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"geo database" or "gene expression omnibus"

Ming Jiang, Yi-Ran Wang, Nan Xu, Liyang Zhou, Qing An
More and more evidence indicate long noncoding RNAs (lncRNAs) as competing endogenous RNAs (ceRNAs) to indirectly regulate messenger RNAs (mRNAs) by acting as microRNA (miRNA) sponges, which represents a novel layer of gene regulation that plays a critical role in the development of cancers. However, functional roles and regulatory mechanisms of lncRNA-mediated ceRNAs network in osteosarcoma are still largely unknown. Here, we comprehensively compared the expression profiles of mRNAs, lncRNAs, and miRNAs between osteosarcoma and normal samples from the Gene Expression Omnibus (GEO) to elaborate related latent mechanisms...
October 15, 2018: Journal of Cellular Biochemistry
Shilpa Harshan, Poulami Dey, Srivatsan Ragunathan
Background: Osteoclast differentiation in the inflamed synovium of rheumatoid arthritis (RA) affected joints leads to the formation of bone lesions. Reconstruction and analysis of protein interaction networks underlying specific disease phenotypes are essential for designing therapeutic interventions. In this study, we have created a network that captures signal flow leading to osteoclast differentiation. Based on transcriptome analysis, we have indicated the potential mechanisms responsible for the phenotype in the RA affected synovium...
2018: PeerJ
Peng-Fei Chen, Fan Wang, Jia-Yan Nie, Jue-Rong Feng, Jing Liu, Rui Zhou, Hong-Ling Wang, Qiu Zhao
Background and aims: Gastric cancer (GC) is one of the most common cancers worldwide, and its pathogenesis is related to a complex network of gene interactions. The aims of our study were to find hub genes associated with the progression and prognosis of GC and illustrate the underlying mechanisms. Methods: Weighted gene co-expression network analysis (WGCNA) was conducted using the microarray dataset and clinical data of GC patients from Gene Expression Omnibus (GEO) database to identify significant gene modules and hub genes associated with TNM stage in GC...
2018: OncoTargets and Therapy
Zhong-Yang Xu, Chao Zhou, Ke-Feng Zhang, Yan-Ping Zheng
Ankylosing spondylitis (AS) is a common form of seronegative spondyloarthritis. We had identified differentially expressed genes (DEGs) in AS based on our previous RNA-sequencing results. Our study aimed to identify key genes in AS by integrated microarray analysis. In this present study, we identified 1328 DEGs between AS and normal control by using integrated analysis of two datasets derived from the Gene Expression Omnibus (GEO) database. Functional annotation of DEGs were performed. Pathways in cancer, Pancreatic cancer and Natural killer cell mediated cytotoxicity were significantly enriched pathways for DEGs...
October 12, 2018: Immunology Letters
Lin Zhang, Shuo Chen, Boxue Wang, Yinan Su, Shuyuan Li, Guisheng Liu, Xipeng Zhang
Long noncoding RNAs (lncRNAs) have recently emerged as important biomarkers of cancer progression. Here, we proposed to develop a lncRNA-based signature with a prognostic value for colorectal cancer (CRC) overall survival (OS). Through mining microarray datasets, we analyzed the lncRNA expression profiles of 122 patients with CRC from Gene Expression Omnibus. Associations between lncRNA and CRC OS were firstly evaluated through univariate Cox regression analysis. A random survival forest method was applied for further screening of the lncRNA signature, which resulted in eight lncRNAs, including PEG3-AS1, LOC100505715, MINCR, DBH-AS1, LINC00664, FAM224A, LOC642852, and LINC00662...
October 15, 2018: Journal of Cellular Biochemistry
Wendong Wang, Zhiwei Xu, Xiaobo Zhu, Xiaotong Chang
The present study aimed to mine therapeutic molecular targets that play an important part in the progression of coronary artery disease (CAD). The gene expression profile GSE28829 dataset and the microRNA (miRNA) expression profile GSE59421 dataset were downloaded from the Gene Expression Omnibus (GEO) database. The GEO2R online analytical tool was used to identify differentially expressed genes (DEGs) and miRNAs (DEMs). The target genes of DEMs were identified using the miRWalk2.0 web‑based tool and 2 miRNA‑gene regulatory networks were constructed using Cytoscape software...
October 10, 2018: Molecular Medicine Reports
ZhaoFang Li, RongQiang Zhang, XiaoLi Yang, DanDan Zhang, BaoRong Li, Di Zhang, Qiang Li, YongMin Xiong
BACKGROUND: Osteoarthritis (OA) is a kind of chronic osteoarthropathy and degenerative joint disease. Epigenetic regulation in the gene expression dynamics has become increasingly important in OA. We performed a combined analysis of two types of microarray datasets (gene expression and DNA methylation) to identify methylation-based key biomarkers to provide a better understanding of molecular biological mechanisms of OA. METHODS: We obtained two expression profiling datasets (GSE55235, GSE55457) and one DNA methylation profiling data set (GSE63695) from the Gene Expression Omnibus...
