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gene expression meta-analysis

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https://www.readbyqxmd.com/read/29786918/novel-genes-and-insights-in-complete-asthma-remission
#1
Judith M Vonk, Maartje A E Nieuwenhuis, F Nicole Dijk, Anne Boudier, Valerie Siroux, Emmanuelle Bouzigon, Nicole Probst-Hensch, Medea Imboden, Dirk Keidel, Don Sin, Yohan Bossé, Ke Hao, Maarten van den Berge, Alen Faiz, Gerard H Koppelman, Dirkje S Postma
BACKGROUND: Asthma is a chronic respiratory disease without a cure, though there exists spontaneous remission. Genome wide association(GWA) studies have pinpointed genes associated with asthma development, but did not investigate asthma remission. OBJECTIVES: We performed a GWA study to develop insights in asthma remission. METHODS: Clinical remission (ClinR) was defined by absence of asthma treatment and wheezing in the last year and asthma attacks in the last 3 years, and complete remission (ComR) similarly but additionally with normal lung function and absence of bronchial hyperresponsiveness (BHR)...
May 22, 2018: Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29786549/pluripotent-stem-cells-induction-and-self-renewal
#2
REVIEW
R Abu-Dawud, N Graffmann, S Ferber, W Wruck, J Adjaye
Pluripotent stem cells (PSCs) lie at the heart of modern regenerative medicine due to their properties of unlimited self-renewal in vitro and their ability to differentiate into cell types representative of the three embryonic germ layers-mesoderm, ectoderm and endoderm. The derivation of induced PSCs bypasses ethical concerns associated with the use of human embryonic stem cells and also enables personalized cell-based therapies. To exploit their regenerative potential, it is essential to have a firm understanding of the molecular processes associated with their induction from somatic cells...
July 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29785040/archetypal-transcriptional-blocks-underpin-yeast-gene-regulation-in-response-to-changes-in-growth-conditions
#3
David Talavera, Christopher J Kershaw, Joseph L Costello, Lydia M Castelli, William Rowe, Paul F G Sims, Mark P Ashe, Chris M Grant, Graham D Pavitt, Simon J Hubbard
The transcriptional responses of yeast cells to diverse stresses typically include gene activation and repression. Specific stress defense, citric acid cycle and oxidative phosphorylation genes are activated, whereas protein synthesis genes are coordinately repressed. This view was achieved from comparative transcriptomic experiments delineating sets of genes whose expression greatly changed with specific stresses. Less attention has been paid to the biological significance of 1) consistent, albeit modest, changes in RNA levels across multiple conditions, and 2) the global gene expression correlations observed when comparing numerous genome-wide studies...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784013/vegf-vascularization-pathway-in-human-intervertebral-disc-does-not-change-during-the-disc-degeneration-process
#4
Simona Capossela, Alessandro Bertolo, Kapila Gunasekera, Tobias Pötzel, Martin Baur, Jivko V Stoyanov
OBJECTIVE: During degeneration of the intervertebral disc ingrowth of blood vessels and nerves into the disc are associated with back pain. Vascular endothelial growth factors promote vasculogenesis by binding to the membrane vascular endothelial growth factor receptor 1, while shorter soluble forms of this receptor can inhibit vascularization. We hypothesized that membrane and soluble receptor forms might change between stages of intervertebral disc degeneration. RESULTS: Expression of soluble and membrane forms of vascular endothelial growth factor receptor 1 in human degenerated intervertebral discs and healthy bovine caudal discs was assessed by qRT-PCR and immunoblot...
May 22, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29779017/-xpg-rs17655-g-c-polymorphism-associated-with-cancer-risk-evidence-from-60-studies
#5
Jie Zhao, Shanshan Chen, Haixia Zhou, Ting Zhang, Yang Liu, Jing He, Jinhong Zhu, Jichen Ruan
Xeroderma pigmentosum group G (XPG), a key component in nucleotide excision repair pathway, functions to cut DNA lesions during DNA repair. Genetic variations that alter DNA repair gene expression or function may decrease DNA repair ability and impair genome integrity, thereby predisposing to cancer. The association between XPG rs17655 G>C polymorphism and cancer risk has been investigated extensively, but the results remain contradictory. To get a more accurate conclusion, we performed a comprehensive meta-analysis of 60 case-control studies, involving 27,098 cancer cases and 30,535 healthy controls...
