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"geo database" or "gene expression omnibus"

Qiuyan Guo, Yanan He, Liyuan Sun, Congcong Kong, Yan Cheng, Peng Wang, Guangmei Zhang
The pathophysiology of ovarian cancer (OV) is complex and depends on multiple biological processes and pathways. Therefore, there is an urgent need to identify reliable prognostic biomarkers for predicting clinical outcomes and helping personalize treatment of OV. A long non-coding RNA (lncRNA)-based risk score model was constructed to infer the prognostic efficacy of transcription factors (TFs) based on the OV dataset from The Cancer Genome Atlas. The risk score model was further validated in other independent cohorts from Gene Expression Omnibus...
December 13, 2018: Journal of Cellular and Molecular Medicine
Yanping Chen, Naiheng Hei, Jianguang Zhao, Shixiong Peng, Kaicheng Yang, He Chen, Zifeng Cui, Linyu Jin, Ran Sun, Jingxin Guo
Oral squamous cell carcinoma (OSCC) represents one of the most common head and neck cancer that with dire prognosis due partly to the lack of reliable prognostic biomarker. Here, we aimed to develop a CpG site-based prognostic signature through which we could accurately predict overall survival (OS) of patients with OSCC. We obtained OSCC-related DNA methylation and gene expression data sets from the public accessible Gene Expression Omnibus. Correlations between methylation level of CpG sites and OS of patients with OSCC were assessed by univariate Cox regression analysis followed by robust likelihood-based survival analysis on those CpG sites with permutation P < 0...
December 12, 2018: Journal of Cellular Biochemistry
Qiandong Zhu, Yunpeng Sun, Qingqing Zhou, Qikuan He, Haixin Qian
Improved insight into the molecular characteristics of hepatocellular carcinoma (HCC) is required to predict prognosis and to develop a new rationale for targeted therapeutic strategy. Bioinformatics methods, including functional enrichment and network analysis combined with survival analysis, are required to process a large volume of data to obtain further information on differentially expressed genes (DEGs). The RNA sequencing data related to HCC in The Cancer Genome Atlas (TCGA) database were analyzed to screen DEGs, which were separately submitted to perform gene enrichment analysis to identify gene sets and signaling pathways, and to construct a protein-protein interaction (PPI) network...
December 2018: Molecular and Clinical Oncology
Hai-Min Lu, Wan-Wan Yi, Yu-Shui Ma, Wei Wu, Fei Yu, Heng-Wei Fan, Zhong-Wei Lv, Hui-Qiong Yang, Zheng-Yan Chang, Chao Zhang, Wen-Ting Xie, Jun-Jian Jiang, Ying-Chun Song, Li Chai, Cheng-You Jia, Gai-Xia Lu, Xiao-Jun Zhong, Li-Kun Hou, Chun-Yan Wu, Min-Xin Shi, Ji-Bin Liu, Da Fu
To investigate the expression level of microRNA-101-3p (miR-101-3p) and its possible association with progression, prognosis and chemotherapy in patients with non-small cell lung cancer (NSCLC), the Gene Expression Omnibus (GEO) database was used. Quantitative polymerase chain reaction was used to verify the expression in 327 NSCLC and 42 adjacent normal lung tissues, of which 42 viable tissues were paired with nearby normal lung tissues. Based on the Cox regression model, univariate and multivariate analyses were used to address the factors that had effects on overall survival (OS) and disease-free survival (DFS) rate...
December 2018: Oncology Letters
Dong-Yue Wen, Jia-Cheng Huang, Jie-Yu Wang, Wen-Ya Pan, Jiang-Hui Zeng, Yu-Yan Pang, Hong Yang
In order to determine the diagnostic efficacy of microRNA (miR)-122-5p and to identify the potential molecular signaling pathways underlying the function of miR-122-5p in hepatocellular carcinoma (HCC), the expression profiles of data collected from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and literature databases were analyzed, along with any associations between clinicopathological characteristics and the diagnostic value of miR-122-5p in HCC. The intersection of 12 online prediction databases and differentially expressed genes from TCGA and GEO were utilized in order to select the prospective target genes of miR-122-5p in HCC...
December 2018: Oncology Letters
Ruoyu Wu, Jihao Ruan, Yongjin Sun, Mengyu Liu, Zhuang Sha, Cunyi Fan, Qingkai Wu
BACKGROUND: This study was aimed to investigate the role and specific molecular mechanism of HIF1A-AS2/miR-665/IL6 axis in regulating osteogenic differentiation of adipose-derived stem cells (ASCs) via the PI3K/Akt signaling pathway. METHODS: RNAs' expression profile in normal/osteogenic differentiation-induced ASCs (osteogenic group) was from the Gene Expression Omnibus database. The analysis was carried out using Bioconductor of R. Gene Set Enrichment Analysis and Kyoto Encyclopedia of Genes and Genomes dataset were applied to identify up- and downregulated signaling pathways...
