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https://www.readbyqxmd.com/read/27911280/clinicopathological-significance-of-wif1-hypermethylation-in-nsclc-a-meta-analysis-and-literature-review
#1
Hao Guo, Shuni Zhou, Lili Tan, Xiaoyu Wu, Zhenfeng Wu, Ruizhi Ran
Methylation of the WIF-1 gene can lead to the loss of WIF-1 expression which has been observed in numerous types of cancer including NSCLC. However, the association and clinicopathological significance between WIF-1 promoter hypermethylation and NSCLC remains unclear. In the present study, we performed a meta-analysis to evaluate the clinicopathological significance of WIF-1 hypermethylation in NSCLC. A systematic literature search was carried out using Pubmed, EMBASE, Web of Science and CNKI. The Cochrane software Review manager 5...
November 29, 2016: Oncotarget
https://www.readbyqxmd.com/read/27902461/whole-exome-sequencing-in-75-high-risk-families-with-validation-and-replication-in-independent-case-control-studies-identifies-tango2-or5h14-and-chad-as-new-prostate-cancer-susceptibility-genes
#2
Danielle M Karyadi, Milan S Geybels, Eric Karlins, Brennan Decker, Laura McIntosh, Amy Hutchinson, Suzanne Kolb, Shannon K McDonnell, Belynda Hicks, Sumit Middha, Liesel M FitzGerald, Melissa S DeRycke, Meredith Yeager, Daniel J Schaid, Stephen J Chanock, Stephen N Thibodeau, Sonja I Berndt, Janet L Stanford, Elaine A Ostrander
Prostate cancer (PCa) susceptibility is defined by a continuum from rare, high-penetrance to common, low-penetrance alleles. Research to date has concentrated on identification of variants at the ends of that continuum. Taking an alternate approach, we focused on the important but elusive class of low-frequency, moderately penetrant variants by performing disease model-based variant filtering of whole exome sequence data from 75 hereditary PCa families. Analysis of 341 candidate risk variants identified nine variants significantly associated with increased PCa risk in a population-based, case-control study of 2,495 men...
November 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/27899990/microarray-analysis-of-differentially-expressed-genes-and-linker-genes-associated-with-the-molecular-mechanism-of-colorectal-cancer
#3
Xingjie Shen, Meng Yue, Fansheng Meng, Jingyu Zhu, Xiaoyan Zhu, Yakun Jiang
Colorectal cancer (CRC) is one of the most prevalent malignancies worldwide and remains the third leading cause of cancer-associated mortality. The present study aimed to fully elucidate the pathogenesis of CRC and identify associated genes in tumor development. Microarray GSE44076, GSE41328 and GSE44861 datasets were downloaded from the Gene Expression Omnibus database and integrated with meta-analysis. Differentially-expressed genes (DEGs) were identified from CRC samples compared with adjacent non-cancerous controls using the Limma package in R, followed by functional analysis using the Database for Annotation, Visualization, and Integrated Discovery online tool...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27899424/genetic-architecture-of-sporadic-frontotemporal-dementia-and-overlap-with-alzheimer-s-and-parkinson-s-diseases
#4
Raffaele Ferrari, Yunpeng Wang, Jana Vandrovcova, Sebastian Guelfi, Aree Witeolar, Celeste M Karch, Andrew J Schork, Chun C Fan, James B Brewer, Parastoo Momeni, Gerard S Schellenberg, William P Dillon, Leo P Sugrue, Christopher P Hess, Jennifer S Yokoyama, Luke W Bonham, Gil D Rabinovici, Bruce L Miller, Ole A Andreassen, Anders M Dale, John Hardy, Rahul S Desikan
BACKGROUND: Clinical, pathological and genetic overlap between sporadic frontotemporal dementia (FTD), Alzheimer's disease (AD) and Parkinson's disease (PD) has been suggested; however, the relationship between these disorders is still not well understood. Here we evaluated genetic overlap between FTD, AD and PD to assess shared pathobiology and identify novel genetic variants associated with increased risk for FTD. METHODS: Summary statistics were obtained from the International FTD Genomics Consortium, International PD Genetics Consortium and International Genomics of AD Project (n>75 000 cases and controls)...