May 20, 2018: Aging
https://www.readbyqxmd.com/read/29777315/the-mdm2-rs937283-a-g-variant-significantly-increases-the-risk-of-lung-and-gastric-cancer-in-chinese-population
#6
Bifeng Chen, Jieling Wang, Yucan Chen, Xiuli Gu, Xianhong Feng
BACKGROUND: Currently, the MDM2 promoter rs937283 A > G variant that is able to alter MDM2 gene expression has been widely studied to explore the association of MDM2 with cancer risk. In this report, we investigate the association of MDM2 rs937283 A > G variant with risk of lung cancer (LC) and gastric cancer (GC) in a Chinese population of Hubei province, which was followed by a meta-analysis. METHODS: The genotyping of rs937283 was performed by polymerase chain reaction-restriction fragment length polymorphism and confirmed by sequencing...
May 18, 2018: International Journal of Clinical Oncology
https://www.readbyqxmd.com/read/29775108/high-trna-transferase-nsun2-gene-expression-is-associated-with-poor-prognosis-in-head-and-neck-squamous-carcinoma
#7
Lingeng Lu, Gongjian Zhu, Hongmei Zeng, Qian Xu, Klaus Holzmann
NSUN2 is a tRNA methyltransferase and plays an important role in cell development via modifying RNA methylation. We aimed to evaluate the expression of NSUN2 and its prognostic value in HNSCC. Random-effects model of meta-analysis shows 1.99-folds (95% CI: 1.89-2.09) upregulation of NSUN2 expression in HNSCC versus normal tissues. Patients with high NSUN2 levels had approximately 22 months shorter overall survival, and had a higher mortality risk than those with low one (p-trend = 0.020). In conclusion, NSUN2 is a potential independent prognostic marker and may be a potential therapeutic target in HNSCC...
April 21, 2018: Cancer Investigation
https://www.readbyqxmd.com/read/29774565/local-and-systemic-regulation-of-psii-efficiency-in-triticale-infected-by-the-hemibiotrophic-pathogen-microdochium-nivale
#8
Mateusz Dyda, Iwona Wąsek, Mirosław Tyrka, Maria Wędzony, Magdalena Szechyńska-Hebda
Microdochium nivale is a fungal pathogen that causes yield losses of cereals during winter. Cold hardening under light conditions induces genotype-dependent resistance of a plant to infection. We aim to show how photosystem II (PSII) regulation contributes to plant resistance. Using mapping population of triticale doubled haploid lines, three M. nivale strains and different infection assays, we demonstrate that plants that maintain a higher maximum quantum efficiency of PSII show less leaf damage upon infection...
May 17, 2018: Physiologia Plantarum
https://www.readbyqxmd.com/read/29769662/novel-internal-regulators-and-candidate-mirnas-within-mir-379-mir-656-mirna-cluster-can-alter-cellular-phenotype-of-human-glioblastoma
#9
Subhashree Nayak, Meghali Aich, Anupam Kumar, Suman Sengupta, Prajakta Bajad, Parashar Dhapola, Deepanjan Paul, Kiran Narta, Suvendu Purkrait, Bharati Mehani, Ashish Suri, Debojyoti Chakraborty, Arijit Mukhopadhyay, Chitra Sarkar
Clustered miRNAs can affect functioning of downstream pathways due to possible coordinated function. We observed 78-88% of the miR-379/miR-656 cluster (C14MC) miRNAs were downregulated in three sub-types of diffuse gliomas, which was also corroborated with analysis from The Cancer Genome Atlas (TCGA) datasets. The miRNA expression levels decreased with increasing tumor grade, indicating this downregulation as an early event in gliomagenesis. Higher expression of the C14MC miRNAs significantly improved glioblastioma prognosis (Pearson's r = 0...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29768622/single-nucleotide-polymorphisms-of-cytokine-related-genes-and-association-with-clinical-outcome-in-a-chagas-disease-case-control-study-from-brazil
#10
Lucia Elena Alvarado-Arnez, Angelica Martins Batista, Silvia Marinho Alves, Gloria Melo, Virgínia Maria Barros de Lorena, Cynthia C Cardoso, Isabela Resende Pereira, Cristina Carrazzone, Antonio G Pacheco, Wilson Oliveira, Milton Ozório Moraes, Joseli Lannes-Vieira
BACKGROUND: The severity of chronic chagasic cardiomyopathy (CCC), the most frequent clinical outcome of Chagas disease (CD), has been associated with cytokine-enriched heart tissue inflammation, and high serum levels of transforming growth factor (TGFβ), interferon-gamma (IFNγ), and tumour necrosis factor (TNF). Conversely, increased interleukin (IL)-10 serum concentrations have been associated with asymptomatic CD. Cytokines and cytokine-related gene polymorphisms may control cytokine expression and have been proposed to contribute to CCC outcomes...
