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Microarray gene expression meta-analysis

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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/28796378/functional-genetic-variants-of-xrcc4-and-ercc1-predict-survival-of-gastric-cancer-patients-treated-with-chemotherapy-by-regulating-the-gene-expression
#13
Lei Cheng, Lixin Qiu, Mengyun Wang, Ruoxin Zhang, Menghong Sun, Xiaodong Zhu, Yanong Wang, Qingyi Wei
DNA repair protects genomic integrity and may modulate chemotherapy efficacy. Few large-scale studies have evaluated predictive roles of genetic variants of DNA repair genes in survival of Chinese gastric cancer (GCa) patients treated with chemotherapy. Here, we assessed the roles of 35 single nucleotide polymorphisms (SNPs) in DNA repair genes in survival of 1002 GCa patients, of whom 694 received chemotherapy and 308 did not. Among patients receiving chemotherapy, the ERCC1 rs2298881A allele was associated with a better survival [hazards ratio (HR) = 0...
August 10, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28782484/gene-expression-meta-analysis-of-potential-metastatic-breast-cancer-markers
#14
R Bell, R Barraclough, O Vasieva
BACKGROUND: Breast cancer metastasis is a highly prevalent cause of death for European females. DNA microarray analysis has established that primary tumors, which remain localized, differ in gene expression from those that metastasize. Crossanalysis of these studies allow to revile the differences that may be used as predictive in the disease prognosis and therapy. OBJECTIVE: The aim of the project was to validate suggested prognostic and therapeutic markers using meta-analysis of data on gene expression in metastatic and primary breast cancer tumors...
2017: Current Molecular Medicine
https://www.readbyqxmd.com/read/28732597/pattern-of-gene-expression-in-different-stages-of-schizophrenia-down-regulation-of-nptx2-gene-revealed-by-a-meta-analysis-of-microarray-datasets
#15
Mirko Manchia, Ignazio S Piras, Matthew J Huentelman, Federica Pinna, Clement C Zai, James L Kennedy, Bernardo Carpiniello
Schizophrenia (SCZ) is a severe psychiatric disorder with a genetic susceptibility. Alterations in neurochemical signaling, as well as changes in brain structure and function, manifest during the course of SCZ and are likely causative of the symptoms shown by affected individuals. However, little is known about the timing of these changes, particularly in the pre-morbid and prodromal phases of SCZ. Here, we performed a gene-based and pathway-based meta-analysis of 5 microarray datasets from human induced pluripotent stem cells (hiPSCs)-derived neurons and post-mortem brain tissue from SCZ and healthy controls (HC), with the underlying assumption they might represent the neurobiological make-up of SCZ in the pre-morbid and chronic stages of illness, respectively...
October 2017: European Neuropsychopharmacology: the Journal of the European College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28719625/differences-of-immune-disorders-between-alzheimer-s-disease-and-breast-cancer-based-on-transcriptional-regulation
#16
COMPARATIVE STUDY
Wei Kong, Xiaoyang Mou, Jin Deng, Benteng Di, Ruxing Zhong, Shuaiqun Wang, Yang Yang, Weiming Zeng
Although chronic inflammation and immune disorders are of great importance to the pathogenesis of both dementia and cancer, the pathophysiological mechanisms are not clearly understood. In recent years, growing epidemiological evidence and meta-analysis data suggest an inverse association between Alzheimer's disease (AD), which is the most common form of dementia, and cancer. It has been revealed that some common genes and biological processes play opposite roles in AD and cancer; however, the biological immune mechanism for the inverse association is not clearly defined...
2017: PloS One
https://www.readbyqxmd.com/read/28713914/systematic-identification-of-human-housekeeping-genes-possibly-useful-as-references-in-gene-expression-studies
#17
Maria Caracausi, Allison Piovesan, Francesca Antonaros, Pierluigi Strippoli, Lorenza Vitale, Maria Chiara Pelleri
The ideal reference, or control, gene for the study of gene expression in a given organism should be expressed at a medium‑high level for easy detection, should be expressed at a constant/stable level throughout different cell types and within the same cell type undergoing different treatments, and should maintain these features through as many different tissues of the organism. From a biological point of view, these theoretical requirements of an ideal reference gene appear to be best suited to housekeeping (HK) genes...
September 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28659725/system-level-meta-analysis-of-microarray-datasets-for-elucidation-of-diabetes-mellitus-pathobiology
#18
Aditya Saxena, Kumar Sachin, Ashok Kumar Bhatia
BACKGROUND: Type 2 diabetes (T2D) is a common multi-factorial disease that is primarily ac-counted to ineffective insulin action in lowering blood glucose level and later escalates to impaired insu-lin secretion by pancreatic β cells. Deregulation in insulin signaling to its target organs is attributed to this disease phenotype. Various genome-wide microarray studies from multiple insulin responsive tis-sues have been conducted in past but due to inherent noise in microarray data and heterogeneity in dis-ease etiology; reproduction of prioritized pathways/genes is very low across various studies...
June 2017: Current Genomics
https://www.readbyqxmd.com/read/28659634/dach1-suppresses-breast-cancer-as-a-negative-regulator-of-cd44
#19
Hanxiao Xu, Shengnan Yu, Xun Yuan, Jing Xiong, Dong Kuang, Richard G Pestell, Kongming Wu
Dachshund homolog 1 (DACH1), a key cell fate determination factor, contributes to tumorigenesis, invasion, metastasis of human breast neoplasm. However, the exact molecular mechanisms for the anti-tumor roles of DACH1 in breast carcinoma are still lack of extensive understanding. Herein, we utilized immunohistochemistry (IHC) staining and public microarray data analysis showing that DACH1 was higher in normal breast, low-grade and luminal-type cancer in comparison with breast carcinoma, high-grade and basal-like tumors respectively...
June 28, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28651018/meta-analysis-of-mirna-expression-profiles-for-prostate-cancer-recurrence-following-radical-prostatectomy
#20
Elnaz Pashaei, Elham Pashaei, Maryam Ahmady, Mustafa Ozen, Nizamettin Aydin
BACKGROUND: Prostate cancer (PCa) is a leading reason of death in men and the most diagnosed malignancies in the western countries at the present time. After radical prostatectomy (RP), nearly 30% of men develop clinical recurrence with high serum prostate-specific antigen levels. An important challenge in PCa research is to identify effective predictors of tumor recurrence. The molecular alterations in microRNAs are associated with PCa initiation and progression. Several miRNA microarray studies have been conducted in recurrence PCa, but the results vary among different studies...
2017: PloS One
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