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gene expression meta analysis

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https://www.readbyqxmd.com/read/29210060/genome-wide-association-study-identifies-the-gldc-il33-locus-associated-with-survival-of-osteosarcoma-patients
#1
Roelof Koster, Orestis A Panagiotou, William A Wheeler, Eric Karlins, Julie M Gastier-Foster, Silvia Regina Caminada de Toledo, Antonio S Petrilli, Adrienne M Flanagan, Roberto Tirabosco, Irene L Andrulis, Jay S Wunder, Nalan Gokgoz, Ana Patiño-Garcia, Fernando Lecanda, Massimo Serra, Claudia Hattinger, Piero Picci, Katia Scotlandi, David M Thomas, Mandy L Ballinger, Richard Gorlick, Donald A Barkauskas, Logan G Spector, Margaret Tucker, D Hicks Belynda, Meredith Yeager, Robert N Hoover, Sholom Wacholder, Stephen J Chanock, Sharon A Savage, Lisa Mirabello
Survival rates for osteosarcoma, the most common primary bone cancer, have changed little over the past three decades and are particularly low for patients with metastatic disease. We conducted a multi-institutional genome-wide association study (GWAS) to identify germline genetic variants associated with overall survival in 632 patients with osteosarcoma including 523 patients of European ancestry and 109 from Brazil. We conducted a time-to-event analysis and estimated hazard ratios (HR) and 95% confidence intervals (CI) using Cox proportional hazards models, with and without adjustment for metastatic disease...
December 6, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29209617/mirroring-the-multiple-potentials-of-micrornas-in-acute-myocardial-infarction
#2
REVIEW
Solenne Paiva, Onnik Agbulut
At present, cardiovascular diseases are depicted to be the leading cause of death worldwide according to the World Health Organization. In the future, projections predict that ischemic heart disease will persist in the top main causes of illness. Within this alarming context, some tiny master regulators of gene expression programs, namely, microRNAs (miRNAs) carry three promising potentials. In fact, miRNAs can prove to be useful not only in terms of biomarkers allowing heart injury detection but also in terms of therapeutics to overcome limitations of past strategies and treat the lesions...
2017: Frontiers in Cardiovascular Medicine
https://www.readbyqxmd.com/read/29207133/potential-role-of-microrna%C3%A2-223%C3%A2-3p-in-the-tumorigenesis-of-hepatocellular-carcinoma-a-comprehensive-study-based-on-data-mining-and-bioinformatics
#3
Rui Zhang, Li-Jie Zhang, Mei-Ling Yang, Lan-Shan Huang, Gang Chen, Zhen-Bo Feng
The aims of the present study were to examine the potential role of microRNA‑233‑3p (miR)‑223‑3p in the tumorigenesis of hepatocellular carcinoma (HCC), and to investigate its diagnostic accuracy and potential molecular mechanisms. The expression data of miR‑223‑3p in HCC were obtained from the Gene Expression Omnibus (GEO). Data for the precursor miR‑223 were obtained from The Cancer Genome Atlas (TCGA). The diagnostic role of miR‑223‑3p was identified by the receiver operating curve (ROC), and the diagnostic value of miR‑223‑3p in HCC was calculated from qualified reports in the literature...
November 27, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29207053/diagnostic-significance-and-potential-function-of-mir-338-5p-in-hepatocellular-carcinoma-a-bioinformatics-study-with-microarray-and-rna-sequencing-data
#4
Liang Liang, Li Gao, Xiao-Ping Zou, Meng-Lan Huang, Gang Chen, Jian-Jun Li, Xiao-Yong Cai
MicroRNA (miR)-338-5p has been studied in hepatocellular carcinoma (HCC); however, the diagnostic value and molecular mechanism underlying its actions remains to be elucidated. The present study aimed to validate the diagnostic ability of miR‑338‑5p and further explore the underlying molecular mechanism. Data from eligible studies, Gene Expression Omnibus (GEO) chips and The Cancer Genome Atlas (TCGA) datasets were gathered in the data mining and the integrated meta‑analysis, to evaluate the significance of miR‑338‑5p in diagnosing HCC comprehensively...