May 14, 2018: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/29763751/integration-of-summary-data-from-gwas-and-eqtl-studies-identified-novel-causal-bmd-genes-with-functional-predictions
#11
Xiang-He Meng, Xiang-Ding Chen, Jonathan Greenbaum, Qin Zeng, Sheng-Lan You, Hong-Mei Xiao, Li-Jun Tan, Hong-Wen Deng
PURPOSE: Osteoporosis is a common global health problem characterized by low bone mineral density (BMD) and increased risk of fracture. Genome-wide association studies (GWAS) have identified >100 genetic loci associated with BMD. However, the functional genes responsible for most associations remain largely unknown. We conducted an innovative summary statistic data-based Mendelian randomization (SMR) analysis to identify novel causal genes associated with BMD and explored their potential functional significance...
May 12, 2018: Bone
https://www.readbyqxmd.com/read/29761469/hymenoptera-genome-database-using-hymenopteramine-to-enhance-genomic-studies-of-hymenopteran-insects
#12
Christine G Elsik, Aditi Tayal, Deepak R Unni, Gregory W Burns, Darren E Hagen
The Hymenoptera Genome Database (HGD; http://hymenopteragenome.org ) is a genome informatics resource for insects of the order Hymenoptera, which includes bees, ants and wasps. HGD provides genome browsers with manual annotation tools (JBrowse/Apollo), BLAST, bulk data download, and a data mining warehouse (HymenopteraMine). This chapter focuses on the use of HymenopteraMine to create annotation data sets that can be exported for use in downstream analyses. HymenopteraMine leverages the InterMine platform to combine genome assemblies and official gene sets with data from OrthoDB, RefSeq, FlyBase, Gene Ontology, UniProt, InterPro, KEGG, Reactome, dbSNP, PubMed, and BioGrid, as well as precomputed gene expression information based on publicly available RNAseq...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29758295/systematic-bioinformatic-approaches-reveal-novel-gene-expression-signatures-associated-with-acquired-resistance-to-egfr-targeted-therapy-in-lung-cancer
#13
Marjan Mojtabavi Naeini, Manoochehr Tavassoli, Kamran Ghaedi
OBJECTIVES: Human non-small cell lung cancer (NSCLC) that harbors activating mutations in epidermal growth factor receptor (EGFR) initially responds to treatment with EGFR tyrosine kinase inhibitors (TKIs) such as gefitinib and erlotinib but eventually tumor cells acquire resistance. To date, several gene expression profiles have been reported in TKIs-resistant EGFR-mutant NSCLC. The objective of this study is to identify robust gene expression signatures, biological processes, and promising overcoming targets for TKIs-resistant EGFR-mutant NSCLC...
May 11, 2018: Gene
https://www.readbyqxmd.com/read/29757366/a-systematic-review-and-meta-analysis-reveals-pervasive-effects-of-germline-mitochondrial-replacement-on-components-of-health
#14
Ralph Dobler, Damian K Dowling, Edward H Morrow, Klaus Reinhardt
BACKGROUND: Mitochondrial replacement, a form of nuclear transfer, has been proposed as a germline therapy to prevent the transmission of mitochondrial diseases. Mitochondrial replacement therapy has been licensed for clinical application in the UK, and already carried out in other countries, but little is known about negative or unintended effects on the health of offspring born using this technique. OBJECTIVE AND RATIONALE: Studies in invertebrate models have used techniques that achieve mitochondrial replacement to create offspring with novel combinations of mitochondrial and nuclear genotype...
May 11, 2018: Human Reproduction Update
https://www.readbyqxmd.com/read/29755398/deconvolution-of-human-brain-cell-type-transcriptomes-unraveled-microglia-specific-potential-biomarkers
#15
R Ayana, Shailja Singh, Soumya Pati
Microglial cells form a context-dependent network of brain immunoeffector cells. Despite their indispensable roles, unresolved questions exist around biomarker discovery relevant to their cellular localization, self-renewing potential, and brain developmental dynamics. To resolve the existent gap in the annotation of candidate biomarkers, we conducted a meta-analysis of brain cells using available high-throughput data sets for deciphering microglia-specific expression profiles. We have identified 3,290 significant genes specific to microglia and further selected the top 20 dysregulated genes on the basis of p -value and log2 FC...