November 29, 2016: Journal of Neurology, Neurosurgery, and Psychiatry
https://www.readbyqxmd.com/read/27899376/gwas-of-clinically-defined-gout-and-subtypes-identifies-multiple-susceptibility-loci-that-include-urate-transporter-genes
#5
Akiyoshi Nakayama, Hirofumi Nakaoka, Ken Yamamoto, Masayuki Sakiyama, Amara Shaukat, Yu Toyoda, Yukinori Okada, Yoichiro Kamatani, Takahiro Nakamura, Tappei Takada, Katsuhisa Inoue, Tomoya Yasujima, Hiroaki Yuasa, Yuko Shirahama, Hiroshi Nakashima, Seiko Shimizu, Toshihide Higashino, Yusuke Kawamura, Hiraku Ogata, Makoto Kawaguchi, Yasuyuki Ohkawa, Inaho Danjoh, Atsumi Tokumasu, Keiko Ooyama, Toshimitsu Ito, Takaaki Kondo, Kenji Wakai, Blanka Stiburkova, Karel Pavelka, Lisa K Stamp, Nicola Dalbeth, Yutaka Sakurai, Hiroshi Suzuki, Makoto Hosoyamada, Shin Fujimori, Takashi Yokoo, Tatsuo Hosoya, Ituro Inoue, Atsushi Takahashi, Michiaki Kubo, Hiroshi Ooyama, Toru Shimizu, Kimiyoshi Ichida, Nariyoshi Shinomiya, Tony R Merriman, Hirotaka Matsuo
OBJECTIVE: A genome-wide association study (GWAS) of gout and its subtypes was performed to identify novel gout loci, including those that are subtype-specific. METHODS: Putative causal association signals from a GWAS of 945 clinically defined gout cases and 1213 controls from Japanese males were replicated with 1396 cases and 1268 controls using a custom chip of 1961 single nucleotide polymorphisms (SNPs). We also first conducted GWASs of gout subtypes. Replication with Caucasian and New Zealand Polynesian samples was done to further validate the loci identified in this study...
November 29, 2016: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/27896981/meta-analysis-of-continuous-phenotypes-identifies-a-gene-signature-that-correlates-with-copd-disease-status
#6
Madeleine Scott, Francesco Vallania, Purvesh Khatri
The utility of multi-cohort two-class meta-analysis to identify robust differentially expressed gene signatures has been well established. However, many biomedical applications, such as gene signatures of disease progression, require one-class analysis. Here we describe an R package, MetaCorrelator, that can identify a reproducible transcriptional signature that is correlated with a continuous disease phenotype across multiple datasets. We successfully applied this framework to extract a pattern of gene expression that can predict lung function in patients with chronic obstructive pulmonary disease (COPD) in both peripheral blood mononuclear cells (PBMCs) and tissue...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896970/empowering-multi-cohort-gene-expression-analysis-to-increase-reproducibility
#7
Winston A Haynes, Francesco Vallania, Charles Liu, Erika Bongen, Aurelie Tomczak, Marta Andres-Terrè, Shane Lofgren, Andrew Tam, Cole A Deisseroth, Matthew D Li, Timothy E Sweeney, Purvesh Khatri
A major contributor to the scientific reproducibility crisis has been that the results from homogeneous, single-center studies do not generalize to heterogeneous, real world populations. Multi-cohort gene expression analysis has helped to increase reproducibility by aggregating data from diverse populations into a single analysis. To make the multi-cohort analysis process more feasible, we have assembled an analysis pipeline which implements rigorously studied meta-analysis best practices. We have compiled and made publicly available the results of our own multi-cohort gene expression analysis of 103 diseases, spanning 615 studies and 36,915 samples, through a novel and interactive web application...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27892526/comprehensive-gene-expression-meta-analysis-and-integrated-bioinformatic-approaches-reveal-shared-signatures-between-thrombosis-and-myeloproliferative-disorders
#8
Prabhash Kumar Jha, Aatira Vijay, Anita Sahu, Mohammad Zahid Ashraf
Thrombosis is a leading cause of morbidity and mortality in patients with myeloproliferative disorders (MPDs), particularly polycythemia vera (PV) and essential thrombocythemia (ET). Despite the attempts to establish a link between them, the shared biological mechanisms are yet to be characterized. An integrated gene expression meta-analysis of five independent publicly available microarray data of the three diseases was conducted to identify shared gene expression signatures and overlapping biological processes...