November 21, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29203636/identification-of-potential-pathogenic-genes-associated-with-osteoporosis
#5
B Xia, Y Li, J Zhou, B Tian, L Feng
OBJECTIVES: Osteoporosis is a chronic disease. The aim of this study was to identify key genes in osteoporosis. METHODS: Microarray data sets GSE56815 and GSE56814, comprising 67 osteoporosis blood samples and 62 control blood samples, were obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified in osteoporosis using Limma package (3.2.1) and Meta-MA packages. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to identify biological functions...
December 2017: Bone & Joint Research
https://www.readbyqxmd.com/read/29203587/nampt-is-a-potent-oncogene-in-colon-cancer-progression-that-modulates-cancer-stem-cell-properties-and-resistance-to-therapy-through-sirt1-and-parp
#6
Amancio Carnero, Antonio Lucena-Cacace, Daniel Otero-Albiol, Manuel P Jimenez-Garcia, Sandra Muñoz-Galvan
PURPOSE: Colorectal cancer (CRC) is the second most common cancer in women and the third most common in men worldwide. However, despite current progress, many patients with advanced and metastatic tumors still die from the malignancy. Refractory disease often relies on nicotinamide adenine dinucleotide(NAD)-dependent mechanisms. NAD metabolism and a stable NAD regeneration circuit are required to maintain tissue homeostasis and metabolism. However, high levels of NAD confer therapy resistance to tumors...
December 4, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29202780/transforming-growth-factor-beta-tgf-%C3%AE-in-adolescent-chronic-fatigue-syndrome
#7
Vegard Bruun Wyller, Chinh Bkrong Nguyen, Judith Anita Ludviksen, Tom Eirik Mollnes
BACKGROUND: Chronic fatigue syndrome (CFS) is a prevalent and disabling condition among adolescent. The disease mechanisms are unknown. Previous studies have suggested elevated plasma levels of several cytokines, but a recent meta-analysis of 38 articles found that of 77 different cytokines measured in plasma, transforming growth factor beta (TGF-β) was the only one that was elevated in patients compared to controls in a sufficient number of articles. In the present study we therefore compared the plasma levels of the three TGF-β isoforms in adolescent CFS patients and healthy controls...
December 4, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29198723/dna-methylation-analysis-identifies-loci-for-blood-pressure-regulation
#8
Melissa A Richard, Tianxiao Huan, Symen Ligthart, Rahul Gondalia, Min A Jhun, Jennifer A Brody, Marguerite R Irvin, Riccardo Marioni, Jincheng Shen, Pei-Chien Tsai, May E Montasser, Yucheng Jia, Catriona Syme, Elias L Salfati, Eric Boerwinkle, Weihua Guan, Thomas H Mosley, Jan Bressler, Alanna C Morrison, Chunyu Liu, Michael M Mendelson, André G Uitterlinden, Joyce B van Meurs, Oscar H Franco, Guosheng Zhang, Yun Li, James D Stewart, Joshua C Bis, Bruce M Psaty, Yii-Der Ida Chen, Sharon L R Kardia, Wei Zhao, Stephen T Turner, Devin Absher, Stella Aslibekyan, John M Starr, Allan F McRae, Lifang Hou, Allan C Just, Joel D Schwartz, Pantel S Vokonas, Cristina Menni, Tim D Spector, Alan Shuldiner, Coleen M Damcott, Jerome I Rotter, Walter Palmas, Yongmei Liu, Tomáš Paus, Steve Horvath, Jeffrey R O'Connell, Xiuqing Guo, Zdenka Pausova, Themistocles L Assimes, Nona Sotoodehnia, Jennifer A Smith, Donna K Arnett, Ian J Deary, Andrea A Baccarelli, Jordana T Bell, Eric Whitsel, Abbas Dehghan, Daniel Levy, Myriam Fornage
Genome-wide association studies have identified hundreds of genetic variants associated with blood pressure (BP), but sequence variation accounts for a small fraction of the phenotypic variance. Epigenetic changes may alter the expression of genes involved in BP regulation and explain part of the missing heritability. We therefore conducted a two-stage meta-analysis of the cross-sectional associations of systolic and diastolic BP with blood-derived genome-wide DNA methylation measured on the Infinium HumanMethylation450 BeadChip in 17,010 individuals of European, African American, and Hispanic ancestry...
