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gene expression meta-analysis

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https://www.readbyqxmd.com/read/29145823/dbmdega-a-database-for-meta-analysis-of-differentially-expressed-genes-in-autism-spectrum-disorder
#1
Shuyun Zhang, Libin Deng, Qiyue Jia, Shaoting Huang, Junwang Gu, Fankun Zhou, Meng Gao, Xinyi Sun, Chang Feng, Guangqin Fan
BACKGROUND: Autism spectrum disorders (ASD) are hereditary, heterogeneous and biologically complex neurodevelopmental disorders. Individual studies on gene expression in ASD cannot provide clear consensus conclusions. Therefore, a systematic review to synthesize the current findings from brain tissues and a search tool to share the meta-analysis results are urgently needed. METHODS: Here, we conducted a meta-analysis of brain gene expression profiles in the current reported human ASD expression datasets (with 84 frozen male cortex samples, 17 female cortex samples, 32 cerebellum samples and 4 formalin fixed samples) and knock-out mouse ASD model expression datasets (with 80 collective brain samples)...
November 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29145283/the-relationship-between-rassf1a-promoter-methylation-and-thyroid-carcinoma-a-meta-analysis-of-14-articles-and-a-bioinformatics-of-2-databases-prisma
#2
Heng Niu, Jingyu Yang, Kunxian Yang, Yingze Huang
BACKGROUND: DNA promoter methylation can suppresses gene expression and shows an important role in the biological functions of Ras association domain family 1A (RASSF1A). Many studies have performed to elucidate the role of RASSF1A promoter methylation in thyroid carcinoma, while the results were conflicting and heterogeneous. Here, we analyzed the data of databases to determine the relationship between RASSF1A promoter methylation and thyroid carcinoma. METHODS: We used the data from 14 cancer-normal studies and Gene Expression Omnibus (GEO) database to analyze RASSF1A promoter methylation in thyroid carcinoma susceptibility...
November 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29145252/identifications-of-potential-therapeutic-targets-and-drugs-in-angiotensin-ii-induced-hypertension
#3
Xiaoli Wu, Ruihua Fan
This study aimed to identify the underlying therapeutic targets of angiotensin II (AngII)-induced hypertension, and screen the related drugs.The gene expression profiles of GSE93579 and GSE75815 were used to identify differentially expressed genes (DEGs) between AngII-induced hypertension and control samples based on meta-analysis. These DEGs were analyzed using Gene-Ontology (GO) function and pathway enrichment methods. Subsequently, the weighed gene coexpression network analysis (WGCNA)-based meta-analysis was applied to determine transcriptional signature with DEGs...
November 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29141020/genomic-analysis-of-atypical-fibroxanthoma
#4
Kevin Lai, Catherine A Harwood, Karin J Purdie, Charlotte M Proby, Irene M Leigh, Namita Ravi, Thaddeus W Mully, Lionel Brooks, Priscilla M Sandoval, Michael D Rosenblum, Sarah T Arron
Atypical fibroxanthoma (AFX), is a rare type of skin cancer affecting older individuals with sun damaged skin. Since there is limited genomic information about AFX, our study seeks to improve the understanding of AFX through whole-exome and RNA sequencing of 8 matched tumor-normal samples. AFX is a highly mutated malignancy with recurrent mutations in a number of genes, including COL11A1, ERBB4, CSMD3, and FAT1. The majority of mutations identified were UV signature (C>T in dipyrimidines). We observed deletion of chromosomal segments on chr9p and chr13q, including tumor suppressor genes such as KANK1 and CDKN2A, but no gene fusions were found...
2017: PloS One
https://www.readbyqxmd.com/read/29140729/gene-expression-and-gene-associations-during-the-development-of-heart-failure-with-preserved-ejection-fraction-in-the-dahl-salt-sensitive-model-of-hypertension
#5
Jeffrey Yim, Hyokeun Cho, Simon W Rabkin
Gene expression and associations were examined in a model of heart failure with preserved ejection fraction (HFpEF), a condition with minimal effective treatment. Genes with at least two studies showing significant changes in Dahl rat with heart failure were examined by meta-analysis. Significantly increased in expression were iNOS, p47phox, ADM, ANP, OPN, ACE, MCP-1, GP91PHOX, ICAM-1, TGF-β1, CTGF, ET-1, p22phox, ETB, BNP, ETA, MMP13, Col1a1, MMP2, TIMP1, Col3a1, Il-1β, β-MHC, ECE1, MMP14, AGT, and MMP9...