November 28, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27890468/genetic-overlap-between-attention-deficit-hyperactivity-disorder-and-bipolar-disorder-evidence-from-genome-wide-association-study-meta-analysis
#9
Kimm J E van Hulzen, Claus J Scholz, Barbara Franke, Stephan Ripke, Marieke Klein, Andrew McQuillin, Edmund J Sonuga-Barke, John R Kelsoe, Mikael Landén, Ole A Andreassen, Klaus-Peter Lesch, Heike Weber, Stephen V Faraone, Alejandro Arias-Vasquez, Andreas Reif
BACKGROUND: Attention-deficit/hyperactivity disorder (ADHD) and bipolar disorder (BPD) are frequently co-occurring and highly heritable mental health conditions. We hypothesized that BPD cases with an early age of onset (≤21 years old) would be particularly likely to show genetic covariation with ADHD. METHODS: Genome-wide association study data were available for 4609 individuals with ADHD, 9650 individuals with BPD (5167 thereof with early-onset BPD), and 21,363 typically developing controls...
October 18, 2016: Biological Psychiatry
https://www.readbyqxmd.com/read/27873492/aberrant-hypomethylation-of-solute-carrier-family-6-member-12-promoter-induces-metastasis-of-ovarian-cancer
#10
Hye Youn Sung, San Duk Yang, Ae Kyung Park, Woong Ju, Jung Hyuck Ahn
PURPOSE: Ovarian cancer (OC) is the most fatal of gynecological malignancies with a high rate of recurrence. We aimed to evaluate the expression of solute carrier family 6, member 12 (SLC6A12) and methylation of its promoter CpG sites in a xenograft mouse model of metastatic OC, and to investigate the regulatory mechanisms that promote aggressive properties during OC progression. MATERIALS AND METHODS: Expression of SLC6A12 mRNA was determined by reverse-transcription quantitative polymerase chain reaction (RT-qPCR), and DNA methylation status of its promoter CpGs was detected by quantitative methylation-specific PCR...
January 2017: Yonsei Medical Journal
https://www.readbyqxmd.com/read/27863190/human-papillomavirus-drives-tumor-development-throughout-the-head-and-neck-improved-prognosis-is-associated-with-an-immune-response-largely-restricted-to-the-oropharynx
#11
Ankur Chakravarthy, Stephen Henderson, Stephen M Thirdborough, Christian H Ottensmeier, Xiaoping Su, Matt Lechner, Andrew Feber, Gareth J Thomas, Tim R Fenton
Purpose In squamous cell carcinomas of the head and neck (HNSCC), the increasing incidence of oropharyngeal squamous cell carcinomas (OPSCCs) is attributable to human papillomavirus (HPV) infection. Despite commonly presenting at late stage, HPV-driven OPSCCs are associated with improved prognosis compared with HPV-negative disease. HPV DNA is also detectable in nonoropharyngeal (non-OPSCC), but its pathogenic role and clinical significance are unclear. The objectives of this study were to determine whether HPV plays a causal role in non-OPSCC and to investigate whether HPV confers a survival benefit in these tumors...
December 2016: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/27862943/blood-transcriptomic-comparison-of-individuals-with-and-without-autism-spectrum-disorder-a-combined-samples-mega-analysis
#12
Daniel S Tylee, Jonathan L Hess, Thomas P Quinn, Rahul Barve, Hailiang Huang, Yanli Zhang-James, Jeffrey Chang, Boryana S Stamova, Frank R Sharp, Irva Hertz-Picciotto, Stephen V Faraone, Sek Won Kong, Stephen J Glatt
Blood-based microarray studies comparing individuals affected with autism spectrum disorder (ASD) and typically developing individuals help characterize differences in circulating immune cell functions and offer potential biomarker signal. We sought to combine the subject-level data from previously published studies by mega-analysis to increase the statistical power. We identified studies that compared ex vivo blood or lymphocytes from ASD-affected individuals and unrelated comparison subjects using Affymetrix or Illumina array platforms...
