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Microarray gene expression meta-analysis

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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
#1
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...
July 18, 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
#2
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
#3
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
#4
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
#5
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
#6
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
https://www.readbyqxmd.com/read/28648455/kinetic-modelling-and-meta-analysis-of-the-b-subtilis-siga-regulatory-network-during-spore-germination-and-outgrowth
#7
O Ramaniuk, M Černý, L Krásný, J Vohradský
This study describes the meta-analysis and kinetic modelling of gene expression control by sigma factor SigA of Bacillus subtilis during germination and outgrowth based on microarray data from 14 time points. The analysis computationally models the direct interaction among SigA, SigA-controlled sigma factor genes (sigM, sigH, sigD, sigX), and their target genes. Of the >800 known genes in the SigA regulon, as extracted from databases, 311 genes were analysed, and 190 were confirmed by the kinetic model as being controlled by SigA...
June 22, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28637422/optimal-alpha-reduces-error-rates-in-gene-expression-studies-a-meta-analysis-approach
#8
J F Mudge, C J Martyniuk, J E Houlahan
BACKGROUND: Transcriptomic approaches (microarray and RNA-seq) have been a tremendous advance for molecular science in all disciplines, but they have made interpretation of hypothesis testing more difficult because of the large number of comparisons that are done within an experiment. The result has been a proliferation of techniques aimed at solving the multiple comparisons problem, techniques that have focused primarily on minimizing Type I error with little or no concern about concomitant increases in Type II errors...
June 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28629367/african-american-esophageal-squamous-cell-carcinoma-expression-profile-reveals-dysregulation-of-stress-response-and-detox-networks
#9
Hayriye Verda Erkizan, Kory Johnson, Svetlana Ghimbovschi, Deepa Karkera, Gregory Trachiotis, Houtan Adib, Eric P Hoffman, Robert G Wadleigh
BACKGROUND: Esophageal carcinoma is the third most common gastrointestinal malignancy worldwide and is largely unresponsive to therapy. African-Americans have an increased risk for esophageal squamous cell carcinoma (ESCC), the subtype that shows marked variation in geographic frequency. The molecular architecture of African-American ESCC is still poorly understood. It is unclear why African-American ESCC is more aggressive and the survival rate in these patients is worse than those of other ethnic groups...
June 19, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28617547/mastl-is-a-potential-poor-prognostic-indicator-in-er-breast-cancer
#10
B-Z Zhuge, B-R Du, X-L Meng, Y-Q Zhang
OBJECTIVE: In this study, we aimed to explore prognostic value of MASTL (microtubule-associated serine/threonine kinase-like) in breast cancer patients on the basis of ER status and molecular subtypes. MATERIALS AND METHODS: The raw microarray data (GDS5666) of 4T1 derived bone-aggressive explant and primary tumor explant were reanalyzed to identify the dysregulated genes. To pool previous annotated genomic data that assessed the association between MASTL expression and metastatic relapse (MR) risk, MR-free survival, any event (AE, defined as any relapse or death) risk, and AE-free survival in breast cancer patients, a meta-analysis was performed by bc-GenExMiner 4...
May 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28574441/gene-expression-mrna-markers-for-differentiating-between-malignant-and-benign-follicular-thyroid-tumours
#11
Bartosz Wojtas, Aleksandra Pfeifer, Malgorzata Oczko-Wojciechowska, Jolanta Krajewska, Agnieszka Czarniecka, Aleksandra Kukulska, Markus Eszlinger, Thomas Musholt, Tomasz Stokowy, Michal Swierniak, Ewa Stobiecka, Ewa Chmielik, Dagmara Rusinek, Tomasz Tyszkiewicz, Monika Halczok, Steffen Hauptmann, Dariusz Lange, Michal Jarzab, Ralf Paschke, Barbara Jarzab
Distinguishing between follicular thyroid cancer (FTC) and follicular thyroid adenoma (FTA) constitutes a long-standing diagnostic problem resulting in equivocal histopathological diagnoses. There is therefore a need for additional molecular markers. To identify molecular differences between FTC and FTA, we analyzed the gene expression microarray data of 52 follicular neoplasms. We also performed a meta-analysis involving 14 studies employing high throughput methods (365 follicular neoplasms analyzed). Based on these two analyses, we selected 18 genes differentially expressed between FTA and FTC...
June 2, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28541721/a-joint-bayesian-model-for-integrating-microarray-and-rna-sequencing-transcriptomic-data
#12
Tianzhou Ma, Faming Liang, Steffi Oesterreich, George C Tseng
As the sequencing cost continued to drop in the past decade, RNA sequencing (RNA-seq) has replaced microarray to become the standard high-throughput experimental tool to analyze transcriptomic profile. As more and more datasets are generated and accumulated in the public domain, meta-analysis to combine multiple transcriptomic studies to increase statistical power has received increasing popularity. In this article, we propose a Bayesian hierarchical model to jointly integrate microarray and RNA-seq studies...
