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Microarray gene expression meta-analysis

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https://www.readbyqxmd.com/read/29328493/meta-analysis-of-mrna-expression-profiles-to-identify-differentially-expressed-genes-in-lung-adenocarcinoma-tissue-from-smokers-and-non-smokers
#1
Xiaona He, Cheng Zhang, Chao Shi, Quqin Lu
Compared to other types of lung cancer, lung adenocarcinoma patients with a history of smoking have a poor prognosis during the treatment of lung cancer. How lung adenocarcinoma-related genes are differentially expressed between smoker and non-smoker patients has yet to be fully elucidated. We performed a meta-analysis of four publicly available microarray datasets related to lung adenocarcinoma tissue in patients with a history of smoking using R statistical software. The top 50 differentially expressed genes (DEGs) in smoking vs...
January 8, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29286069/a-16-gene-expression-signature-to-distinguish-stage%C3%A2-i-from-stage%C3%A2-ii-lung-squamous-carcinoma
#2
Rui Wang, Yuxing Cai, Baoping Zhang, Zhengxia Wu
The present study aimed to perform screening of a gene signature for the discrimination and prognostic prediction of stage I and II lung squamous carcinoma. A microarray meta‑analysis was performed to identify differentially expressed genes (DEGs) between stage I and II lung squamous carcinoma samples in seven microarray datasets collected from the Gene Expression Omnibus database via the MetaQC and MetaDE package in R. The important DEGs were selected according to the betweenness centrality value of the protein‑protein interaction (PPI) network...
December 19, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29258768/role-of-mir-1-expression-in-clear-cell-renal-cell-carcinoma-ccrcc-a-bioinformatics-study-based-on-geo-arrayexpress-microarrays-and-tcga-database
#3
Hai-Biao Yan, Jia-Cheng Huang, You-Rong Chen, Jian-Ni Yao, Wei-Ning Cen, Jia-Yi Li, Yi-Fan Jiang, Gang Chen, Sheng-Hua Li
PURPOSE: To investigate the clinical value and potential molecular mechanisms of miR-1 in clear cell renal cell carcinoma (ccRCC). METHODS: We searched the Gene Expression Omnibus (GEO), ArrayExpress, several online publication databases and the Cancer Genome Atlas (TCGA). Continuous variable meta-analysis and diagnostic meta-analysis were conducted, both in Stata 14, to show the expression of miR-1 in ccRCC. Furthermore, we acquired the potential targets of miR-1 from datasets that transfected miR-1 into ccRCC cells, online prediction databases, differentially expressed genes from TCGA and literature...
December 2, 2017: Pathology, Research and Practice
https://www.readbyqxmd.com/read/29207133/potential-role-of-microrna%C3%A2-223%C3%A2-3p-in-the-tumorigenesis-of-hepatocellular-carcinoma-a-comprehensive-study-based-on-data-mining-and-bioinformatics
#4
Rui Zhang, Li-Jie Zhang, Mei-Ling Yang, Lan-Shan Huang, Gang Chen, Zhen-Bo Feng
The aims of the present study were to examine the potential role of microRNA‑233‑3p (miR)‑223‑3p in the tumorigenesis of hepatocellular carcinoma (HCC), and to investigate its diagnostic accuracy and potential molecular mechanisms. The expression data of miR‑223‑3p in HCC were obtained from the Gene Expression Omnibus (GEO). Data for the precursor miR‑223 were obtained from The Cancer Genome Atlas (TCGA). The diagnostic role of miR‑223‑3p was identified by the receiver operating curve (ROC), and the diagnostic value of miR‑223‑3p in HCC was calculated from qualified reports in the literature...
November 27, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29207053/diagnostic-significance-and-potential-function-of-mir-338-5p-in-hepatocellular-carcinoma-a-bioinformatics-study-with-microarray-and-rna-sequencing-data
#5
Liang Liang, Li Gao, Xiao-Ping Zou, Meng-Lan Huang, Gang Chen, Jian-Jun Li, Xiao-Yong Cai
MicroRNA (miR)-338-5p has been studied in hepatocellular carcinoma (HCC); however, the diagnostic value and molecular mechanism underlying its actions remains to be elucidated. The present study aimed to validate the diagnostic ability of miR‑338‑5p and further explore the underlying molecular mechanism. Data from eligible studies, Gene Expression Omnibus (GEO) chips and The Cancer Genome Atlas (TCGA) datasets were gathered in the data mining and the integrated meta‑analysis, to evaluate the significance of miR‑338‑5p in diagnosing HCC comprehensively...