November 30, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29198719/multiethnic-gwas-reveals-polygenic-architecture-of-earlobe-attachment
#9
John R Shaffer, Jinxi Li, Myoung Keun Lee, Jasmien Roosenboom, Ekaterina Orlova, Kaustabh Adhikari, Carla Gallo, Giovanni Poletti, Lavinia Schuler-Faccini, Maria-Cátira Bortolini, Samuel Canizales-Quinteros, Francisco Rothhammer, Gabriel Bedoya, Rolando González-José, Paige E Pfeffer, Christopher A Wollenschlaeger, Jacqueline T Hecht, George L Wehby, Lina M Moreno, Anan Ding, Li Jin, Yajun Yang, Jenna C Carlson, Elizabeth J Leslie, Eleanor Feingold, Mary L Marazita, David A Hinds, Timothy C Cox, Sijia Wang, Andrés Ruiz-Linares, Seth M Weinberg
The genetic basis of earlobe attachment has been a matter of debate since the early 20th century, such that geneticists argue both for and against polygenic inheritance. Recent genetic studies have identified a few loci associated with the trait, but large-scale analyses are still lacking. Here, we performed a genome-wide association study of lobe attachment in a multiethnic sample of 74,660 individuals from four cohorts (three with the trait scored by an expert rater and one with the trait self-reported). Meta-analysis of the three expert-rater-scored cohorts revealed six associated loci harboring numerous candidate genes, including EDAR, SP5, MRPS22, ADGRG6 (GPR126), KIAA1217, and PAX9...
November 21, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29197182/protection-of-macrophages-from-intracellular-pathogens-by-mir-182-5p-mimic-a-gene-expression-meta-analysis-approach
#10
David J Gregory, Igor Kramnik, Lester Kobzik
The goals of this study were to i) define which host genes are of particular importance during the interactions between macrophages and intracellular pathogens, and ii) use this knowledge to gain fresh, experimental understanding of how macrophage activities may be manipulated during host defence. We designed an in silico method for meta-analysis of microarray gene expression data, and used this to combine data from 16 different studies of cells in the monocyte-macrophage lineage infected with 7 different pathogens...
December 2, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29194095/is-nonmetastatic-cutaneous-melanoma-predictable-through-genomic-biomarkers
#11
Mattia Branca, Samuel Orso, Roberto C Molinari, Haotian Xu, Stéphane Guerrier, Yuming Zhang, Nabil Mili
Cutaneous melanoma is a highly aggressive skin cancer whose treatment and prognosis are critically affected by the presence of metastasis. In this study, we address the following issue: which gene transcripts and what kind of interactions between them can allow to predict nonmetastatic from metastatic melanomas with a high level of accuracy? We carry out a meta-analysis on the first gene expression set of the Leeds melanoma cohort, as made available online on 11 May 2016 through the ArrayExpress platform with MicroArray Gene Expression number 4725...
November 29, 2017: Melanoma Research
https://www.readbyqxmd.com/read/29187960/meta-analysis-of-liver-and-heart-transcriptomic-data-for-functional-annotation-transfer-in-mammalian-orthologs
#12
Pía Francesca Loren Reyes, Tom Michoel, Anagha Joshi, Guillaume Devailly
Functional annotation transfer across multi-gene family orthologs can lead to functional misannotations. We hypothesised that co-expression network will help predict functional orthologs amongst complex homologous gene families. To explore the use of transcriptomic data available in public domain to identify functionally equivalent ones from all predicted orthologs, we collected genome wide expression data in mouse and rat liver from over 1500 experiments with varied treatments. We used a hyper-graph clustering method to identify clusters of orthologous genes co-expressed in both mouse and rat...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29187571/the-brassicaceae-family-displays-divergent-shoot-skewed-nlr-resistance-gene-expression
#13
David Munch, Vikas Gupta, Terry Mun, Asger Bachmann, Wolfgang Busch, Simon Kelly, Stig U Andersen
Nucleotide-binding site leucine-rich repeat resistance genes (NLRs) allow plants to detect microbial effectors. We hypothesized that NLR expression patterns could reflect organ-specific differences in effector challenge and tested this by carrying out a meta-analysis of expression data for 1,235 NLRs from 9 plant species. We found stable NLR root/shoot expression ratios within species, suggesting organ-specific hardwiring of NLR expression patterns in anticipation of distinct challenges. Most monocot and dicot plant species preferentially expressed NLRs in roots...
