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gene expression meta-analysis

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https://www.readbyqxmd.com/read/28542306/gene-signature-associated-with-benign-neurofibroma-transformation-to-malignant-peripheral-nerve-sheath-tumors
#1
Marta Martínez, Carlos O S Sorzano, Alberto Pascual-Montano, Jose M Carazo
Benign neurofibromas, the main phenotypic manifestations of the rare neurological disorder neurofibromatosis type 1, degenerate to malignant tumors associated to poor prognosis in about 10% of patients. Despite efforts in the field of (epi)genomics, the lack of prognostic biomarkers with which to predict disease evolution frustrates the adoption of appropriate early therapeutic measures. To identify potential biomarkers of malignant neurofibroma transformation, we integrated four human experimental studies and one for mouse, using a gene score-based meta-analysis method, from which we obtained a score-ranked signature of 579 genes...
2017: PloS One
https://www.readbyqxmd.com/read/28541721/a-joint-bayesian-model-for-integrating-microarray-and-rna-sequencing-transcriptomic-data
#2
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...
May 25, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28540642/plasma-and-white-blood-cells-show-different-mirna-expression-profiles-in-parkinson-s-disease
#3
Christine Schwienbacher, Luisa Foco, Anne Picard, Eloina Corradi, Alice Serafin, Jörg Panzer, Stefano Zanigni, Hagen Blankenburg, Maurizio F Facheris, Giulia Giannini, Marika Falla, Pietro Cortelli, Peter P Pramstaller, Andrew A Hicks
Parkinson's disease (PD) diagnosis is based on the assessment of motor symptoms, which manifest when more than 50% of dopaminergic neurons are degenerated. To date, no validated biomarkers are available for the diagnosis of PD. The aims of the present study are to evaluate whether plasma and white blood cells (WBCs) are interchangeable biomarker sources and to identify circulating plasma-based microRNA (miRNA) biomarkers for an early detection of PD. We profiled plasma miRNA levels in 99 L-dopa-treated PD patients from two independent data collections, in ten drug-naïve PD patients, and in unaffected controls matched by sex and age...
May 24, 2017: Journal of Molecular Neuroscience: MN
https://www.readbyqxmd.com/read/28538665/molecular-basis-of-alcohol-related-gastric-and-colon-cancer
#4
REVIEW
Hye-Kyung Na, Ja Young Lee
Many meta-analysis, large cohort studies, and experimental studies suggest that chronic alcohol consumption increases the risk of gastric and colon cancer. Ethanol is metabolized by alcohol dehydrogenases (ADH), catalase or cytochrome P450 2E1 (CYP2E1) to acetaldehyde, which is then further oxidized to acetate by aldehyde dehydrogenase (ALDH). Acetaldehyde has been classified by the International Agency for Research on Cancer (IARC) as a Group 1 carcinogen to humans. The acetaldehyde level in the stomach and colon is locally influenced by gastric colonization by Helicobacter pylori or colonic microbes, as well as polymorphisms in the genes encoding tissue alcohol metabolizing enzymes, especially ALDH2...
May 24, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28533425/brms1gene-expressionmay-be-associated-with-clinico-pathological-features-of-breast-cancer
#5
Li-Zhong Lin, Miao-Guo Cai, Yue-Chu Dai, Zhi-Bao Zheng, Fang-Fang Jiang, Li-Li Shi, Yin Pan, Han-Bing Song
Our aim is to investigate whether or not the breast cancer metastasis suppressor 1 ( BRMS1 ) gene expression is directly linked to clinico-pathological features of breast cancer. Following a stringent inclusion and exclusion criteria, case-control studies with associations between BRMS1 and breast cancer were selected from articles obtained by way of searches conducted through an electronic database. All statistical analyses were performed with Stata 12.0 (Stata Corp, College Station, TX, USA). Ultimately, 1,263 patients with breast cancer were found in a meta-analysis retrieved from a total that included 12 studies...
