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gene expression meta analysis

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https://www.readbyqxmd.com/read/29040973/sulforaphane-and-epigallocatechin-gallate-restore-estrogen-receptor-expression-by-modulating-epigenetic-events-in-the-breast-cancer-cell-line-mda-mb-231-a-systematic-review-and-meta-analysis
#1
Vincenza Gianfredi, Samuele Vannini, Massimo Moretti, Milena Villarini, Nicola Luigi Bragazzi, Alberto Izzotti, Daniele Nucci
BACKGROUND/AIMS: Epigenetics refers to modifications in gene activity and expression without alteration at the DNA sequence. Environment and diet could influence gene expression. Diet modifications may be meaningful in preventing and treating chronic diseases, cancer included. Dietary bioactive compounds, such as polyphenols (e.g., curcumin, resveratrol, or epigallocatechin gallate [EGCG]) or isothiocyanate (e.g., sulforaphane [SFN]), can regulate histone acetylation. The aim of this systematic review and meta-analysis was to evaluate the effect of SFN and EGCG on breast cancer (BC) cells cultured in vitro...
October 18, 2017: Journal of Nutrigenetics and Nutrigenomics
https://www.readbyqxmd.com/read/29035442/long-noncoding-rna-pvt1-as-a-potent-predictor-of-prognosis-in-cancers-a-meta-analysis
#2
Xuefeng Pan, Baohui Li, Naijun Fan, Juntang Li, Fengbo Cai, Guang Zhao, Guobao Zheng, Chunfang Gao
BACKGROUND: Plasmacytoma variant translocation 1 (PVT1), an oncogenic long noncoding RNA located in a recognized cancer-risk gene region-8q24, is significantly overexpressed in various cancers. Many studies have found that high expression of PVT1 was correlated with poor prognosis. METHODS: This meta-analysis was performed by searching electronic databases Pubmed, Web of Science, Chinese National Knowledge Infrastructure, WanFang, and ChongQing VIP for eligible papers on the prognostic impact and clinicopathological characteristics of PVT1 expression in cancer from inception to January 31, 2017...
October 1, 2017: Clinical Laboratory
https://www.readbyqxmd.com/read/29030403/new-blood-pressure-associated-loci-identified-in-meta-analyses-of-475%C3%A2-000-individuals
#3
Aldi T Kraja, James P Cook, Helen R Warren, Praveen Surendran, Chunyu Liu, Evangelos Evangelou, Alisa K Manning, Niels Grarup, Fotios Drenos, Xueling Sim, Albert Vernon Smith, Najaf Amin, Alexandra I F Blakemore, Jette Bork-Jensen, Ivan Brandslund, Aliki-Eleni Farmaki, Cristiano Fava, Teresa Ferreira, Karl-Heinz Herzig, Ayush Giri, Franco Giulianini, Megan L Grove, Xiuqing Guo, Sarah E Harris, Christian T Have, Aki S Havulinna, He Zhang, Marit E Jørgensen, AnneMari Käräjämäki, Charles Kooperberg, Allan Linneberg, Louis Little, Yongmei Liu, Lori L Bonnycastle, Yingchang Lu, Reedik Mägi, Anubha Mahajan, Giovanni Malerba, Riccardo E Marioni, Hao Mei, Cristina Menni, Alanna C Morrison, Sandosh Padmanabhan, Walter Palmas, Alaitz Poveda, Rainer Rauramaa, Nigel William Rayner, Muhammad Riaz, Ken Rice, Melissa A Richard, Jennifer A Smith, Lorraine Southam, Alena Stančáková, Kathleen E Stirrups, Vinicius Tragante, Tiinamaija Tuomi, Ioanna Tzoulaki, Tibor V Varga, Stefan Weiss, Andrianos M Yiorkas, Robin Young, Weihua Zhang, Michael R Barnes, Claudia