November 15, 2017: Clinical and Experimental Hypertension: CHE
https://www.readbyqxmd.com/read/29138855/integrated-bioinformatics-analysis-of-the-osteoarthritis%C3%A2-associated-microrna-expression-signature
#6
Xi Wang, Yujie Ning, Bing Zhou, Lei Yang, Yingting Wang, Xiong Guo
Numerous studies have focused on osteoarthritis (OA) cartilage injuries, with observations of abnormalities in microRNA (miRNA) expression levels. The aim of the present study was to consolidate and assess the results of these studies to identify potential miRNA biomarkers of OA. A comprehensive meta‑analysis of eight independent miRNA expression studies in OA was performed using the robust rank aggregation method (RRA), which contained a total of 82 OA and 39 normal cartilage samples. The targets of meta‑signature miRNA were predicted using TargetScan v6...
November 14, 2017: Molecular Medicine Reports
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
#7
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/29136636/screening-of-skin-lesion-associated-genes-in-patients-with-psoriasis-by-meta-integration-analysis
#8
Rong Mei, Xiaofeng Mei
AIM: Psoriasis is an inflammatory skin disease, and approximately one quarter of individuals with psoriasis develop painful and debilitating arthritis. As a complex and polygenetic hereditary disease, it is significant to investigate skin lesion-associated genes of psoriasis. METHOD: In the present study, a total of 3,047 differentially expressed genes between lesional and nonlesional skin of psoriasis patients were screened based on 4 data sets in GEO DataSets...
November 15, 2017: Dermatology: International Journal for Clinical and Investigative Dermatology
https://www.readbyqxmd.com/read/29132337/gene-expression-signatures-of-neuroendocrine-prostate-cancer-and-primary-small-cell-prostatic-carcinoma
#9
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
#10
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/29122639/the-p2rx7-polymorphism-rs2230912-is-associated-with-depression-a-meta-analysis
#11
D Czamara, B Müller-Myhsok, S Lucae
Various studies have investigated whether single nucleotide polymorphisms (SNPs) in the gene purinergic receptor P2X7 (P2RX7), and rs2230912 specifically, were associated with mood disorders. While some studies found positive evidence, a large number of studies reported no significant associations. In a previously published meta-analysis, Feng et al. did not find a significant association and only moderate odds ratios (ORs) in case-control studies. They reported significant findings only for family-based studies...
November 6, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/29121939/case-definition-terminology-for-paratuberculosis-johne-s-disease
#12
R J Whittington, D J Begg, K de Silva, A C Purdie, N K Dhand, K M Plain
Paratuberculosis (Johne's disease) is an economically significant condition caused by Mycobacterium avium subsp. paratuberculosis. However, difficulties in diagnosis and classification of individual animals with the condition have hampered research and impeded efforts to halt its progressive spread in the global livestock industry. Descriptive terms applied to individual animals and herds such as exposed, infected, diseased, clinical, sub-clinical, infectious and resistant need to be defined so that they can be incorporated consistently into well-understood and reproducible case definitions...
November 9, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/29118919/integrative-analysis-of-bsg-expression-in-npc-through-immunohistochemistry-and-public-high-throughput-gene-expression-data
#13
Li Gao, Jin-Cai Zhong, Wen-Ting Huang, Yi-Wu Dang, Min Kang, Gang Chen
BACKGROUND: Though basigin (BSG) was reported to be overexpressed in nasopharyngeal carcinoma (NPC) and correlate with the development of NPC, the molecular basis of BSG in NPC remained elusive. The aim of the research was to investigate BSG expression in NPC and the potential molecular mechanism underlying it. MATERIALS AND METHODS: BSG expression in NPC tissues was detected with immunohistochemistry. Chi-square test, Kruskal-Wallis test and Spearman correlation test were performed to examine the relationship between BSG expression and the clinico-pathological features as well as EGFR and P-53 expression in NPC...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/29115927/transcriptomic-responses-to-wounding-meta-analysis-of-gene-expression-microarray-data
#14
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/29114920/integrative-sparse-principal-component-analysis-of-gene-expression-data
#15
Mengque Liu, Xinyan Fan, Kuangnan Fang, Qingzhao Zhang, Shuangge Ma
In the analysis of gene expression data, dimension reduction techniques have been extensively adopted. The most popular one is perhaps the PCA (principal component analysis). To generate more reliable and more interpretable results, the SPCA (sparse PCA) technique has been developed. With the "small sample size, high dimensionality" characteristic of gene expression data, the analysis results generated from a single dataset are often unsatisfactory. Under contexts other than dimension reduction, integrative analysis techniques, which jointly analyze the raw data of multiple independent datasets, have been developed and shown to outperform "classic" meta-analysis and other multidatasets techniques and single-dataset analysis...
