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TCGA meta

Xiao-Zhu Zhong, Yun Deng, Gang Chen, Hong Yang
To investigate the prospective roles and the clinicopathological application of microRNA-21-5p (miR-21-5p) in hepatocellular carcinoma (HCC), the present review is based on 24 studies and bioinformatics investigation. Firstly, HCC-associated miR-21-5p data were aggregated from literature databases and two public genomic data repositories, including the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). Potential target genes of miR-21-5p in HCC were identified using TCGA and GEO, Natural Language Processing and 14 online software packages...
January 2019: Oncology Letters
Jie-Yu Liu, Xing-Xuan Dong, Jia-Nan Lu, Yue Zhang, Kai-Fan Liu, Ling-Feng Liu, Qing-Zhi E, Xiao-Jing Lu, Jie-Yun Yin, Yue-Ping Shen
It was recently suggested that growth differentiation factor-15 (GDF-15) is associated with gastric cancer (GC) carcinogenesis. However, the diagnostic potential of GDF-15 for GC remains unclear. To address this issue, we obtained RNA sequencing and microarray data from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases, and searched PubMed, Google Scholar and Web of Science for relevant literature. We then used STATA to perform a meta-analysis. In total, reports of 253 GC patients and 112 healthy controls who contributed peripheral blood samples were taken from the four literature sources, while information on 754 GC tumor and 263 gastric normal tissues was drawn from TCGA and seven GEO datasets...
January 2019: FEBS Open Bio
He-San Luo, De-Hua Wu
Accumulating evidence has demonstrated that aberrantly expressed miRNAs in cancer tissues regulated various cellular processes related to carcinogenesis. The present study aimed to identify the differentially expressed miRNAs between esophageal squamous cell cancer (ESCC) and adjacent normal esophageal tissue (ANET). In our present study, we identified 129 differentially expressed miRNAs between ESCC and ANET by analyzing high-throughput miRNA data downloaded from TCGA database. After investigating the prognostic value of the 129 differential expressed miRNAs, eight miRNAs were found to be associated with prognosis of patients with ESCC...
January 7, 2019: Pathology, Research and Practice
Yuanyuan Wang, Yang Han, Zhongliang Guo, Yanan Yang, Tao Ren
The transcription co-factor TAZ plays critical roles in the regulation of human carcinogenesis. However, the pathological role for TAZ in lung cancer has remained incompletely understood. TAZ expression was examined by immunohistochemistry for 163 NSCLC tissues. TAZ expression was also examined by western blotting for 20 frozen paired NSCLC and adjacent normal lung tissues. We report that TAZ is overexpressed in non-small cell lung cancer (NSCLC) tissues and correlates with shorter patient survival. Intriguingly, we find that TAZ is overexpressed primarily in lung squamous cell carcinomas (LUSC) but not lung adenocarcinomas (LUAD) compared to normal lung tissues, and that the expression levels of TAZ are significantly higher in LUSC than LUAD...
January 10, 2019: Biochemical and Biophysical Research Communications
Farhad Ghasemi, Stephenie D Prokopec, Danielle MacNeil, Neil Mundi, Steven F Gameiro, Christopher Howlett, William Stecho, Paul Plantinga, Nicole Pinto, Kara M Ruicci, Mohammed Imran Khan, John Yoo, Kevin Fung, Axel Sahovaler, David A Palma, Eric Winquist, Joe S Mymryk, John W Barrett, Paul C Boutros, Anthony C Nichols
Smoking has historically been recognized as a negative prognostic factor in head and neck squamous cell carcinoma (HNSCC). This study aimed to assess the mutational differences between heavy smokers (>20 pack years) and never smokers among the HNSCC patients within The Cancer Genome Atlas (TCGA). Single nucleotide variation and copy number aberration differences between heavy smokers and never smokers were compared within human papillomavirus-positive (HPV-positive) (n = 67) and HPV-negative (n = 431) TCGA cohorts with HNSCC, and the impact of these mutations on survival were assessed...
January 10, 2019: JCI Insight
Yu Zhang, Li-Jie Zhang, Yi-Wu Dang, Sheng-Hua Li, Hai-Biao Yan, Gang Chen
Background: Overexpression of metadherin/astrocyte elevated gene-1 (MTDH/AEG-1) has been implicated in various cancers. However, the clinical significance and the potential biological functions of MTDH/AEG-1 in bladder urothelial carcinoma (BUC) are not established. Methods: In this study, the expression of MTDH/AEG-1in BUC was measured using the Cancer Genome Atlas (TCGA) database and immunohistochemistry, together with a meta-analysis, to investigate the expression and diagnostic value of MTDH/AEG-1...