November 11, 2016: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/27854507/sex-based-genetic-association-study-identifies-celsr1-as-a-possible-copd-risk-locus-among-women
#13
Megan Hardin, Michael H Cho, Sunita S Sharma, Kimberly Glass, Peter J Castaldi, Merry-Lynn McDonald, Hugues Aschard, Jody Senter-Sylvia, Kelan Tantisira, Scott T Weiss, Craig P Hersh, Jarrett D Morrow, David Lomas, Alvar Agusti, Per Bakke, Amund Gulsvik, George T O'Connor, Josée Dupuis, John Hokanson, James Crapo, Terri H Beaty, Nan Laird, Edwin K Silverman, Dawn L DeMeo
BACKGROUND: Chronic Obstructive Pulmonary Disease (COPD) is a complex disease with strong environmental and genetic influences and sexually dimorphic features. Although genetic risk factors for COPD have been identified, much of the heritability remains unexplained. Sex-based genetic association studies may uncover additional COPD genetic risk factors. METHODS: We studied current and former smokers from COPD case-control cohorts (COPDGene non-Hispanic whites and African Americans, ECLIPSE, and GenKOLS)...
November 17, 2016: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/27852052/micrornas-for-osteosarcoma-in-the-mouse-a-meta-analysis
#14
REVIEW
Junli Chang, Min Yao, Yimian Li, Dongfeng Zhao, Shaopu Hu, Xuejun Cui, Gang Liu, Qi Shi, Yongjun Wang, Yanping Yang
Osteosarcoma (OS) is the most common primary malignant bone carcinoma with high morbidity that happens mainly in children and young adults. As the key components of gene-regulatory networks, microRNAs (miRNAs) control many critical pathophysiological processes, including initiation and progression of cancers. The objective of this study is to summarize and evaluate the potential of miRNAs as targets for prevention and treatment of OS in mouse models, and to explore the methodological quality of current studies...
November 12, 2016: Oncotarget
https://www.readbyqxmd.com/read/27846842/a-meta-analysis-of-public-microarray-data-identifies-gene-regulatory-pathways-deregulated-in-peripheral-blood-mononuclear-cells-from-individuals-with-systemic-lupus-erythematosus-compared-to-those-without
#15
Wendy Kröger, Darlington Mapiye, Jean-Baka Domelevo Entfellner, Nicki Tiffin
BACKGROUND: Systemic Lupus Erythematosus (SLE) is a complex, multi-systemic, autoimmune disease for which the underlying aetiological mechanisms are poorly understood. The genetic and molecular processes underlying lupus have been extensively investigated using a variety of -omics approaches, including genome-wide association studies, candidate gene studies and microarray experiments of differential gene expression in lupus samples compared to controls. METHODS: This study analyses a combination of existing microarray data sets to identify differentially regulated genetic pathways that are dysregulated in human peripheral blood mononuclear cells from SLE patients compared to unaffected controls...
November 15, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27843151/a-dna-methylation-biomarker-of-alcohol-consumption
#16
C Liu, R E Marioni, Å K Hedman, L Pfeiffer, P-C Tsai, L M Reynolds, A C Just, Q Duan, C G Boer, T Tanaka, C E Elks, S Aslibekyan, J A Brody, B Kühnel, C Herder, L M Almli, D Zhi, Y Wang, T Huan, C Yao, M M Mendelson, R Joehanes, L Liang, S-A Love, W Guan, S Shah, A F McRae, A Kretschmer, H Prokisch, K Strauch, A Peters, P M Visscher, N R Wray, X Guo, K L Wiggins, A K Smith, E B Binder, K J Ressler, M R Irvin, D M Absher, D Hernandez, L Ferrucci, S Bandinelli, K Lohman, J Ding, L Trevisi, S Gustafsson, J H Sandling, L Stolk, A G Uitterlinden, I Yet, J E Castillo-Fernandez, T D Spector, J D Schwartz, P Vokonas, L Lind, Y Li, M Fornage, D K Arnett, N J Wareham, N Sotoodehnia, K K Ong, J B J van Meurs, K N Conneely, A A Baccarelli, I J Deary, J T Bell, K E North, Y Liu, M Waldenberger, S J London, E Ingelsson, D Levy
The lack of reliable measures of alcohol intake is a major obstacle to the diagnosis and treatment of alcohol-related diseases. Epigenetic modifications such as DNA methylation may provide novel biomarkers of alcohol use. To examine this possibility, we performed an epigenome-wide association study of methylation of cytosine-phosphate-guanine dinucleotide (CpG) sites in relation to alcohol intake in 13 population-based cohorts (ntotal=13 317; 54% women; mean age across cohorts 42-76 years) using whole blood (9643 European and 2423 African ancestries) or monocyte-derived DNA (588 European, 263 African and 400 Hispanic ancestry) samples...