December 13, 2018: Stem Cell Research & Therapy
Yi-Jen Chen, Wei-An Chang, Ling-Yu Wu, Ya-Ling Hsu, Chia-Hsin Chen, Po-Lin Kuo
The phenotypic change of chondrocytes and the interplay between cartilage and subchondral bone in osteoarthritis (OA) has received much attention. Structural changes with nerve ingrowth and vascular penetration within OA cartilage may contribute to arthritic joint pain. The aim of this study was to identify differentially expressed genes and potential miRNA regulations in OA knee chondrocytes through next-generation sequencing and bioinformatics analysis. Results suggested the involvement of SMAD family member 3 ( SMAD3 ) and Wnt family member 5A ( WNT5A ) in the growth of blood vessels and cell aggregation, representing features of cartilage damage in OA...
December 10, 2018: Journal of Clinical Medicine
Xue Xia Liu, Li Cai, Fu Jun Liu
Asthenozoospermia is the most common clinical symptom of male infertility. Molecular markers associated with asthenozoospermia spermatozoa are scarcely identified. The objective of this study was to screen the differentially expressed genes (DEGs) in asthenozoospermia spermatozoa and assess the underlying bioinformatics roles in regulation of sperm quality.Based on gene expression omnibus (GEO) database, the GSE22331, GSE1133, and GSE4193 expression profile data were downloaded. The DEGs of asthenozoospermia spermatozoa were identified...
December 2018: Medicine (Baltimore)
Zhong Jun Chen, You Ji Yan, Hao Shen, Jia Jie Zhou, Guang Hua Yang, Yi Xiang Liao, Jin Min Zeng, Tao Yang
OBJECTIVE: Prostate cancer (PCa) is one of the most prevalent types of cancer among men worldwide. The incidence of PCa is increasing in China. Therefore, there is an urgent need to identify novel diagnostic and prognostic markers for PCa to improve the treatment of the disease. METHODS: The Cancer Genome Atlas (TCGA) and GEO database were used to analyze the expression of miR-192, and the relationship between miR-192 and the Clinical features of patients in PCa...
December 13, 2018: Medical Principles and Practice: International Journal of the Kuwait University, Health Science Centre
Sahika Cingir Koker, Ermira Jahja, Huma Shehwana, Ayse Gokce Keskus, Ozlen Konu
Cholinergic Receptor Nicotinic Alpha 5 (CHRNA5) is an important susceptibility locus for nicotine addiction and lung cancer. Depletion of CHRNA5 has been associated with reduced cell viability, increased apoptosis and alterations in cellular motility in different cancers yet not in breast cancer. Herein we first showed the expression of CHRNA5 was variable and positively correlated with the fraction of total genomic alterations in breast cancer cell lines and tumors indicating its potential role in DNA damage response (DDR)...
2018: PloS One
Mingwei Chen, Xiaonan Xu, Haiqing Ma
Oral carcinoma (OC) is the major cancer type in the head and neck region; however, the molecular mechanisms of its pathogenesis and progression remain poorly understood. In recent years, the long noncoding RNAs (lncRNAs) have been uncovered as critical regulators in the development and progression of multiple human cancers, but most of the lncRNAs expression patterns, clinical relevance, and biological functions in OC are still unclear. To better understand the significance of lncRNAs in OC carcinogenesis, we analyzed the expression levels of lncRNAs between OC and healthy oral mucosa using The Cancer Genome Atlas Cancer Genome RNA sequencing data and another three independent microarray datasets from Gene Expression Omnibus...
December 12, 2018: Anti-cancer Drugs
Bin-Liang Gan, Li-Jie Zhang, Li Gao, Fu-Chao Ma, Rong-Quan He, Gang Chen, Jie Ma, Jin-Cai Zhong, Xiao-Hua Hu
The function of the expression of microRNA (miR)‑224‑5p in prostate adenocarcinoma (PCa) remains to be elucidated, therefore, the present study aimed to investigate the clinical significance and potential molecular mechanism of miR‑224‑5p in PCa. Data on the expression of miR‑224‑5p in PCa were extracted from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), ArrayExpress and previous literature, and meta‑analyses with standardized mean difference (SMD) and summary receiver operating characteristic (sROC) methods were performed for statistical analyses...
October 3, 2018: Oncology Reports
Tao Zhang, Jianrong Guo, Jian Gu, Zheng Wang, Guobin Wang, Huili Li, Jiliang Wang
Colorectal cancer (CRC) is one of the principal causes of cancer‑associated mortality worldwide. The high incidence of liver metastasis is the leading risk factor of mortality in patients with CRC, and the mechanisms of CRC liver metastasis are poorly understood. In the present study, 7 datasets, including 3 gene expression profile datasets and 4 microRNA (miRNA) expression profile datasets were downloaded from the NCBI Gene Expression Omnibus (GEO) database to identify potential key genes and miRNAs, which may be candidate biomarkers for CRC liver metastasis...
