, Yu-Tao Qin, Kai Hu, Fang Wu, Ye-Ying Fang
MicroRNAs (miRNAs) are confirmed to be tumor promoters or suppressors in multiple squamous cell carcinomas (SCCs). miR-99a-5p has been demonstrated to be downregulated in cancerous tissues, but its functional role in head and neck SCC (HNSCC) and its mechanism of action have not been fully elucidated. Here, we studied the expression of miR-99a-5p in HNSCC and performed a clinical value assessment and then extracted mature expression data from The Cancer Genome Atlas (TCGA) and microarrays from Gene Expression Omnibus (GEO)...
August 2018: FEBS Open Bio
Hongshun Shi, Hui Li, Ronghua Yuan, Wen Guan, Xiaomei Zhang, Shaoyang Zhang, Wenliang Zhang, Fang Tong, Li Li, Zhihong Song, Changwei Wang, Shulan Yang, Haihe Wang
BACKGROUND: Poly C Binding Protein 1 (PCBP1) is an RNA-binding protein that binds and regulates translational activity of subsets of cellular mRNAs. Depletion of PCBP1 is implicated in various carcinomas, but the underlying mechanism in tumorigenesis remains elusive. METHODS: We performed a transcriptome-wide screen to identify novel bounding mRNA of PCBP1. The bind regions between PCBP1 with target mRNA were investigated by using point mutation and luciferase assay...
August 7, 2018: Journal of Experimental & Clinical Cancer Research: CR
Jinjing Cun, Qifeng Yang
The abnormal expression of miR-92a-3p was detected in multiple cancers. However, the biological role and underlying mechanism of miR-92a-3p in tamoxifen-resistant cells are still unknown. The main objective of our study was to find potential miR-92a-3p regulating pathways involved in tamoxifen resistance and to construct their regulatory network using bioinformatics. Four gene expression profiles were retrieved from GEO database and the GEO2R tool was used for analysis. GSE41922 and GSE42072 were applied to investigate aberrant miR-92a-3p expression in breast cancer serum and tissue...
August 4, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Meghan L Ruebel, Peter Z Schall, Uros Midic, Kailey A Vincent, Benjamin Goheen, Catherine A VandeVoort, Keith E Latham
STUDY QUESTION: Which different pathways and functions are altered in rhesus monkey oocytes that fail to mature after an ovulatory stimulus? SUMMARY ANSWER: FTM oocytes complete a large portion of the transition in transcriptome composition associated with normal maturation, but also manifest numerous differences that indicate incomplete transcriptional repression and cytoplasmic maturation affecting multiple processes. WHAT IS KNOWN ALREADY: Oocyte maturation defects contribute to unexplained female infertility...
August 3, 2018: Molecular Human Reproduction
Jia Li, Yajuan Sun, Jiajun Chen
The purpose of this study was to explore the key mechanism involved in the pathogenesis of Parkinson's disease (PD) based on microarray analysis. The expression profile data of GSE7621, which contained 9 substantia nigra tissues isolated from normals and 16 substantia nigra tissues isolated from PD patients, was obtained from Gene Expression Omnibus. The differentially expressed genes (DEGs) were screened, followed by functional enrichment analysis and protein-protein interaction (PPI) network construction...
August 6, 2018: Journal of Molecular Neuroscience: MN
Lei Wang, Xin Hu, Peng Wang, Zhi-Ming Shao
BACKGROUND: Sentinel lymph node biopsy is the standard surgical staging approach for operable triple-negative breast cancer (TNBC) with clinically negative axillae. In this study, we sought to develop a model to predict TNBC patients with negative nodal involvement, who would benefit from the exemption of the axillary staging surgery. MATERIALS AND METHODS: We evaluated 3' untranslated region (3'UTR) profiles using microarray data of TNBC from two Gene Expression Omnibus datasets...
August 6, 2018: Oncologist
C Puttipanyalears, A Arayataweegool, K Chalertpet, P Rattanachayoto, P Mahattanasakul, N Tangjaturonsasme, V Kerekhanjanarong, A Mutirangura, N Kitkumthorn
BACKGROUND: The incidence of oral squamous cell carcinoma (OSCC) continues to increase each year. Clinical examination and biopsy usually detect OSCC at an advanced stage that is difficult to treat, leading to poor prognosis. DNA methylation pattern is tissue specific and has emerged as a biomarker for the detection of cancers of tissue origin. Herein, we aimed to discover a novel site-specific methylation marker for OSCC. METHODS: We selected OSCC datasets analyzed using the IlluminaHumanMethylation27 BeadChip from the Gene Expression Omnibus repository of the National Center for Biotechnology Information using a bioinformatics approach...
August 6, 2018: BMC Cancer
Wei Liu, Ling Li, Yiruo He, Sen Cai, Wenjie Zhao, Hao Zheng, Yuexian Zhong, Shaobo Wang, Yang Zou, Zhenhua Xu, Yu Zhang, Wei Tu
Caenorhabditis elegans ( C. elegans ) is a well-characterized metazoan, whose transcriptome has been profiled in different tissues, development stages, or other conditions. Large-scale transcriptomes can be reused for gene function annotation through systematic analysis of gene co-expression relationships. We collected 2101 microarray data from National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO), and identified 48 modules of co-expressed genes that correspond to tissues, development stages, and other experimental conditions...
August 3, 2018: Biomolecules
Xinyuan Zhao, Minlu Liang, Xiaona Li, Xiaoling Qiu, Li Cui
Adipose stem cells (ASCs) are considered a great alternative source of mesenchymal stem cells (MSCs) and have shown great promise on tissue engineering and regenerative medicine applications, including bone repair. However, the underlying mechanisms regulating the osteogenic differentiation of ASCs remain poorly known. Gene expression profiles of GSE63754 and GSE37329 were downloaded from gene expression omnibus database. R software and Bioconductor packages were used to compare and identify the differentially expressed genes (DEGs) before and after ASC osteogenic differentiation...
August 5, 2018: Journal of Cellular Physiology
Hsin-Han Chang, Yu-Chen Cheng, Wen-Chiuan Tsai, Min-Jen Tsao, Ying Chen
BACKGROUND/AIMS: Glioblastoma, also known as glioblastoma multiforme (GBM), is a fast-growing type of tumor that is the most aggressive brain malignancy in adults. According to GEO profile analysis, patients with high transient receptor potential canonical 3 (TRPC3) expression have poor survival rates. The aim of this study is to evaluate the effects of Ethyl-1-(4-(2,3,3-trichloroacrylamide)phenyl)-5-(trifluoromethyl)-1H-pyrazole-4-carboxylate (Pyr3), a selective TRPC3 channel blocker, on the proliferation and migration of human glioblastoma cells...
August 3, 2018: Cellular Physiology and Biochemistry
Feng Xu, Feng Gao
This study aimed to investigate the potential therapeutic targets of Liuwei Dihuang pill (LDP) in the treatment of postmenopausal osteoporosis with kidney-Yin deficiency (PMO-KY).Gene expression data were downloaded from the GEO database, including 4 PMO-KY samples and 3 healthy postmenopausal controls from GSE56116, as well as 3 PMO-KY samples before LDP treatment and 3 PMO-KY samples after three months of LDP treatment from GSE57273. Limma package was used to identify differentially expressed genes (DEGs)...
August 2018: Medicine (Baltimore)
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