November 15, 2016: Molecular Psychiatry
https://www.readbyqxmd.com/read/27835872/targeting-abcb1-mdr1-in-multi-drug-resistant-osteosarcoma-cells-using-the-crispr-cas9-system-to-reverse-drug-resistance
#17
Tang Liu, Zhihong Li, Qing Zhang, Karen De Amorim Bernstein, Santiago Lozano-Calderon, Edwin Choy, Francis J Hornicek, Zhenfeng Duan
BACKGROUND: Multi-drug resistance (MDR) remains a significant obstacle to successful chemotherapy treatment for osteosarcoma patients. One of the central causes of MDR is the overexpression of the membrane bound drug transporter protein P-glycoprotein (P-gp), which is the protein product of the MDR gene ABCB1. Though several methods have been reported to reverse MDR in vitro and in vivo when combined with anticancer drugs, they have yet to be proven useful in the clinical setting. RESULTS: The meta-analysis demonstrated that a high level of P-gp may predict poor survival in patients with osteosarcoma...
November 7, 2016: Oncotarget
https://www.readbyqxmd.com/read/27835655/a-transcriptome-meta-analysis-proposes-novel-biological-roles-for-the-antifungal-protein-anafp-in-aspergillus-niger
#18
Norman Paege, Sascha Jung, Paul Schäpe, Dirk Müller-Hagen, Jean-Paul Ouedraogo, Caroline Heiderich, Johanna Jedamzick, Benjamin M Nitsche, Cees A van den Hondel, Arthur F Ram, Vera Meyer
Understanding the genetic, molecular and evolutionary basis of cysteine-stabilized antifungal proteins (AFPs) from fungi is important for understanding whether their function is mainly defensive or associated with fungal growth and development. In the current study, a transcriptome meta-analysis of the Aspergillus niger γ-core protein AnAFP was performed to explore co-expressed genes and pathways, based on independent expression profiling microarrays covering 155 distinct cultivation conditions. This analysis uncovered that anafp displays a highly coordinated temporal and spatial transcriptional profile which is concomitant with key nutritional and developmental processes...
2016: PloS One
https://www.readbyqxmd.com/read/27830726/meta-analysis-of-gene-expression-studies-in-endometrial-cancer-identifies-gene-expression-profiles-associated-with-aggressive-disease-and-patient-outcome
#19
Tracy A O'Mara, Min Zhao, Amanda B Spurdle
Although endometrioid endometrial cancer (EEC; comprising ~80% of all endometrial cancers diagnosed) is typically associated with favourable patient outcome, a significant portion (~20%) of women with this subtype will relapse. We hypothesised that gene expression predictors of the more aggressive non-endometrioid endometrial cancers (NEEC) could be used to predict EEC patients with poor prognosis. To explore this hypothesis, we performed meta-analysis of 12 gene expression microarray studies followed by validation using RNA-Seq data from The Cancer Genome Atlas (TCGA) and identified 1,253 genes differentially expressed between EEC and NEEC...
November 10, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27824868/drug-repositioning-through-systematic-mining-of-gene-coexpression-networks-in-cancer
#20
Alexander E Ivliev, Peter A C 't Hoen, Dmitrii Borisevich, Yuri Nikolsky, Marina G Sergeeva
Gene coexpression network analysis is a powerful "data-driven" approach essential for understanding cancer biology and mechanisms of tumor development. Yet, despite the completion of thousands of studies on cancer gene expression, there have been few attempts to normalize and integrate co-expression data from scattered sources in a concise "meta-analysis" framework. We generated such a resource by exploring gene coexpression networks in 82 microarray datasets from 9 major human cancer types. The analysis was conducted using an elaborate weighted gene coexpression network (WGCNA) methodology and identified over 3,000 robust gene coexpression modules...
2016: PloS One
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