2018: Frontiers in Neurology
https://www.readbyqxmd.com/read/29750799/population-specific-genetic-modification-of-huntington-s-disease-in-venezuela
#16
Michael J Chao, Kyung-Hee Kim, Jun Wan Shin, Diane Lucente, Vanessa C Wheeler, Hong Li, Jared C Roach, Leroy Hood, Nancy S Wexler, Laura B Jardim, Peter Holmans, Lesley Jones, Michael Orth, Seung Kwak, Marcy E MacDonald, James F Gusella, Jong-Min Lee
Modifiers of Mendelian disorders can provide insights into disease mechanisms and guide therapeutic strategies. A recent genome-wide association (GWA) study discovered genetic modifiers of Huntington's disease (HD) onset in Europeans. Here, we performed whole genome sequencing and GWA analysis of a Venezuelan HD cluster whose families were crucial for the original mapping of the HD gene defect. The Venezuelan HD subjects develop motor symptoms earlier than their European counterparts, implying the potential for population-specific modifiers...
May 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29749535/oncogenic-role-of-mir%C3%A2-183%C3%A2-5p-in-lung-adenocarcinoma-a-comprehensive-study-of-qpcr-in-vitro-experiments-and-bioinformatic-analysis
#17
Rong-Quan He, Li Gao, Jie Ma, Zu-Yun Li, Xiao-Hua Hu, Gang Chen
Despite the fact that previous studies have reported the aberrant expression of miR‑183‑5p in lung adenocarcinoma (LUAD), the oncogenic role of miR‑183‑5p in LUAD and its underlying mechanisms have remained elusive. Hence, we attempted to elucidate the clinicopathological significance of miR‑183‑5p expression in LUAD and identify the biological function of miR‑183‑5p in LUAD in this study. Meta‑analysis of Gene Expression Omnibus (GEO) data, data mining of The Cancer Genome Atlas (TCGA) and real‑time quantitative polymerase chain reaction (qPCR) were performed to evaluate the clinicopathological significance of miR‑183‑5p in LUAD...
May 9, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29748761/gene-expression-in-triple-negative-breast-cancer-in-relation-to-survival
#18
Shuyang Wang, Alicia Beeghly-Fadiel, Qiuyin Cai, Hui Cai, Xingyi Guo, Liang Shi, Jie Wu, Fei Ye, Qingchao Qiu, Ying Zheng, Wei Zheng, Ping-Ping Bao, Xiao-Ou Shu
PURPOSE: The identification of biomarkers related to the prognosis of triple-negative breast cancer (TNBC) is critically important for improved understanding of the biology that drives TNBC progression. METHODS: We evaluated gene expression in total RNA isolated from formalin-fixed paraffin-embedded tumor samples using the NanoString nCounter assay for 469 TNBC cases from the Shanghai Breast Cancer Survival Study. We used Cox regression to quantify Hazard Ratios (HR) and corresponding confidence intervals (CI) for overall survival (OS) and disease-free survival (DFS) in models that included adjustment for breast cancer intrinsic subtype...
May 10, 2018: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29745833/differential-networking-meta-analysis-of-gastric-cancer-across-asian-and-american-racial-groups
#19
Wentao Dai, Quanxue Li, Bing-Ya Liu, Yi-Xue Li, Yuan-Yuan Li
BACKGROUND: Gastric Carcinoma is one of the most lethal cancer around the world, and is also the most common cancers in Eastern Asia. A lot of differentially expressed genes have been detected as being associated with Gastric Carcinoma (GC) progression, however, little is known about the underlying dysfunctional regulation mechanisms. To address this problem, we previously developed a differential networking approach that is characterized by involving differential coexpression analysis (DCEA), stage-specific gene regulatory network (GRN) modelling and differential regulation networking (DRN) analysis...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29740474/integrated-quantitative-transcriptome-maps-of-human-trisomy-21-tissues-and-cells
#20
Maria Chiara Pelleri, Chiara Cattani, Lorenza Vitale, Francesca Antonaros, Pierluigi Strippoli, Chiara Locatelli, Guido Cocchi, Allison Piovesan, Maria Caracausi
Down syndrome (DS) is due to the presence of an extra full or partial chromosome 21 (Hsa21). The identification of genes contributing to DS pathogenesis could be the key to any rational therapy of the associated intellectual disability. We aim at generating quantitative transcriptome maps in DS integrating all gene expression profile datasets available for any cell type or tissue, to obtain a complete model of the transcriptome in terms of both expression values for each gene and segmental trend of gene expression along each chromosome...
2018: Frontiers in Genetics
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