November 8, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/29112949/integrative-analysis-of-genome-wide-gene-copy-number-changes-and-gene-expression-in-non-small-cell-lung-cancer
#16
Verena Jabs, Karolina Edlund, Helena König, Marianna Grinberg, Katrin Madjar, Jörg Rahnenführer, Simon Ekman, Michael Bergkvist, Lars Holmberg, Katja Ickstadt, Johan Botling, Jan G Hengstler, Patrick Micke
Non-small cell lung cancer (NSCLC) represents a genomically unstable cancer type with extensive copy number aberrations. The relationship of gene copy number alterations and subsequent mRNA levels has only fragmentarily been described. The aim of this study was to conduct a genome-wide analysis of gene copy number gains and corresponding gene expression levels in a clinically well annotated NSCLC patient cohort (n = 190) and their association with survival. While more than half of all analyzed gene copy number-gene expression pairs showed statistically significant correlations (10,296 of 18,756 genes), high correlations, with a correlation coefficient >0...
2017: PloS One
https://www.readbyqxmd.com/read/29108269/microarray-analyses-reveal-genes-related-to-progression-and-prognosis-of-esophageal-squamous-cell-carcinoma
#17
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/29103177/matrix-metalloproteinase-14-modulates-diabetes-and-alzheimer-s-disease-cross-talk-a-meta-analysis
#18
Jack Cheng, Hsin-Ping Liu, Cheng-Chun Lee, Mei-Ying Chen, Wei-Yong Lin, Fuu-Jen Tsai
Diabetes mellitus is associated with dementia, but whether diabetes is associated with Alzheimer's disease remains controversial. Alzheimer's disease is characterized by amyloid beta aggregation. We hypothesized that genes, involved in amyloid beta degradation, may be altered due to diabetes and thus participate in progression of Alzheimer's disease. Expression profiling of amyloid beta-degrading enzymes in streptozotocin-induced diabetic mice and their correlation with expression of amyloid precursor protein in hippocampus of Alzheimer's disease patients were accessed...
November 4, 2017: Neurological Sciences
https://www.readbyqxmd.com/read/29102815/combining-genetic-and-epigenetic-parameters-of-the-serotonin-transporter-gene-in-obsessive-compulsive-disorder
#19
Edna Grünblatt, Zoya Marinova, Alexander Roth, Elena Gardini, Juliane Ball, Julia Geissler, Tomasz K Wojdacz, Marcel Romanos, Susanne Walitza
While genetic variants have been reported to be associated with obsessive-compulsive disorder (OCD), the small effect sizes suggest that epigenetic mechanisms such as DNA methylation may also be relevant. The serotonin transporter (SLC6A4) gene has been extensively investigated in relation to OCD, since serotonin reuptake inhibitors are the pharmacological treatment of choice for the disorder. The current study set three questions: Firstly, whether the high expressing loci of the SLC6A4 polymorphisms, 5-HTTLPR + rs25531, rs25532 and rs16965628 are associated with family-based (n = 164 trios) and case-control OCD (n = 186, 152, respectively)...
October 16, 2017: Journal of Psychiatric Research
https://www.readbyqxmd.com/read/29100317/the-30-kb-deletion-in-the-apobec3-cluster-decreases-apobec3a-and-apobec3b-expression-and-creates-a-transcriptionally-active-hybrid-gene-but-does-not-associate-with-breast-cancer-in-the-european-population
#20
Katarzyna Klonowska, Wojciech Kluzniak, Bogna Rusak, Anna Jakubowska, Magdalena Ratajska, Natalia Krawczynska, Danuta Vasilevska, Karol Czubak, Marzena Wojciechowska, Cezary Cybulski, Jan Lubinski, Piotr Kozlowski
APOBEC3B, in addition to other members of the APOBEC3 gene family, has recently been intensively studied due to its identification as a gene whose activation in cancer is responsible for a specific pattern of massively occurring somatic mutations. It was recently shown that a common large deletion in the APOBEC3 cluster (the APOBEC3B deletion) may increase the risk of breast cancer. However, conflicting evidence regarding this association was also reported. In the first step of our study, using different approaches, including an in-house designed multiplex ligation-dependent probe amplification assay, we analyzed the structure of the deletion and showed that although the breakpoints are located in highly homologous regions, which may generate recurrent occurrence of similar but not identical deletions, there is no sign of deletion heterogeneity...
September 29, 2017: Oncotarget
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