May 22, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28530674/fifteen-new-risk-loci-for-coronary-artery-disease-highlight-arterial-wall-specific-mechanisms
#6
Joanna M M Howson, Wei Zhao, Daniel R Barnes, Weang-Kee Ho, Robin Young, Dirk S Paul, Lindsay L Waite, Daniel F Freitag, Eric B Fauman, Elias L Salfati, Benjamin B Sun, John D Eicher, Andrew D Johnson, Wayne H H Sheu, Sune F Nielsen, Wei-Yu Lin, Praveen Surendran, Anders Malarstig, Jemma B Wilk, Anne Tybjærg-Hansen, Katrine L Rasmussen, Pia R Kamstrup, Panos Deloukas, Jeanette Erdmann, Sekar Kathiresan, Nilesh J Samani, Heribert Schunkert, Hugh Watkins, Ron Do, Daniel J Rader, Julie A Johnson, Stanley L Hazen, Arshed A Quyyumi, John A Spertus, Carl J Pepine, Nora Franceschini, Anne Justice, Alex P Reiner, Steven Buyske, Lucia A Hindorff, Cara L Carty, Kari E North, Charles Kooperberg, Eric Boerwinkle, Kristin Young, Mariaelisa Graff, Ulrike Peters, Devin Absher, Chao A Hsiung, Wen-Jane Lee, Kent D Taylor, Ying-Hsiang Chen, I-Te Lee, Xiuqing Guo, Ren-Hua Chung, Yi-Jen Hung, Jerome I Rotter, Jyh-Ming J Juang, Thomas Quertermous, Tzung-Dau Wang, Asif Rasheed, Philippe Frossard, Dewan S Alam, Abdulla Al Shafi Majumder, Emanuele Di Angelantonio, Rajiv Chowdhury, Yii-Der Ida Chen, Børge G Nordestgaard, Themistocles L Assimes, John Danesh, Adam S Butterworth, Danish Saleheen
Coronary artery disease (CAD) is a leading cause of morbidity and mortality worldwide. Although 58 genomic regions have been associated with CAD thus far, most of the heritability is unexplained, indicating that additional susceptibility loci await identification. An efficient discovery strategy may be larger-scale evaluation of promising associations suggested by genome-wide association studies (GWAS). Hence, we genotyped 56,309 participants using a targeted gene array derived from earlier GWAS results and performed meta-analysis of results with 194,427 participants previously genotyped, totaling 88,192 CAD cases and 162,544 controls...
May 22, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28530673/genome-wide-association-meta-analysis-of-78-308-individuals-identifies-new-loci-and-genes-influencing-human-intelligence
#7
Suzanne Sniekers, Sven Stringer, Kyoko Watanabe, Philip R Jansen, Jonathan R I Coleman, Eva Krapohl, Erdogan Taskesen, Anke R Hammerschlag, Aysu Okbay, Delilah Zabaneh, Najaf Amin, Gerome Breen, David Cesarini, Christopher F Chabris, William G Iacono, M Arfan Ikram, Magnus Johannesson, Philipp Koellinger, James J Lee, Patrik K E Magnusson, Matt McGue, Mike B Miller, William E R Ollier, Antony Payton, Neil Pendleton, Robert Plomin, Cornelius A Rietveld, Henning Tiemeier, Cornelia M van Duijn, Danielle Posthuma
Intelligence is associated with important economic and health-related life outcomes. Despite intelligence having substantial heritability (0.54) and a confirmed polygenic nature, initial genetic studies were mostly underpowered. Here we report a meta-analysis for intelligence of 78,308 individuals. We identify 336 associated SNPs (METAL P < 5 × 10(-8)) in 18 genomic loci, of which 15 are new. Around half of the SNPs are located inside a gene, implicating 22 genes, of which 11 are new findings. Gene-based analyses identified an additional 30 genes (MAGMA P < 2...
May 22, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28530463/association-of-il-6-174-g-c-polymorphism-with-the-risk-of-sle-among-south-indians-evidence-from-case-control-study-and-meta-analysis
#8
S K Katkam, L Rajasekhar, K Kumaraswami, V K Kutala
Cytokines play a direct role in disease pathogenesis of systemic lupus erythematosus (SLE). Elevated levels of serum IL-6 are well documented with the disease activity and anti-dsDNA antibodies in SLE. The 5' promoter region of the IL-6 gene has been shown to play a significant role in the regulation of gene expression. In view of this, the current study aimed to investigate the possible association of 5' promoter polymorphisms G-597A (rs1800797), G-572C (rs1800796) and G-174C (rs1800795) with the risk of SLE...