November 29, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29186694/large-scale-cognitive-gwas-meta-analysis-reveals-tissue-specific-neural-expression-and-potential-nootropic-drug-targets
#14
Max Lam, Joey W Trampush, Jin Yu, Emma Knowles, Gail Davies, David C Liewald, John M Starr, Srdjan Djurovic, Ingrid Melle, Kjetil Sundet, Andrea Christoforou, Ivar Reinvang, Pamela DeRosse, Astri J Lundervold, Vidar M Steen, Thomas Espeseth, Katri Räikkönen, Elisabeth Widen, Aarno Palotie, Johan G Eriksson, Ina Giegling, Bettina Konte, Panos Roussos, Stella Giakoumaki, Katherine E Burdick, Antony Payton, William Ollier, Ornit Chiba-Falek, Deborah K Attix, Anna C Need, Elizabeth T Cirulli, Aristotle N Voineskos, Nikos C Stefanis, Dimitrios Avramopoulos, Alex Hatzimanolis, Dan E Arking, Nikolaos Smyrnis, Robert M Bilder, Nelson A Freimer, Tyrone D Cannon, Edythe London, Russell A Poldrack, Fred W Sabb, Eliza Congdon, Emily Drabant Conley, Matthew A Scult, Dwight Dickinson, Richard E Straub, Gary Donohoe, Derek Morris, Aiden Corvin, Michael Gill, Ahmad R Hariri, Daniel R Weinberger, Neil Pendleton, Panos Bitsios, Dan Rujescu, Jari Lahti, Stephanie Le Hellard, Matthew C Keller, Ole A Andreassen, Ian J Deary, David C Glahn, Anil K Malhotra, Todd Lencz
Here, we present a large (n = 107,207) genome-wide association study (GWAS) of general cognitive ability ("g"), further enhanced by combining results with a large-scale GWAS of educational attainment. We identified 70 independent genomic loci associated with general cognitive ability. Results showed significant enrichment for genes causing Mendelian disorders with an intellectual disability phenotype. Competitive pathway analysis implicated the biological processes of neurogenesis and synaptic regulation, as well as the gene targets of two pharmacologic agents: cinnarizine, a T-type calcium channel blocker, and LY97241, a potassium channel inhibitor...
November 28, 2017: Cell Reports
https://www.readbyqxmd.com/read/29186428/genome-wide-meta-analysis-identifies-novel-determinants-of-circulating-serum-progranulin
#15
Anke Tönjes, Markus Scholz, Jacqueline Krüger, Kerstin Krause, Dorit Schleinitz, Holger Kirsten, Claudia Gebhardt, Carola Marzi, Harald Grallert, Claes Ladenvall, Henrike Heyne, Esa Laurila, Jennifer Kriebel, Christa Meisinger, Wolfgang Rathmann, Christian Gieger, Leif Groop, Inga Prokopenko, Bo Isomaa, Frank Beutner, Jürgen Kratzsch, Antje Fischer-Rosinsky, Andreas Pfeiffer, Knut Krohn, Joachim Spranger, Joachim Thiery, Matthias Blüher, Michael Stumvoll, Peter Kovacs
Progranulin is a secreted protein with important functions in processes including immune and inflammatory response, metabolism and embryonic development. The present study aimed at identification of genetic factors determining progranulin concentrations.We conducted a genome-wide association meta-analysis for serum progranulin in three independent cohorts from Europe: Sorbs (N = 848) and KORA (N = 1,628) from Germany and PPP-Botnia (N = 335) from Finland (total N = 2,811). SNPs associated with progranulin levels were replicated in two additional German cohorts: LIFE Heart Study (Leipzig; N = 967) and Metabolic Syndrome Berlin Potsdam (Berlin cohort; N = 833)...