November 21, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29203636/identification-of-potential-pathogenic-genes-associated-with-osteoporosis
#6
B Xia, Y Li, J Zhou, B Tian, L Feng
OBJECTIVES: Osteoporosis is a chronic disease. The aim of this study was to identify key genes in osteoporosis. METHODS: Microarray data sets GSE56815 and GSE56814, comprising 67 osteoporosis blood samples and 62 control blood samples, were obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified in osteoporosis using Limma package (3.2.1) and Meta-MA packages. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to identify biological functions...
December 2017: Bone & Joint Research
https://www.readbyqxmd.com/read/29197182/protection-of-macrophages-from-intracellular-pathogens-by-mir-182-5p-mimic-a-gene-expression-meta-analysis-approach
#7
David J Gregory, Igor Kramnik, Lester Kobzik
The goals of this study were to i) define which host genes are of particular importance during the interactions between macrophages and intracellular pathogens, and ii) use this knowledge to gain fresh, experimental understanding of how macrophage activities may be manipulated during host defence. We designed an in silico method for meta-analysis of microarray gene expression data, and used this to combine data from 16 different studies of cells in the monocyte-macrophage lineage infected with 7 different pathogens...
December 2, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29194095/is-nonmetastatic-cutaneous-melanoma-predictable-through-genomic-biomarkers
#8
Mattia Branca, Samuel Orso, Roberto C Molinari, Haotian Xu, Stéphane Guerrier, Yuming Zhang, Nabil Mili
Cutaneous melanoma is a highly aggressive skin cancer whose treatment and prognosis are critically affected by the presence of metastasis. In this study, we address the following issue: which gene transcripts and what kind of interactions between them can allow to predict nonmetastatic from metastatic melanomas with a high level of accuracy? We carry out a meta-analysis on the first gene expression set of the Leeds melanoma cohort, as made available online on 11 May 2016 through the ArrayExpress platform with MicroArray Gene Expression number 4725...
February 2018: Melanoma Research
https://www.readbyqxmd.com/read/29138825/utility-of-mir%C3%A2-133a%C3%A2-3p-as-a-diagnostic-indicator-for-hepatocellular-carcinoma-an-investigation-combined-with-geo-tcga-meta%C3%A2-analysis-and-bioinformatics
#9
Hai-Wei Liang, Xia Yang, Dong-Yue Wen, Li Gao, Xiang-Yu Zhang, Zhi-Hua Ye, Jie Luo, Zu-Yun Li, Yun He, Yu-Yan Pang, Gang Chen
Increasing evidence has demonstrated that microRNA (miR)‑133a‑3p is an important regulator of hepatocellular carcinoma (HCC). In the present study, the diagnostic role of miR‑133a‑3p in HCC, and the potential functional pathways, were both explored based on publicly available data. Eligible microarray datasets were collected from NCBI Gene Expression Omnibus (GEO) database and ArrayExpress database. The data related to HCC and matched adjacent normal tissues were also downloaded from The Cancer Genome Atlas (TCGA)...
November 14, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29132337/gene-expression-signatures-of-neuroendocrine-prostate-cancer-and-primary-small-cell-prostatic-carcinoma
#10
Harrison K Tsai, Jonathan Lehrer, Mohammed Alshalalfa, Nicholas Erho, Elai Davicioni, Tamara L Lotan
BACKGROUND: Neuroendocrine prostate cancer (NEPC) may be rising in prevalence as patients with advanced prostate cancer potentially develop resistance to contemporary anti-androgen treatment through a neuroendocrine phenotype. While prior studies comparing NEPC and prostatic adenocarcinoma have identified important candidates for targeted therapy, most have relied on few NEPC patients due to disease rarity, resulting in thousands of differentially expressed genes collectively and offering an opportunity for meta-analysis...