July 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28521438/identification-of-differentially-expressed-genes-between-early-stage-adenocarcinoma-and-squamous-cell-carcinoma-lung-cancer-using-meta-analysis-methods
#13
Tianjiao Wang, Lei Zhang, Pu Tian, Suyan Tian
Lung adenocarcinoma (AC) and squamous cell lung carcinoma (SCC) are two major subtypes of non-small cell lung cancer (NSCLC). Previous studies have demonstrated that fundamental differences exist in the underlying mechanisms of tumor development, growth and invasion between these subtypes. The investigation of differentially-expressed genes (DEGs) between these two NSCLC subtypes is useful for determining and understanding such differences. The present study aimed to identify those DEGs using meta-analysis and the data from four microarray experiments, consisting of 164 AC and 161 SCC samples...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28510204/microarray-meta-analysis-to-explore-abiotic-stress-specific-gene-expression-patterns-in-arabidopsis
#14
Po-Chih Shen, Ai-Ling Hour, Li-Yu Daisy Liu
BACKGROUND: Abiotic stresses are the major limiting factors that affect plant growth, development, yield and final quality. Deciphering the underlying mechanisms of plants' adaptations to stresses using few datasets might overlook the different aspects of stress tolerance in plants, which might be simultaneously and consequently operated in the system. Fortunately, the accumulated microarray expression data offer an opportunity to infer abiotic stress-specific gene expression patterns through meta-analysis...
December 2017: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/28500854/systematic-analysis-of-coronary-artery-disease-datasets-revealed-the-potential-biomarker-and-treatment-target
#15
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...
April 26, 2017: Oncotarget
https://www.readbyqxmd.com/read/28474265/gene-expression-signatures-for-head-and-neck-cancer-patient-stratification-are-results-ready-for-clinical-application
#16
REVIEW
Luca Tonella, Marco Giannoccaro, Salvatore Alfieri, Silvana Canevari, Loris De Cecco
Head and neck squamous cell carcinoma (HNSCC) is the sixth leading cancer by incidence worldwide and considering the recent EUROCARE-5 population-based study the 5-year survival rate of HNSCC patients in Europe ranges between 69% in localized cases and 34% in patients with regional involvement. The development of high-throughput gene expression assays in the last two decades has provided the invaluable opportunity to improve our knowledge on cancer biology and to identify predictive signatures in the most deeply analyzed malignancies, such as hematological and breast cancers...
May 2017: Current Treatment Options in Oncology
https://www.readbyqxmd.com/read/28396836/down-regulation-of-mir-146a-5p-and-its-potential-targets-in-hepatocellular-carcinoma-validated-by-a-tcga-and-geo-based-study
#17
Xin Zhang, Zhi-Hua Ye, Hai-Wei Liang, Fang-Hui Ren, Ping Li, Yi-Wu Dang, Gang Chen
Our previous research has demonstrated that miR-146a-5p is down-regulated in hepatocellular carcinoma (HCC) and might play a tumor-suppressive role. In this study, we sought to validate the decreased expression with a larger cohort and to explore potential molecular mechanisms. GEO and TCGA databases were used to gather miR-146a-5p expression data in HCC, which included 762 HCC and 454 noncancerous liver tissues. A meta-analysis of the GEO-based microarrays, TCGA-based RNA-seq data, and additional qRT-PCR data validated the down-regulation of miR-146a-5p in HCC and no publication bias was observed...
April 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/28347234/clinical-value-of-mir-145-5p-in-nsclc-and-potential-molecular-mechanism-exploration-a-retrospective-study-based-on-geo-qrt-pcr-and-tcga-data
#18
Ting-Qing Gan, Zu-Cheng Xie, Rui-Xue Tang, Tong-Tong Zhang, Dong-Yao Li, Zu-Yun Li, Gang Chen
MicroRNAs have been reported to be involved in various biological processes. Here, we performed a systematic analysis to explore the clinical value and potential molecular mechanism of miR-145-5p in non-small cell lung cancer. First, a meta-analysis was performed with eligible literature, followed by microRNA microarrays in the Gene Expression Omnibus database, to verify the diagnostic and prognostic values of miR-145-5p. A cohort of 125 clinical paired non-small cell lung cancer samples was next used to detect the level of miR-145-5p and to explore the relationship of miR-145-5p with clinicopathological parameters...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28335819/concordance-analysis-of-microarray-studies-identifies-representative-gene-expression-changes-in-parkinson-s-disease-a-comparison-of-33-human-and-animal-studies
#19
COMPARATIVE STUDY
Erin Oerton, Andreas Bender
BACKGROUND: As the popularity of transcriptomic analysis has grown, the reported lack of concordance between different studies of the same condition has become a growing concern, raising questions as to the representativeness of different study types, such as non-human disease models or studies of surrogate tissues, to gene expression in the human condition. METHODS: In a comparison of 33 microarray studies of Parkinson's disease, correlation and clustering analyses were used to determine the factors influencing concordance between studies, including agreement between different tissue types, different microarray platforms, and between neurotoxic and genetic disease models and human Parkinson's disease...
March 23, 2017: BMC Neurology
https://www.readbyqxmd.com/read/28334340/meta-analytic-framework-for-liquid-association
#20
Lin Wang, Silvia Liu, Ying Ding, Shin-Sheng Yuan, Yen-Yi Ho, George C Tseng
Motivation: Although coexpression analysis via pair-wise expression correlation is popularly used to elucidate gene-gene interactions at the whole-genome scale, many complicated multi-gene regulations require more advanced detection methods. Liquid association is a powerful tool to detect the dynamic correlation of two gene variables depending on the expression level of a third variable (LA scouting gene). Liquid association detection from single transcriptomic study, however, is often unstable and not generalizable due to cohort bias, biological variation, and limited sample size...
March 11, 2017: Bioinformatics
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