Read by QxMD icon Read

TCGA meta

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...
November 21, 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...
October 31, 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
Tongwu Zhang, Jiyeon Choi, Michael A Kovacs, Jianxin Shi, Mai Xu, Alisa M Goldstein, Adam J Trower, D Timothy Bishop, Mark M Iles, David L Duffy, Stuart MacGregor, Laufey T Amundadottir, Matthew H Law, Stacie K Loftus, William J Pavan, Kevin M Brown
Most expression quantitative trait locus (eQTL) studies to date have been performed in heterogeneous tissues as opposed to specific cell types. To better understand the cell-type-specific regulatory landscape of human melanocytes, which give rise to melanoma but account for <5% of typical human skin biopsies, we performed an eQTL analysis in primary melanocyte cultures from 106 newborn males. We identified 597,335 cis -eQTL SNPs prior to linkage disequilibrium (LD) pruning and 4997 eGenes (FDR < 0.05)...
November 2018: Genome Research
Jianan Chen, Yan Yu, Chen Xue, Xiaolong Chen, Guangying Cui, Juan Li, Kongfei Li, Zhigang Ren, Ranran Sun
BACKGROUND: microRNA-139 (miR-139) is dysregulated in various types of tumors and plays a key role in carcinogenesis. miR-139 may be used as a diagnostic and prognostic biomarker of cancers. However, the data from the literature are not consistent. The present study aimed to verify the prognostic and diagnostic values of miR-139 in solid tumors. DATA SOURCES: PubMed, Web of Science and Embase databases were searched and publications from January 2011 to August 2017 were included...
September 26, 2018: Hepatobiliary & Pancreatic Diseases International: HBPD INT
Peixin Dong, Ying Xiong, Junming Yue, Sharon J B Hanley, Hidemichi Watari
Although the role of PD-L1 in suppressing the anti-tumor immune response is extensively documented, recent discoveries indicate a distinct tumor-intrinsic role for PD-L1 in modulating epithelial-to-mesenchymal transition (EMT), cancer stem cell (CSC)-like phenotype, metastasis and resistance to therapy. In this review, we will focus on the newly discovered functions of PD-L1 in the regulation of cancer development, describe underlying molecular mechanisms responsible for PD-L1 upregulation and discuss current insights into novel components of PD-L1 signaling...
2018: Frontiers in Oncology
Yuexiong Yi, Yanyan Liu, Wanrong Wu, Kejia Wu, Wei Zhang
This study aims to investigate the role of miR-106b-5p in cervical cancer by performing a comprehensive analysis on its expression and identifying its putative molecular targets and pathways based on The Cancer Genome Atlas (TCGA) dataset, Gene Expression Omnibus (GEO) dataset, and literature review. Significant upregulation of miR-106b-5p in cervical cancer is confirmed by meta-analysis with the data from TCGA, GEO, and literature. Moreover, the expression of miR-106b-5p is significantly correlated with the number of metastatic lymph nodes...
2018: Cell Death Discovery
Sara S Oltra, Maria Peña-Chilet, Victoria Vidal-Tomas, Kirsty Flower, María Teresa Martinez, Elisa Alonso, Octavio Burgues, Ana Lluch, James M Flanagan, Gloria Ribas
MiRNAs are part of the epigenetic machinery, and are also epigenetically modified by DNA methylation. MiRNAs regulate expression of different genes, so any alteration in their methylation status may affect their expression. We aimed to identify methylation differences in miRNA encoding genes in breast cancer affecting women under 35 years old (BCVY), in order to identify potential biomarkers in these patients. In Illumina Infinium MethylationEPIC BeadChip samples (metEPICVal), we analysed the methylation of 9,961 CpG site regulators of miRNA-encoding genes present in the array...
September 26, 2018: Scientific Reports
Wei-Ning Cen, Jin-Shu Pang, Jia-Cheng Huang, Jia-Yin Hou, Wen-Guang Bao, Rong-Quan He, Jie Ma, Zhi-Gang Peng, Xiao-Hua Hu, Fu-Chao Ma
BACKGROUND: The specific expression level and clinical significance of miR-375-3p in HNSCC had not been fully stated, as well as the overall biological function and molecular mechanisms. Therefore, we purpose to carry out a comprehensive meta-analysis to further explore the clinical significance and potential function mechanism of miR-375-3p in HNSCC. METHODS: HNSCC-related data was gained from Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA), and peer-reviewed journals...
November 2018: Pathology, Research and Practice
Kumardeep Chaudhary, Olivier B Poirion, Liangqun Lu, Sijia Huang, Travers Ching, Lana X Garmire
Although driver genes in hepatocellular carcinoma (HCC) have been investigated in various previous genetic studies, prevalence of key driver genes among heterogeneous populations is unknown. Moreover, the phenotypic associations of these driver genes are poorly understood. This report aims to reveal the phenotypic impacts of a group of consensus driver genes in HCC. We used MutSigCV and OncodriveFM modules implemented in the IntOGen pipeline to identify consensus driver genes across six HCC cohorts comprising 1,494 samples in total...
September 21, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Kashif Rafiq Zahid, Shiming Han, Fuling Zhou, Umar Raza
BACKGROUND: Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-associated deaths worldwide. Although recent studies have proposed different biomarkers for HCC progression and therapy resistance, a better understanding of the molecular mechanisms underlying HCC progression and recurrence, as well as the identification of molecular markers with a higher diagnostic accuracy, are necessary for the development of more effective clinical management strategies. Here, we aimed to identify novel players in HCC progression...
September 20, 2018: Cellular Oncology (Dordrecht)
Jie Ruan, Peipei Xu, Wei Fan, Qiaoling Deng, Mingxia Yu
Epigenetic alteration of P16INK4a is conventionally thought to induce the initiation of carcinoma. However, the role of P16INK4a methylation in ovarian cancer still remains controversial. Therefore, we performed a meta-analysis to further elucidate the relationship between P16INK4a promoter methylation and ovarian cancer. A total of 24 studies, including 20 on risk, 10 on clinicopathological features, and 3 on prognosis, were included in our meta-analysis. Our results indicated that the frequency of P16INK4a methylation in cancer tissues was significantly higher than normal tissues and low malignant potential tumor tissues (odds ratio [OR] =5...
2018: Cancer Management and Research
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"