November 13, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29132026/integrated-omics-analysis-of-root-preferred-genes-across-diverse-rice-varieties-including-japonica-and-indica-cultivars
#11
Sunok Moon, Anil Kumar Nalini Chandran, Yun-Shil Gho, Sun-A Park, Sung-Ryul Kim, Yo-Han Yoo, Ki-Hong Jung
Plant root systems play essential roles in developmental processes, such as the absorption of water and inorganic nutrients, and structural support. Gene expression is affected by growth conditions and the genetic background of plants. To identify highly conserved root-preferred genes in rice across diverse growth conditions and varieties, we used two independent meta-anatomical expression profiles based on a large collection of Affymetrix and Agilent 44K microarray data sets available for public use. We then identified 684 loci with root-preferred expression, which were validated with in silico analysis using both meta-expression profiles...
October 26, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/29115927/transcriptomic-responses-to-wounding-meta-analysis-of-gene-expression-microarray-data
#12
Piotr Andrzej Sass, Michał Dąbrowski, Agata Charzyńska, Paweł Sachadyn
BACKGROUND: A vast amount of microarray data on transcriptomic response to injury has been collected so far. We designed the analysis in order to identify the genes displaying significant changes in expression after wounding in different organisms and tissues. This meta-analysis is the first study to compare gene expression profiles in response to wounding in as different tissues as heart, liver, skin, bones, and spinal cord, and species, including rat, mouse and human. RESULTS: We collected available microarray transcriptomic profiles obtained from different tissue injury experiments and selected the genes showing a minimum twofold change in expression in response to wounding in prevailing number of experiments for each of five wound healing stages we distinguished: haemostasis & early inflammation, inflammation, early repair, late repair and remodelling...
November 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29108269/microarray-analyses-reveal-genes-related-to-progression-and-prognosis-of-esophageal-squamous-cell-carcinoma
#13
Mao Qixing, Dong Gaochao, Xia Wenjie, Wang Anpeng, Chen Bing, Ma Weidong, Xu Lin, Jiang Feng
Esophageal squamous cell carcinoma is a high morbidity and mortality cancer in China. Here are few biomarkers and therapeutic targets. Our study was aimed to identify candidate genes correlated to ESCC. Oncomine, The Cancer Genome Atlas, Gene Expression Omnibus were retrieved for eligible ESCC data. Deregulated genes were identified by meta-analysis and validated by an independent dataset. Survival analyses and bioinformatics analyses were used to explore potential mechanisms. Copy number variant analyses identified upstream mechanisms of candidate genes...
October 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/29066959/gene-network-construction-from-microarray-data-identifies-a-key-network-module-and-several-candidate-hub-genes-in-age-associated-spatial-learning-impairment
#14
Raihan Uddin, Shiva M Singh
As humans age many suffer from a decrease in normal brain functions including spatial learning impairments. This study aimed to better understand the molecular mechanisms in age-associated spatial learning impairment (ASLI). We used a mathematical modeling approach implemented in Weighted Gene Co-expression Network Analysis (WGCNA) to create and compare gene network models of young (learning unimpaired) and aged (predominantly learning impaired) brains from a set of exploratory datasets in rats in the context of ASLI...
2017: Frontiers in Systems Neuroscience
https://www.readbyqxmd.com/read/29060744/identification-of-differentially-expressed-genes-through-a-meta-analysis-approach-for-oral-cancer-classification
#15
Konstantina Kourou, Costas Papaloukas, Dimitrios I Fotiadis
We propose a meta-analysis scheme for identifying differentially expressed genes in Oral Squamous Cell Carcinoma (OSCC) from different microarray studies. We detect a subset of relevant features and further classify samples under two experimental conditions (i.e healthy and cancer samples) for better patient stratification. A well-established meta-analysis method is adopted and gene expression data sets are derived from a public functional genomics data repository. Our primary aim is the accurate identification of up- and down-regulated genes in order to extract valuable biological information concerning the changes in expression between healthy and cancer samples...