2018: Cancer Management and Research
Kai-Teng Cai, An-Gui Liu, Ze-Feng Wang, Hang-Wei Jiang, Jing-Jing Zeng, Rong-Quan He, Jie Ma, Gang Chen, Jin-Cai Zhong
Breast cancer (BC) is the most common cancer among women worldwide. However, there is insufficient research that focuses on the expression and molecular mechanisms of microRNA (miR)‑204‑5p in BC. In the current study, data were downloaded from the Cancer Genome Atlas (TCGA), the Gene Expression Omnibus (GEO) and the University of California Santa Cruz (UCSC) Xena databases. They were then used to undertake a meta‑analysis that leveraged the standard mean difference (SMD) and summarized receiver operating characteristic (sROC) to evaluate the expression of the precursor miR‑204 and mature miR‑204‑5p in BC...
December 14, 2018: Molecular Medicine Reports
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
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
Wenwu He, Linxin Chen, Kun Yuan, Qiuxi Zhou, Lin Peng, Yongtao Han
Background: Esophageal squamous cell carcinoma (ESCC) is a common malignancy with high mortality. Because of the lack of clarity in the relevant genes and mechanisms involved, and the current difficulty for oncotherapy in providing therapeutic solutions, there is an urgent need to study this matter. While gene probe studies have been used to select the most virulent genes and pathways, paucity of case controls during gene screening and lack of conclusive results to expound the etiology and pathogenesis of the disease, have reduced study reliability...
October 2018: Journal of Thoracic Disease
Jia-Yin Hou, Hua-Yu Wu, Rong-Quan He, Peng Lin, Yi-Wu Dang, Gang Chen
Liver cancer is one of the few tumors with a steadily increasing morbidity and mortality; hepatocellular carcinoma (HCC) is the most common type of primary liver cancer. We combined the expression profiles of Chaperonin Containing T-complex 1 Subunit 3 (CCT3) in HCC tissues based on microarray and RNA-sequencing data. The CCT3 expression levels were extracted and examined based on 421 samples from The Cancer Genome Atlas (TCGA) (HCC, n = 371; non-HCC, n = 50) and 3851 samples from 31 microarray or RNA-sequencing datasets (HCC, n = 1975; non-tumor = 1876)...
November 10, 2018: Pathology, Research and Practice
Fuhong Zhang, Xiaowan Chen, Kehu Xi, Zhiqiang Qiu, Youhu Wang, Yan Gui, Yun Hou, Kangbing Chen, Xiaobing Zhang
Background and aims: HOXD antisense growth-associated long noncoding RNA (HOXD-AS1) was reported to be upregulated in various cancers, such as gastric cancer, hepatocellular carcinoma, colorectal cancer, and glioma. Here, we conducted a meta-analysis and The Cancer Genome Atlas data review to investigate the clinicopathologic and prognostic value of HOXD-AS1 in patients with malignant tumors. Materials and methods: Systematic literatures were searched from PubMed, Medline, Cochrane Library, Web of Science, EMBASE database, Ovid, Chinese CNKI, and the Chinese WanFang database...
2018: OncoTargets and Therapy
Zhu Hongzhen, Liu Yanyu, Liu Xuexiang, Dai Meiyu, Chen Xiaoli, Gao Yun, Chen Jingfan, Dai Shengming
BACKGROUND: Accumulating evidence has confirmed that CRNDE is significantly expressed in various cancers, suggesting that it may be a potential biomarker for cancer. However, its diagnostic and prognostic values of CRNDE in cancer are not completely clear. Therefore, we conduct a comprehensive study on CRNDE in cancer. MATERIALS AND METHODS: CRNDE expression data were downloaded from The Cancer Genome Atlas (TCGA). Microarray data were derived from the Gene Expression Omnibus (GEO) database to validate its differential expression...
November 12, 2018: Pathology, Research and Practice
Zi-Qing Yang, Chang-An Wu, Yi-Xing Cheng
BACKGROUND: The role of microRNA-133a (miR-133a) in non-small cell lung cancers (NSCLCs) is controversial. Thus, we conducted a comprehensive study based on meta-analysis and The Cancer Genome Atlas (TCGA) database. METHODS: Publications were searched in both English and Chinese databases, and meta-analysis was performed using Stata 12.0. The clinical value of miR-133a in NSCLC was investigated by collecting and calculating data from the TCGA database, and the statistical analysis was performed in R 3...