P Cabrera, He Gao, Michael Boehnke, Eric Boerwinkle, John C Chambers, John M Connell, Cramer K Christensen, Rudolf A de Boer, Ian J Deary, George Dedoussis, Panos Deloukas, Anna F Dominiczak, Marcus Dörr, Roby Joehanes, Todd L Edwards, Tõnu Esko, Myriam Fornage, Nora Franceschini, Paul W Franks, Giovanni Gambaro, Leif Groop, Göran Hallmans, Torben Hansen, Caroline Hayward, Oksa Heikki, Erik Ingelsson, Jaakko Tuomilehto, Marjo-Riitta Jarvelin, Sharon L R Kardia, Fredrik Karpe, Jaspal S Kooner, Timo A Lakka, Claudia Langenberg, Lars Lind, Ruth J F Loos, Markku Laakso, Mark I McCarthy, Olle Melander, Karen L Mohlke, Andrew P Morris, Colin N A Palmer, Oluf Pedersen, Ozren Polasek, Neil R Poulter, Michael A Province, Bruce M Psaty, Paul M Ridker, Jerome I Rotter, Igor Rudan, Veikko Salomaa, Nilesh J Samani, Peter J Sever, Tea Skaaby, Jeanette M Stafford, John M Starr, Pim van der Harst, Peter van der Meer, Cornelia M van Duijn, Anne-Claire Vergnaud, Vilmundur Gudnason, Nicholas J Wareham, James G Wilson, Cristen J Willer, Daniel R Witte, Eleftheria Zeggini, Danish Saleheen, Adam S Butterworth, John Danesh, Folkert W Asselbergs, Louise V Wain, Georg B Ehret, Daniel I Chasman, Mark J Caulfield, Paul Elliott, Cecilia M Lindgren, Daniel Levy, Christopher Newton-Cheh, Patricia B Munroe, Joanna M M Howson
BACKGROUND: Genome-wide association studies have recently identified >400 loci that harbor DNA sequence variants that influence blood pressure (BP). Our earlier studies identified and validated 56 single nucleotide variants (SNVs) associated with BP from meta-analyses of exome chip genotype data. An additional 100 variants yielded suggestive evidence of association. METHODS AND RESULTS: Here, we augment the sample with 140 886 European individuals from the UK Biobank, in whom 77 of the 100 suggestive SNVs were available for association analysis with systolic BP or diastolic BP or pulse pressure...
October 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/29030101/genome-wide-association-study-and-meta-analysis-in-multiple-populations-identifies-new-loci-for-peanut-allergy-and-establishes-c11orf30-emsy-as-a-genetic-risk-factor-for-food-allergy
#4
Yuka Asai, Aida Eslami, C Dorien van Ginkel, Loubna Akhabir, Ming Wan, George Ellis, Moshe Ben-Shoshan, David Martino, Manuel A Ferreira, Katrina Allen, Bruce Mazer, Hans de Groot, Nicolette W de Jong, Roy N Gerth van Wijk, Anthony E J Dubois, Rick Chin, Steven Cheuk, Joshua Hoffman, Eric Jorgensen, John S Witte, Ronald B Melles, Xiumei Hong, Xiaobin Wang, Jennie Hui, Arthur W Bill Musk, Michael Hunter, Alan L James, Gerard H Koppelman, Andrew J Sandford, Ann E Clarke, Denise Daley
BACKGROUND: Peanut allergy (PA) is a complex disease with both environmental and genetic risk factors. Previously PA loci were identified in FLG and HLA in candidate gene studies, and loci in HLA in a genome-wide association study and meta-analysis. OBJECTIVE: To investigate genetic susceptibility to PA. METHODS: Eight hundred and fifty cases and 926 hyper-controls and >7.8 million genotyped and imputed single nucleotide polymorphisms (SNPs) were analyzed in a genome-wide association study to identify susceptibility variants for PA in the Canadian population...