July 2017: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/29024942/loss-of-myosin-vb-in-colorectal-cancer-is-a-strong-prognostic-factor-for-disease-recurrence
#16
Elisabeth Letellier, Martine Schmitz, Aurélien Ginolhac, Fabien Rodriguez, Pit Ullmann, Komal Qureshi-Baig, Sonia Frasquilho, Laurent Antunes, Serge Haan
BACKGROUND: Selecting the most beneficial treatment regimens for colorectal cancer (CRC) patients remains challenging due to a lack of prognostic markers. Members of the Myosin family, proteins recognised to have a major role in trafficking and polarisation of cells, have recently been reported to be closely associated with several types of cancer and might thus serve as potential prognostic markers in the context of CRC. METHODS: We used a previously established meta-analysis of publicly available gene expression data to analyse the expression of different members of the Myosin V family, namely MYO5A, 5B, and 5C, in CRC...
October 12, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28973476/meta-analysis-of-transcriptomic-datasets-identifies-genes-enriched-in-the-mammalian-circadian-pacemaker
#17
Laurence A Brown, John Williams, Lewis Taylor, Ross J Thomson, Patrick M Nolan, Russell G Foster, Stuart N Peirson
The master circadian pacemaker in mammals is located in the suprachiasmatic nuclei (SCN) which regulate physiology and behaviour, as well as coordinating peripheral clocks throughout the body. Investigating the function of the SCN has often focused on the identification of rhythmically expressed genes. However, not all genes critical for SCN function are rhythmically expressed. An alternative strategy is to characterize those genes that are selectively enriched in the SCN. Here, we examined the transcriptome of the SCN and whole brain (WB) of mice using meta-analysis of publicly deposited data across a range of microarray platforms and RNA-Seq data...
September 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28924174/gene-expression-meta-analysis-in-diffuse-low-grade-glioma-and-the-corresponding-histological-subtypes
#18
Siqi Wang, Feng Jin, Wenliang Fan, Fang Liu, Yan Zou, Xuehan Hu, Haibo Xu, Ping Han
Diffuse low-grade glioma (DLGG) is a well-differentiated, slow-growing tumour with an inherent tendency to progress to high-grade glioma. The potential roles of genetic alterations in DLGG development have not yet been fully delineated. Therefore, the current study performed an integrated gene expression meta-analysis of eight independent, publicly available microarray datasets including 291 DLGGs and 83 non-glioma (NG) samples to identify gene expression signatures associated with DLGG. Using INMEX, 708 differentially expressed genes (DEGs) (385 upregulated and 323 downregulated genes) were identified in DLGG compared to NG...
September 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28903366/systematic-analysis-of-coronary-artery-disease-datasets-revealed-the-potential-biomarker-and-treatment-target
#19
Yan Shi, Sijin Yang, Man Luo, Wei-Dong Zhang, Zun-Ping Ke
Coronary artery disease caused about 1 of every 7 deaths in the United States and early prevention was potential to decrease the incidence and mortality. We aimed to figure the genes involving in the coronary artery disease using meta-anlaysis. Five datasets of coronary heart disease from GEO series were retrieved and data preprocessing and quality control were carried out. Moderated t-test was used to decide the differentially expressed genes for a single dataset. And the combined p-value using systematic-analysis methods were conducted using MetaDE...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28899396/transcriptomic-meta-analysis-identifies-gene-expression-characteristics-in-various-samples-of-hiv-infected-patients-with-nonprogressive-disease
#20
Le-Le Zhang, Zi-Ning Zhang, Xian Wu, Yong-Jun Jiang, Ya-Jing Fu, Hong Shang
BACKGROUND: A small proportion of HIV-infected patients remain clinically and/or immunologically stable for years, including elite controllers (ECs) who have undetectable viremia (<50 copies/ml) and long-term nonprogressors (LTNPs) who maintain normal CD4(+) T cell counts for prolonged periods (>10 years). However, the mechanism of nonprogression needs to be further resolved. In this study, a transcriptome meta-analysis was performed on nonprogressor and progressor microarray data to identify differential transcriptome pathways and potential biomarkers...
September 12, 2017: Journal of Translational Medicine
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