January 1, 2017: Lupus
https://www.readbyqxmd.com/read/28525560/activity-dependent-gene-expression-in-the-mammalian-olfactory-epithelium
#9
Qiang Wang, William B Titlow, Declan A McClintock, Arnold J Stromberg, Timothy S McClintock
Activity-dependent processes are important to olfactory sensory neurons (OSNs) in several ways, such as cell survival and the specificity of axonal convergence. The identification of activity-dependent mRNAs has contributed to our understanding of OSN axon convergence, but has revealed surprisingly little about other processes. Published studies of activity-dependent mRNAs in olfactory mucosae overlap poorly, but by combining these agreements with meta-analysis of existing data we identify 443 mRNAs that respond to methods that alter OSN activity...
May 19, 2017: Chemical Senses
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
#10
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/28510328/genetic-variants-in-the-genes-encoding-rho-gtpases-and-related-regulators-predict-cutaneous-melanoma-specific-survival
#11
Shun Liu, Yanru Wang, William Xue, Hongliang Liu, Yinghui Xu, Qiong Shi, Wenting Wu, Dakai Zhu, Christopher I Amos, Shenying Fang, Jeffrey E Lee, Terry Hyslop, Yi Li, Jiali Han, Qingyi Wei
Rho GTPases control cell division, motility, adhesion, vesicular trafficking and phagocytosis, which may affect progression and/or prognosis of cancers. Here, we investigated associations between genetic variants of Rho GTPases-related genes and cutaneous melanoma-specific survival (CMSS) by re-analyzing a published melanoma genome-wide association study (GWAS) and validating the results in another melanoma GWAS. In the single-locus analysis of 36,018 SNPs in 129 Rho-related genes, 427 SNPs were significantly associated with CMSS (P<0...
May 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28510306/a-polymorphism-in-mir-1262-regulatory-region-confers-the-risk-of-lung-cancer-in-chinese-population
#12
Kaipeng Xie, Mengxi Chen, Meng Zhu, Cheng Wang, Na Qin, Cheng Liang, Ci Song, Juncheng Dai, Guangfu Jin, Hongbing Shen, Dongxing Lin, Hongxia Ma, Zhibin Hu
It has been proposed that the majority of disease-associated loci identified by genome-wide association studies (GWAS) are enriched in non-coding regions, such as the promoter, enhancer or non-coding RNA genes. Thus, we performed a two-stage case-control study to systematically evaluate the association of genetic variants in miRNA regulatory regions (promoter and enhancer) with lung cancer risk in 7,763 subjects (discovery stage: 2,331 cases and 3,077 controls; validation stage: 1,065 cases and 1,290 controls)...
May 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28510302/association-study-of-genetic-variation-in-dna-repair-pathway-genes-and-risk-of-basal-cell-carcinoma
#13
Yuan Lin, Harvind S Chahal, Wenting Wu, Hyunje G Cho, Katherine J Ransohoff, Fengju Song, Jean Y Tang, Kavita Y Sarin, Jiali Han
DNA repair plays a critical role in protecting the genome from ultraviolet radiation and maintaining the genomic integrity of cells. Genetic variants in DNA repair-related genes can influence an individual's DNA repair capacity, which may be related to the risk of developing basal cell carcinoma (BCC). We comprehensively assessed the associations of 2,965 independent single-nucleotide polymorphisms (SNPs) across 165 DNA repair pathway genes with BCC risk in a genome-wide association meta-analysis totaling 17,187 BCC cases and 287,054 controls from two data sets...