October 10, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29029529/the-roles-of-maspin-expression-in-gastric-cancer-a-meta-and-bioinformatics-analysis
#5
Hua-Chuan Zheng, Bao-Cheng Gong
Maspin is a mammary serine protease inhibitor that is encoded by human SERPINB5 gene, and inhibits invasion and metastasis of cancer cells as a tumor suppressor. We performed a systematic meta- and bioinformatics analysis through multiple online databases up to Feb 10, 2017. We found down-regulated maspin expression in gastric cancer, compared with normal mucosa and dysplasia (p < 0.05). Maspin expression was negatively correlated with depth of invasion, TNM staging and dedifferentiation of gastric cancer (p < 0...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29029461/prognostic-value-of-long-non-coding-rna-tug1-in-various-tumors
#6
Na Li, Ke Shi, Xinmei Kang, Wei Li
Taurine up-regulated gene 1 (TUG1) is a long non-coding RNA (lncRNA), has been reported that be dysregulated in various tumors, involved in proliferation and apoptosis in a variety of tumor cells. To detect the clinical significance of TUG1 expression in tumor patients, we carried out current systematic review and meta-analysis investigating its relation with the prognosis and clinicopathological features of cancers. A total of 15 studies comprise 1560 patients were analyzed. The pooled results showed that no significant relationship between high TUG1 expression and overall survival (OS) (HR = 1...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29028988/quasar-mpra-accurate-allele-specific-analysis-for-massively-parallel-reporter-assays
#7
Cynthia A Kalita, Gregory A Moyerbrailean, Christopher Brown, Xiaoquan Wen, Francesca Luca, Roger Pique-Regi
Motivation: The majority of the human genome is composed of non-coding regions containing regulatory elements such as enhancers, which are crucial for controlling gene expression. Many variants associated with complex traits are in these regions, and may disrupt gene regulatory sequences. Consequently, it is important to not only identify true enhancers but also to test if a variant within an enhancer affects gene regulation. Recently, allele-specific analysis in high-throughput reporter assays, such as massively parallel reporter assays (MPRA), have been used to functionally validate non-coding variants...
September 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29024942/loss-of-myosin-vb-in-colorectal-cancer-is-a-strong-prognostic-factor-for-disease-recurrence
#8
Elisabeth Letellier, Martine Schmitz, Aurélien Ginolhac, Fabien Rodriguez, Pit Ullmann, Komal Qureshi-Baig, Sonia Frasquilho, Laurent Antunes, Serge Haan
BACKGROUND: Selecting the most beneficial treatment regimens for colorectal cancer (CRC) patients remains challenging due to a lack of prognostic markers. Members of the Myosin family, proteins recognised to have a major role in trafficking and polarisation of cells, have recently been reported to be closely associated with several types of cancer and might thus serve as potential prognostic markers in the context of CRC. METHODS: We used a previously established meta-analysis of publicly available gene expression data to analyse the expression of different members of the Myosin V family, namely MYO5A, 5B, and 5C, in CRC...
October 12, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/29024936/glucose-insult-elicits-hyperactivation-of-cancer-stem-cells-through-mir-424-cdc42-prdm14-signalling-axis
#9
Sushmita Bose Nandy, Alexis Orozco, Rebecca Lopez-Valdez, Rene Roberts, Ramadevi Subramani, Arunkumar Arumugam, Alok Kumar Dwivedi, Viktoria Stewart, Gautham Prabhakaran, Stephanie Jones, Rajkumar Lakshmanaswamy
BACKGROUND: Meta-analysis shows that women with diabetes have a 20% increased risk of breast cancer and also an increased risk for distant metastasis and mortality. The molecular mechanisms for distant metastasis and mortality in breast cancer patients with diabetes are not very well understood. METHODS: We compared the effect of physiological (5 mM) and diabetic (10 mM) levels of glucose on malignant breast epithelial cell invasion and stemness capabilities...
October 12, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/29024729/integrating-genome-wide-association-study-and-expression-quantitative-trait-locus-study-identifies-multiple-genes-and-gene-sets-associated-with-schizophrenia
#10
Yan Zhao, Awen He, Feng Zhu, Miao Ding, Jingcan Hao, Qianrui Fan, Ping Li, Li Liu, Yanan Du, Xiao Liang, Xiong Guo, Feng Zhang, Xiancang Ma
Schizophrenia is a serious mental disease with high heritability. To better understand the genetic basis of schizophrenia, we conducted a large scale integrative analysis of genome-wide association study (GWAS) and expression quantitative trait loci (eQTLs) data. GWAS summary data was derived from a published GWAS of schizophrenia, containing 9394 schizophrenia patients and 12,462 healthy controls. The eQTLs dataset was obtained from an eQTLs meta-analysis of 5311 subjects, containing 923,021 cis-eQTLs for 14,329 genes and 4732 trans-eQTLs for 2612 genes...