November 27, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29182646/transcriptome-wide-analysis-of-the-trypanosoma-cruzi-proliferative-cycle-identifies-the-periodically-expressed-mrnas-and-their-multiple-levels-of-control
#16
Santiago Chávez, Guillermo Eastman, Pablo Smircich, Lorena Lourdes Becco, Carolina Oliveira-Rizzo, Rafael Fort, Mariana Potenza, Beatriz Garat, José Roberto Sotelo-Silveira, María Ana Duhagon
Trypanosoma cruzi is the protozoan parasite causing American trypanosomiasis or Chagas disease, a neglected parasitosis with important human health impact in Latin America. The efficacy of current therapy is limited, and its toxicity is high. Since parasite proliferation is a fundamental target for rational drug design, we sought to progress into its understanding by applying a genome-wide approach. Treating a TcI linage strain with hydroxyurea, we isolated epimastigotes in late G1, S and G2/M cell cycle stages at 70% purity...
2017: PloS One
https://www.readbyqxmd.com/read/29180674/why-is-there-selective-subcortical-vulnerability-in-adhd-clues-from-postmortem-brain-gene-expression-data
#17
J L Hess, G C Akutagava-Martins, J D Patak, S J Glatt, S V Faraone
Sub-cortical volumetric differences were associated with attention-deficit/hyperactivity disorder (ADHD) in a recent multi-site, mega-analysis of 1713 ADHD persons and 1529 controls. As there was a wide range of effect sizes among the sub-cortical volumes, it is possible that selective neuronal vulnerability has a role in these volumetric losses. To address this possibility, we used data from Allen Brain Atlas to investigate variability in gene expression profiles between subcortical regions of typically developing brains...
November 28, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/29179508/homeobox-protein-cdx2-as-a-prognostic-biomarker-in-solid-malignancies-a-meta-analysis
#18
Jingsheng Yuan, Zhijie Yin, Kaixiong Tao, Guobing Wang, Jinbo Gao
Background: CDX2 is a caudal-homeobox gene and its expression is abnormal in numerous tumour cell types. Nevertheless, its prognostic value for solid tumours requires further investigation. Hence, we conducted a meta-analysis to determine the significance of CDX2 as a prognostic biomarker in solid malignancies systematically. Materials and Methods: We performed a systematic literature search in PUBMED and EMBASE up to May 2017. Retrospective studies comparing the prognostic value of different CDX2 levels in human malignancies were included...
October 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/29172257/clinicopathological-significance-of-mta-1-expression-in-patients-with-non-small-cell-lung-cancer-a-meta-analysis
#19
Wei Zhu, Guixian Li, Haina Guo, Honglang Chen, Xiujuan Xu, Jiali Long, Chao Zeng, Xiaojun Wang
Background: Metastasis associated gene 1(MTA1) is one of the most deregulated molecules in human cancer and leads to cancer progression and metastasis. We performed a meta-analysis to determine the correlations between MTA1 expression and the clinicopathological characteristics of non-small cell lung cancer (NSCLC). Methods: We searched PubMed, Springer, Science Direct, Google Scholar and China National Knowledge Infrastructure (CNKI) for relevant articles. For statistical analyses, we used R3.1.1 software...
November 26, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/29167564/whole-transcriptome-sequencing-analyses-reveal-molecular-markers-of-blood-pressure-response-to-thiazide-diuretics
#20
Ana Caroline C Sá, Amy Webb, Yan Gong, Caitrin W McDonough, Somnath Datta, Taimour Y Langaee, Stephen T Turner, Amber L Beitelshees, Arlene B Chapman, Eric Boerwinkle, John G Gums, Steven E Scherer, Rhonda M Cooper-DeHoff, Wolfgang Sadee, Julie A Johnson
Thiazide diuretics (TD) are commonly prescribed anti-hypertensives worldwide. However, <40% of patients treated with thiazide monotherapy achieve BP control. This study uses whole transcriptome sequencing to identify novel molecular markers associated with BP response to TD. We assessed global RNA expression levels in whole blood samples from 150 participants, representing patients in the upper and lower quartile of BP response to TD from the Pharmacogenomic Evaluation of Antihypertensive Responses (PEAR) (50 whites) and from PEAR-2 (50 whites and 50 blacks)...
November 22, 2017: Scientific Reports
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