October 14, 2018: Journal of Cellular Physiology
Yan-Zhe Wang, Ding-Yu Zhu, Xin-Miao Xie, Miao Ding, Yong-Lan Wang, Lin-Lin Sun, Nan Zhang, E Shen, Xiao-Xia Wang
This study aimed to investigate the molecular mechanisms of diabetic kidney disease (DKD) and to explore new potential therapeutic strategies and biomarkers for DKD. First we analyzed the differentially expressed changes between patients with DKD and the control group using the chip data in Gene Expression Omnibus (GEO) database. Then the gene chip was subjected to be annotated again, so as to screen long noncoding RNAs (lncRNAs) and study expression differences of these lncRNAs in DKD and controlled samples...
October 14, 2018: Journal of Cellular Physiology
Zhaoju Tian, Shuang Cao, Cheng Li, Mingfang Xu, Huaiqing Wei, Han Yang, Qiyu Sun, Qikui Ren, Le Zhang
PURPOSE: The aim of our study was to validate the sway of long noncoding RNA (lncRNA) plasmacytoma variant translocation 1 (PVT1) on the metabolism and growth of bladder cancer cells by microRNA-31 (miR-31)/cyclin-dependent kinase 1 ( CDK1). METHODS: The Gene Expression Omnibus database was used for analyzing the differentially expressed lncRNA and messenger RNA (mRNA) in bladder cancer tissues, with the highly expressed lncRNA PVT1 and mRNA CDK1 screened out. The expression level of PVT1 was detected by quantitative reverse-transcription polymerase chain reaction, cell viability by Cell Counting Kit-8 assay, cell proliferation and scratch by 5-bromo-2'-deoxyuridine assay, cell migration and invasion by transwell assays, the expression level of CDK1 by immunohistochemistry and western blot analysis, transcription factor targeting by dual-luciferase assay, and the effect of PVT1 on bladder cancer growth by nude mice tumor formation experiment...
October 14, 2018: Journal of Cellular Physiology
Xuefei Shi, Zhili Liu, Zhicong Liu, Xueren Feng, Feng Hua, Xixian Hu, Bin Wang, Kaihua Lu, Fengqi Nie
BACKGROUND: NSCLC (non-small-cell lung cancer) is the leading cause of cancer-related mortality worldwide. Both epigenetic and genetic changes contribute to the initiation, development and metastasis of NSCLC. Recently, accumulating data have begun to support the notion that long noncoding RNAs (lncRNAs) function as new crucial regulators of diverse biological processes, including proliferation, apoptosis and metastasis, and play crucial roles in tumorigenesis. Nevertheless, further study is warranted to comprehensively determine lncRNAs' functions and potential mechanism...
October 9, 2018: EBioMedicine
Sara Franceschi, Debora Corsinovi, Francesca Lessi, Elena Tantillo, Paolo Aretini, Michele Menicagli, Claudia Scopelliti, Prospero Civita, Francesco Pasqualetti, Antonio G Naccarato, Michela Ori, Chiara M Mazzanti
BACKGROUND: Glioblastoma (GBM) is the most frequent and malignant primary brain tumor in adults and despite the progress in surgical procedures and therapy options, the overall survival remains very poor. Glutamate and α-KG are fundamental elements necessary to support the growth and proliferation of GBM cells. Glutamate oxidative deamination, catalyzed by GLUD2, is the predominant pathway for the production of α-KG. METHODS: GLUD2 emerged from the RNA-seq analysis of 13 GBM patients, performed in our laboratory and a microarray analysis of 77 high-grade gliomas available on the Geo database...
October 9, 2018: EBioMedicine
Qing Guo, Ge-Fei Guan, Wen Cheng, Cun-Yi Zou, Chen Zhu, Peng Cheng, An-Hua Wu
AIMS: Glioblastoma (GBM) is a lethal disease of the central nervous system with high mortality, and novel therapeutic targets and strategies for GBM are urgently needed. Caveolae-associated protein 1 (CAVIN1) is an essential caveolar component-encoding gene and has been poorly studied in glioma. To this end, in this study, we evaluated CAVIN1 expression in glioma tissue as well as the correlation between CAVIN1 expression and prognosis in glioma patients using the data collected from clinical samples or from the Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA), Rembrandt, and Gene Expression Omnibus (GEO) data sets...
October 11, 2018: CNS Neuroscience & Therapeutics
Wenzong Lu, Zhe Ding
The aim of this study was to identify key candidate genes in prostate cancer. The gene expression profiles of GSE32448, GSE45016, GSE46602 and GSE104749 were downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) between prostate cancer and normal samples were identified by R language. The gene ontology functional and pathway enrichment analyses of DEGs were performed by the Database for Annotation, Visualization and Integrated Discovery software followed by the construction of protein-protein interaction network...