October 9, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/29016655/meta-analysis-of-peripheral-blood-gene-expression-modules-for-copd-phenotypes
#11
Dominik Reinhold, Jarrett D Morrow, Sean Jacobson, Junxiao Hu, Benjamin Ringel, Max A Seibold, Craig P Hersh, Katerina J Kechris, Russell P Bowler
Chronic obstructive pulmonary disease (COPD) occurs typically in current or former smokers, but only a minority of people with smoking history develops the disease. Besides environmental factors, genetics is an important risk factor for COPD. However, the relationship between genetics, environment and phenotypes is not well understood. Sample sizes for genome-wide expression studies based on lung tissue have been small due to the invasive nature of sample collection. Increasing evidence for the systemic nature of the disease makes blood a good alternative source to study the disease, but there have also been few large-scale blood genomic studies in COPD...
2017: PloS One
https://www.readbyqxmd.com/read/28990594/the-gene-encoding-protocadherin-9-pcdh9-a-novel-risk-factor-for-major-depressive-disorder
#12
Xiao Xiao, Fanfan Zheng, Hong Chang, Yina Ma, Yong-Gang Yao, Xiong-Jian Luo, Ming Li
Genomic analyses have identified only a handful of robust risk loci for major depressive disorder (MDD). In addition to the published genome-wide significant genes, it is believed that there are undiscovered 'treasures' underlying the current MDD genome-wide association studies (GWAS) and gene expression datasets, and digging into these data will allow better understanding of the illness and development of new therapeutic approaches. For this purpose, we performed a meta-analytic study combining three MDD GWAS datasets (23andMe, CONVERGE and PGC), then conducted independent replications of significant loci in two additional samples...
October 9, 2017: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28990294/genetic-and-molecular-risk-factors-within-the-newly-identified-primate-specific-exon-of-the-sap97-dlg1-gene-in-the-3q29-schizophrenia-associated-locus
#13
Akihito Uezato, Naoki Yamamoto, Daisuke Jitoku, Emiko Haramo, Eri Hiraaki, Yoshimi Iwayama, Tomoko Toyota, Masakazu Umino, Asami Umino, Yasuhide Iwata, Katsuaki Suzuki, Mitsuru Kikuchi, Tasuku Hashimoto, Nobuhisa Kanahara, Akeo Kurumaji, Takeo Yoshikawa, Toru Nishikawa
The synapse-associated protein 97/discs, large homolog 1 of Drosophila (DLG1) gene encodes synaptic scaffold PDZ proteins interacting with ionotropic glutamate receptors including the N-methyl-D-aspartate type glutamate receptor (NMDAR) that is presumed to be hypoactive in brains of patients with schizophrenia. The DLG1 gene resides in the chromosomal position 3q29, the microdeletion of which confers a 40-fold increase in the risk for schizophrenia. In the present study, we performed genetic association analyses for DLG1 gene using a Japanese cohort with 1808 schizophrenia patients and 2170 controls...
October 9, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28984201/identification-of-common-oncogenic-and-early-developmental-pathways-in-the-ovarian-carcinomas-controlling-by-distinct-prognostically-significant-microrna-subsets
#14
Vladimir A Kuznetsov, Zhiqun Tang, Anna V Ivshina
BACKGROUND: High-grade serous ovarian carcinoma (HG-SOC) is the dominant tumor histologic type in epithelial ovarian cancers, exhibiting highly aberrant microRNA expression profiles and diverse pathways that collectively determine the disease aggressiveness and clinical outcomes. However, the functional relationships between microRNAs, the common pathways controlled by the microRNAs and their prognostic and therapeutic significance remain poorly understood. METHODS: We investigated the gene expression patterns of microRNAs in the tumors of 582 HG-SOC patients to identify prognosis signatures and pathways controlled by tumor miRNAs...
October 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28983737/the-chromosome-6q22-33-region-is-associated-with-age-at-diagnosis-of-type-1-diabetes-and-disease-risk-in-those-diagnosed-under-5%C3%A2-years-of-age
#15
Jamie R J Inshaw, Neil M Walker, Chris Wallace, Leonardo Bottolo, John A Todd
AIMS/HYPOTHESIS: The genetic risk of type 1 diabetes has been extensively studied. However, the genetic determinants of age at diagnosis (AAD) of type 1 diabetes remain relatively unexplained. Identification of AAD genes and pathways could provide insight into the earliest events in the disease process. METHODS: Using ImmunoChip data from 15,696 cases, we aimed to identify regions in the genome associated with AAD. RESULTS: Two regions were convincingly associated with AAD (p < 5 × 10(-8)): the MHC on 6p21, and 6q22...