2018: Oncology Research and Treatment
Linhai Zhu, Yiqing Wang, Jing He, Jie Tang, Wang Lv, Jian Hu
Aims: SQSTM1/p62, as an autophagy marker, is a key molecule involved in the autophagy process. Recent studies have demonstrated that p62 has a close relationship with tumorigenesis and progression, but the impact of p62 on patients' survival has not been comprehensively understood. Therefore, we conducted this study to assess the expression level of p62 in tumor cells and the prognostic role of p62 expression in various malignant tumors. Methods: We searched PubMed, PubMed Central (PMC), Embase, Ovid and Web of Science databases and identified 30 eligible studies containing 14,072 patients to include in the meta-analysis...
2018: Journal of Cancer
Zhang Kaishang, Pan Xue, Zheng Shaozhong, Fan Yingying, Zhang Yan, Sun Chanjun, Li Zhenzhen, Li Xiangnan
AIM: Twinfilin-1 (TWF1) has been implicated in cell motility, invasion and migration. However, its exact role in lung cancer progression is still unclear. In the present study, we explored clinical and prognostic relevance of Twinfilin-1 (TWF1) levels for non-small cell lung carcinoma (NSCLC). MAIN METHODS: The Cancer Genome Atlas (TCGA) dataset was analyzed for possible association between TWF1 expressions in NSCLC tissues and patient prognosis. The meta-analysis data was validated in our clinical study through techniques of immunoblotting, expression analysis and immunohistochemistry...
December 15, 2018: Life Sciences
Yasemin Oztemur Islakoglu, Senem Noyan, Alp Aydos, Bala Gur Dedeoglu
Breast cancer is one of the leading causes of morbidity and mortality that is in need of novel diagnostics and therapeutics. Meta-analysis of microarray data offers promise to combine studies and provide more robust results. We report here a molecular classification of pathological subtypes (estrogen receptor [ER], progesterone receptor [PR], and Human Epidermal Growth Factor Receptor 2 [HER2]) of breast cancers with microRNA (miRNA)-dependent signatures. A ranking-based meta-analysis approach was applied to eight independent microarray data sets and meta-miRNA lists were obtained that are specific to each breast cancer subtype...
November 2018: Omics: a Journal of Integrative Biology
Mu Liu, Yu-Lu Qiu, Tong Jin, Yin Zhou, Zhi-Yuan Mao, Yong-Jie Zhang
Aim: Anaplastic thyroid carcinoma (ATC) is the most lethal thyroid malignancy. Identification of novel drug targets is urgently needed. Materials & Methods: We re-analyzed several GEO datasets by systematic retrieval and data merging. Differentially expressed genes (DEGs) were filtered out. We also performed pathway enrichment analysis to interpret the data. We predicted key genes based on protein-protein interaction networks, weighted gene co-expression network analysis and genes' cancer/testis expression pattern...
2018: PeerJ
Xianxiong Ma, Ruikang Tao, Lei Li, Hengyu Chen, Zongtao Liu, Jie Bai, Xiaoming Shuai, Chuanqing Wu, Kaixiong Tao
miRNA‑gene axes have been reported to serve an important role in the carcinogenesis of pancreatic cancer (PC). The aim of the present study was to systematically identity the microRNA signature and hub molecules, as well as hub miRNA‑gene axes, and to explore the potential biomarkers and mechanisms associated with the carcinogenesis of PC. Eleven microRNA profile datasets were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) and ArrayExpress databases, and a meta‑analysis was performed to identify the differentially expressed miRNAs (DEMs) between tumor tissue and normal tissue...
October 24, 2018: Oncology Reports
Jialin Meng, Xinyao Fan, Meng Zhang, Zongyao Hao, Chaozhao Liang
BACKGROUND: Currently, several studies have demonstrated that PRKAA1 polymorphisms conduce to the development of cancer. PRKAA1 gene encodes the AMP-activated protein kinase summit-α1, and plays an important role in cell metabolism. Thus, we performed a systematic review and meta-analysis of all enrolled eligible case-control studies to obtain a precise correlation between PRKAA1 polymorphism and cancer susceptibility. METHODS: Extensive retrieve was performed in Web of Science, Google Scholar, PubMed, EMbase, CNKI and Wanfang databases up to August 26, 2018...
October 19, 2018: BMC Medical Genetics
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