October 11, 2018: Andrologia
Yancun Yin, Ling Zhou, Renhui Zhan, Qiang Zhang, Minjing Li
Background: Hepatocellular carcinoma (HCC) is one of the most common malignant cancer worldwide. Importantly, the precise mechanisms causing HCC pathogenicity are still unknown. The identification of potential oncogenes plays significant roles in finding novel therapeutic targets for human HCC. Purpose: WDR12 (WD repeat protein 12), a member of WD repeats family, plays crucial roles in the ribosome biogenesis pathway. However, Whether WDR12 contributes to HCC development remains unknown...
2018: Cancer Management and Research
Divya Niveditha, Sudeshna Mukherjee, Syamantak Majumder, Rajdeep Chowdhury, Shibashish Chowdhury
Motivation: Traditional cancer therapy is focused on eradicating fast proliferating population of tumor cells. However, existing evidences suggest survival of sub-population of cancer cells that can resist chemotherapy by entering a 'persister' state of minimal growth. These cells eventually survive to produce cells resistant to drugs. The identifying of appropriate targets that can eliminate the drug-tolerant "persisters" remains a challenge. Hence, a deeper understanding of the distinctive genetic signatures that lead to resistance is of utmost importance to design an appropriate therapy...
October 11, 2018: Bioinformatics
Lei Liu, Minxin Shi, Zhiwei Wang, Haimin Lu, Chang Li, Yu Tao, Xiaoyan Chen, Jun Zhao
BACKGROUND: The current TNM staging system is far from perfect in predicting the survival of individual non-small cell lung cancer (NSCLC) patients. In this study, we aim to combine clinical variables and molecular biomarkers to develop a prognostic model for patients with NSCLC. METHODS: Candidate molecular biomarkers were extracted from the Gene Expression Omnibus (GEO), and Cox regression analysis was performed to determine significant prognostic factors. The survival prediction model was constructed based on multivariable Cox regression analysis in a cohort of 152 NSCLC patients...
October 11, 2018: BMC Cancer
Su Zhang, Yong-Yan Chang, Yu-Wen Gong, Yan-Jun Gao, Qi Guo, Yu-Han Wang, You-Li Zhao, Zhi-Ping Wang
Chemotherapy is still a standard treatment of unresectable bladder cancer or distant metastases. The chemotherapy resistance always occurs after a period of treatment indicating poor prognosis. The current study aimed to explore the molecular mechanism of chemoresistance in bladder cancer cells. The gene expression profiles of GSE77883, including three untreated T24 cells samples and three gemcitabine-resistant T24 cells samples, was downloaded from Gene Expression Omnibus database. The screening of differentially expressed genes (DEGs), gene function analysis, and interaction prediction between microRNAs (miRNAs) and DEGs were performed by R software...
October 10, 2018: Journal of Cellular Biochemistry
Ya Wang, Min Qian, Peifeng Ruan, Andrew E Teschendorff, Shuang Wang
Identifying epigenetic field defects, notably early DNA methylation alterations, is important for early cancer detection. Research has suggested these early methylation alterations are infrequent across samples and identifiable as outlier samples. Here we developed a weighted epigenetic distance-based method characterizing (dis)similarity in methylation measures at multiple CpGs in a gene or a genetic region between pairwise samples, with weights to up-weight signal CpGs and down-weight noise CpGs. Using distance-based approaches, weak signals that might be filtered out in a CpG site-level analysis could be accumulated and therefore boost the overall study power...
October 10, 2018: Nucleic Acids Research
Leimarembi Devi Naorem, Mathavan Muthaiyan, Amouda Venkatesan
Triple-negative breast cancer (TNBC) has attracted more attention compared with other breast cancer subtypes due to its aggressive nature, poor prognosis, and chemotherapy remains the mainstay of treatment with no other approved targeted therapy. Therefore, the study aimed to discover more promising therapeutic targets and investigating new insights of biological mechanism of TNBC. Six microarray data sets consisting of 463 non-TNBC and 405 TNBC samples were mined from Gene Expression Omnibus. The data sets were integrated by meta-analysis and identified 1075 differentially expressed genes...
October 9, 2018: Journal of Cellular Biochemistry
Courtney L Andersen, Michelle M Boisen, Matthew J Sikora, Tianzhou Ma, George Tseng, Swati Suryawanshi, Anda Vlad, Esther Elishaev, Robert P Edwards, Steffi Oesterreich
To investigate changes in estrogen receptor alpha (ERα) signaling during progression of endometriosis to endometriosis-associated ovarian cancer (EAOC) as a driver of malignant transformation. We procured tissue samples of normal endometrium, endometriosis (benign, atypical, concurrent with EAOC), and EAOC. We evaluated expression of a 236-gene signature of estrogen signaling. ANOVA and unsupervised clustering were used to identify gene expression profiles across disease states. These profiles were compared to profiles of estrogen regulation in cancer models from the Gene Expression Omnibus (GEO)...
October 9, 2018: Hormones & Cancer
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