November 1, 2018: Oncology Reports
Yi Wang, Ling Jiang, Guogang Dai, Shengwu Li, Xiaoyuan Mu
Degeneration of the intervertebral disc (IVD), which consists of the annulus fibrosus (AF) and nucleus pulposus (NP), is a multifactorial physiological process associated with lower back pain. Despite decades of research, the knowledge of the underlying molecular mechanisms of IVD degeneration (IDD) has remained limited. The present study aimed to reveal the differential gene expression patterns in AF and NP during the process of IDD and to identify key biomarkers contributing to these differences. The microarray dataset GSE70362 containing 24 AF and 24 NP samples was retrieved from the Gene Expression Omnibus database...
December 2018: Experimental and Therapeutic Medicine
Chunhong Li, Dan Mo, Meiqin Li, Yanyan Zheng, Qiao Li, Shiyan Ou, Zhiyong Zhang
Human lifespan is determined by genetic and environmental factors. Potential longevity genes are neither specific nor reproducible, and longevity-related genes are constantly confused with age-related genes. To distinguish specific age- and longevity-related genes, we analyzed a Gene Expression Omnibus (GEO) dataset established by the Leiden Longevity Study. The individuals were classified into longevity (mean age, 93.4 ± 3.0 years), longevity offspring (60.8 ± 6.1) and control (61.9 ± 6.9) groups. The series matrix files were downloaded, and average expression values were calculated...
December 11, 2018: Genes & Genetic Systems
Shawn Kant, Edward G Stopa, Conrad E Johanson, Andrew Baird, Gerald D Silverberg
BACKGROUND: The roles of the choroid plexus (CP) and cerebrospinal fluid (CSF) production have drawn increasing attention in Alzheimer's disease (AD) research. Specifically, studies document markedly decreased CSF production and turnover in moderate-to-severe AD. Moreover, reduced CP function and CSF turnover lead to impaired clearance of toxic metabolites, likely promote neuroinflammation, and may facilitate neuronal death during AD progression. We analyzed CP gene expression in AD compared with control subjects, specifically considering those genes involved with CSF production and CP structural integrity...
December 12, 2018: Fluids and Barriers of the CNS
Rosa Martin-Mateos, Thiago M De Assuncao, Juan Pablo Arab, Nidhi Jalan-Sakrikar, Usman Yaqoob, Thomas Greuter, Vikas K Verma, Angela J Mathison, Sheng Cao, Gwen Lomberk, Philippe Mathurin, Raul Urrutia, Robert C Huebert, Vijay H Shah
BACKGROUND & AIMS: Transdifferentiation of hepatic stellate cells (HSCs) into myofibroblasts is a key event in the pathogenesis of liver fibrosis. Transforming growth factor β (TGF-β) and platelet-derived growth factor (PDGF) are canonical HSC activators after liver injury. The aim of this study was to analyze the epigenetic modulators that differentially control TGF-β and PDGF signaling pathways. METHODS: We performed a transcriptomic comparison of HSCs treated with TGF-β or PDGF-BB using RNA sequencing...
September 15, 2018: Cellular and Molecular Gastroenterology and Hepatology
Ke Zhang, Cuilin Li, Jianqiu Liu, Zhi Li, Chao Ma
APTR has been employed as a potential biomarker attributing to it was involved in carcinogenesis and malignancy's progression. However, the roles of APTR in papillary thyroid cancer (PTC) and anaplastic thyroid cancer (ATC) are unclear. In the present study, we aimed to explore the relative expression of APTR in PTC and ATC tissues and the relation between APTR expression and PTC clinicopathological features. We analyzed APTR expression in PTC and ATC by investigating data obtained from the Gene Expression Omnibus (GEO) database...
December 11, 2018: Pathology Oncology Research: POR
Ying-Jian Song, Juan Tan, Xin-Huai Gao, Li-Xin Wang
Background: Lung cancer is one of the most common malignant tumors. Despite advances in lung cancer therapies, prognosis of non-small-cell lung cancer is still unfavorable. The aim of this study was to identify the prognostic value of key genes in lung tumorigenesis. Methods: Differentially expressed genes (DEGs) were screened out by GEO2R from three Gene Expression Omnibus cohorts. Common DEGs were selected for Kyoto Encyclopedia of Genes and Genomes pathway analysis and Gene Ontology enrichment analysis...
2018: Cancer Management and Research
Yujia Zheng, Yulin Liu, Songfeng Zhao, Zhetian Zheng, Chunyi Shen, Li An, Yongliang Yuan
Background: Hepatocellular carcinoma (HCC) is a major cause of cancer mortality and an increasing incidence worldwide; however, there are very few effective diagnostic approaches and prognostic biomarkers. Materials and methods: One hundred forty-nine pairs of HCC samples from Gene Expression Omnibus (GEO) were obtained to screen differentially expressed genes (DEGs) between HCC and normal samples. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, Gene ontology enrichment analyses, and protein-protein interaction network were used...
2018: Cancer Management and Research
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