October 5, 2017: Diabetologia
https://www.readbyqxmd.com/read/28978351/the-caspase-8-ripk3-signaling-axis-in-antigen-presenting-cells-controls-the-inflammatory-arthritic-response
#16
Salina Dominguez, Anna B Montgomery, G Kenneth Haines, Christina L Bloomfield, Carla M Cuda
BACKGROUND: Caspase-8 is a well-established initiator of apoptosis and suppressor of necroptosis, but maintains functions beyond cell death that involve suppression of receptor-interacting serine-threonine kinases (RIPKs). A genome-wide association study meta-analysis revealed an SNP associated with risk of rheumatoid arthritis (RA) development within the locus containing the gene encoding for caspase-8. Innate immune cells, like macrophages and dendritic cells, are gaining momentum as facilitators of autoimmune disease pathogenesis, and, in particular, RA...
October 4, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28978122/correlation-between-protein-kinase-catalytic-subunit-alpha-1-gene-rs13361707-polymorphism-and-gastric-cancer-susceptibility-in-asian-populations
#17
Jianfeng Ni, Nan Shen, Jilei Tang, Kewei Ren
A single nucleotide polymorphism (SNP) of the protein kinase catalytic subunit alpha-1 gene (PRKAA1) that confers susceptibility to gastric cancer (GC) was identified by genome-wide association in several case-control studies. However, the results remained controversial and ambiguous. Therefore, we performed a larger meta-analysis to confirm this association. We searched the PubMed, Embase, WanFang, and CNKI databases, without any restriction on language, covering all papers published until Feb 22, 2017. Overall, 14 case-control studies with 14,485 cases and 14,792 controls were retrieved based on the search criteria...
September 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28977969/a-meta-analysis-of-transcriptomic-characterization-revealed-extracellular-matrix-pathway-involved-in-the-h5n1-and-h7n9-infections
#18
Feng Wen, Jinyue Guo, Guangzhi Tong, Dingren Bi, Qi Wang, Xiaomin Liu, Shuaiyong Wang, Tonglin Shan, Wu Tong, Yanjun Zhou, Guoxin Li, Hai Yu
Avian-origin H5N1 and H7N9 influenza A viruses are capable of causing lethal infection in humans, with serious lung pathology and leading to acute respiratory distress syndrome. The contribution of host response associated with the poor prognosis of H5N1 and H7N9 infections remains unclear. The aim of this study was to identify the host factors involved in the high pathogenicity of H5N1 and H7N9 by a systematical meta-analysis. The RNA-seq datasets related to H5N1, H7N9, and H1N1 infections with time series were retrieved from GEO...
September 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28977959/long-non-coding-rna-tug1-as-a-potential-prognostic-biomarker-in-human-cancers-a-meta-analysis
#19
Peng-Ju Ma, Qing-Kai Guan, Lei Meng, Nan Qin, Jia Zhao, Bao-Zhe Jin
LncRNA taurine upregulated gene 1 (TUG1) is reportedly dysregulated in various cancers. We performed this meta-analysis to clarify the usefulness of TUG1 as a prognostic marker in malignant tumors. The PubMed, Medline, OVID, Cochrane Library, and Web of Science databases were searched from inception to Jan 11, 2017. Hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated to explore the relationship between TUG1 expression and overall survival (OS). Odds ratios (ORs) were calculated to assess the association between TUG1 expression and pathological parameters...
September 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28973476/meta-analysis-of-transcriptomic-datasets-identifies-genes-enriched-in-the-mammalian-circadian-pacemaker
#20
Laurence A Brown, John Williams, Lewis Taylor, Ross J Thomson, Patrick M Nolan, Russell G Foster, Stuart N Peirson
The master circadian pacemaker in mammals is located in the suprachiasmatic nuclei (SCN) which regulate physiology and behaviour, as well as coordinating peripheral clocks throughout the body. Investigating the function of the SCN has often focused on the identification of rhythmically expressed genes. However, not all genes critical for SCN function are rhythmically expressed. An alternative strategy is to characterize those genes that are selectively enriched in the SCN. Here, we examined the transcriptome of the SCN and whole brain (WB) of mice using meta-analysis of publicly deposited data across a range of microarray platforms and RNA-Seq data...
September 29, 2017: Nucleic Acids Research
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