May 16, 2017: International Journal of Cancer. Journal International du Cancer
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/28507441/clinicopathological-significance-of-p14-arf-expression-in-lung-cancer-a-meta-analysis
#15
Fang Wang, Heping Li, Jianting Long, Sheng Ye
BACKGROUND: p14(ARF), a tumor suppressor protein, encoded by the p16 tumor suppressor gene, has been reported to be associated with the clinicopathological features of lung cancer. However, the evaluated outcomes were inconsistent and remained inconclusive. In this study, we conducted a meta-analysis to clarify the significance of p14(ARF) expression in lung cancer pathogenesis. MATERIALS AND METHODS: Electronic databases, PubMed, Web of Knowledge, Embase, and CNKI, were retrieved to collect relevant articles with inclusion and exclusion criteria...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28506689/genetic-factors-interact-with-tobacco-smoke-to-modify-risk-for-inflammatory-bowel-disease-in-humans-and-mice
#16
Pankaj Yadav, David Ellinghaus, Gaëlle Rémy, Sandra Freitag-Wolf, Anabelle Cesaro, Frauke Degenhardt, Gabrielle Boucher, Myriam Delacre, Laurent Peyrin-Biroulet, Muriel Pichavant, John D Rioux, Philippe Gosset, Andre Franke, L Philip Schumm, Michael Krawczak, Mathias Chamaillard, Astrid Dempfle, Vibeke Andersen
BACKGROUND & AIMS: The role of tobacco smoke in the etiology of inflammatory bowel disease (IBD) is unclear. We investigated interactions between genes and smoking (gene-smoking interactions) that affect risk for Crohn's disease (CD) and ulcerative colitis (UC) in a case-only study of patients and in mouse models of IBD. METHODS: We used 55 immunochip-wide data sets that included 19,735 IBD cases (10,856 CD cases and 8879 UC cases) of known smoking status. We performed 3 meta-analyses each for CD, UC, and IBD (CD and UC combined), comparing data for never vs ever smokers, never vs current smokers, and never vs former smokers...
May 12, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28505379/analysis-of-cfb-a-cytokinin-responsive-gene-of-arabidopsis-thaliana-encoding-a-novel-f-box-protein-regulating-sterol-biosynthesis
#17
Wolfram G Brenner, Jan Erik Leuendorf, Anne Cortleven, Laetitia B B Martin, Hubert Schaller, Thomas Schmülling
Protein degradation by the ubiquitin-26S proteasome pathway is important for the regulation of cellular processes, but the function of most F-box proteins relevant to substrate recognition is unknown. We describe the analysis of the gene Cytokinin-induced F-box encoding (CFB, AT3G44326), identified in a meta-analysis of cytokinin-related transcriptome studies as one of the most robust cytokinin response genes. F-box domain-dependent interaction with the E3 ubiquitin ligase complex component ASK1 classifies CFB as a functional F-box protein...
May 12, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28501628/evolutionary-expansion-and-structural-functionalism-of-the-ancient-family-of-profilin-proteins
#18
Dhananjay K Pandey, Bhupendra Chaudhary
Structure and functional similarities of a recent protein's orthologs with its ancient counterpart are largely determined by the configuration of evolutionary preservation of amino acids. The emergence of genome sequencing databases allowed dissecting the evolutionarily important gene families at a comprehensive and genome-wide scale. The profilin multi-gene family is an ancient, universal, and functionally diverged across kingdoms, which regulates various aspects of cellular development in both prokarya and eukarya, especially cell-wall maintenance through actin sequestering, nucleation and cytokinesis...
May 10, 2017: Gene
https://www.readbyqxmd.com/read/28500854/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...
April 26, 2017: Oncotarget
https://www.readbyqxmd.com/read/28500704/meta-analysis-of-the-transcriptome-reveals-a-core-set-of-shade-avoidance-genes-in-arabidopsis
#20
Romina Sellaro, Manuel Pacín, Jorge J Casal
The presence of neighboring vegetation modifies the light input perceived by photo-sensory receptors, initiating a signaling cascade that adjusts plant growth and physiology. Thousands of genes can change their expression during this process, but the structure of the transcriptional circuit is poorly understood. Here we present a meta-analysis of transcriptome data from Arabidopsis thaliana exposed to neighbor signals in different contexts, including organs where growth is promoted or inhibited by these signals...
May 2017: Photochemistry and Photobiology
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