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gene expression meta analysis

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https://www.readbyqxmd.com/read/29675033/identification-and-validation-of-a-diagnostic-and-prognostic-multi-gene-biomarker-panel-for-pancreatic-ductal-adenocarcinoma
#1
Hagen Klett, Hannah Fuellgraf, Ella Levit-Zerdoun, Saskia Hussung, Silke Kowar, Simon Küsters, Peter Bronsert, Martin Werner, Uwe Wittel, Ralph Fritsch, Hauke Busch, Melanie Boerries
Late diagnosis and systemic dissemination essentially contribute to the invariably poor prognosis of pancreatic ductal adenocarcinoma (PDAC). Therefore, the development of diagnostic biomarkers for PDAC are urgently needed to improve patient stratification and outcome in the clinic. By studying the transcriptomes of independent PDAC patient cohorts of tumor and non-tumor tissues, we identified 81 robustly regulated genes, through a novel, generally applicable meta-analysis. Using consensus clustering on co-expression values revealed four distinct clusters with genes originating from exocrine/endocrine pancreas, stromal and tumor cells...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29673008/a-gwas-meta-analysis-from-5-population-based-cohorts-implicates-ion-channel-genes-in-the-pathogenesis-of-irritable-bowel-syndrome
#2
F Bonfiglio, M Henström, A Nag, F Hadizadeh, T Zheng, M C Cenit, E Tigchelaar, F Williams, A Reznichenko, W E Ek, N V Rivera, G Homuth, A A Aghdassi, T Kacprowski, M Männikkö, V Karhunen, L Bujanda, J Rafter, C Wijmenga, J Ronkainen, P Hysi, A Zhernakova, M D'Amato
BACKGROUND: Irritable bowel syndrome (IBS) shows genetic predisposition, however, large-scale, powered gene mapping studies are lacking. We sought to exploit existing genetic (genotype) and epidemiological (questionnaire) data from a series of population-based cohorts for IBS genome-wide association studies (GWAS) and their meta-analysis. METHODS: Based on questionnaire data compatible with Rome III Criteria, we identified a total of 1335 IBS cases and 9768 asymptomatic individuals from 5 independent European genotyped cohorts...
April 19, 2018: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
https://www.readbyqxmd.com/read/29669324/clinical-significance-of-mir-210-and-its-prospective-signaling-pathways-in-non-small-cell-lung-cancer-evidence-from-gene-expression-omnibus-and-the-cancer-genome-atlas-data-mining-with-2763-samples-and-validation-via-real-time-quantitative-pcr
#3
Rong-Quan He, Wei-Luan Cen, Jie-Mei Cen, Wei-Ning Cen, Jia-Yi Li, Mei-Wei Li, Ting-Qing Gan, Xiao-Hua Hu, Gang Chen
BACKGROUND/AIMS: Since the function of microRNA (miR)-210 in non-small cell lung cancer (NSCLC) remains unclear, we aimed to explore the clinical significance of miR-210 in NSCLC. METHODS: NSCLC-related data from 1673 samples on Gene Expression Omnibus and 1090 samples on The Cancer Genome Atlas were obtained and analyzed. The expression level of miR-210 was validated via real-time quantitative PCR analysis with 125 paired clinical samples. A meta-analysis was performed to generate a comprehensive understanding of miR-210 expression and its clinical significance in NSCLC...
April 13, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29668885/follicle-capacitation-a-meta-analysis-to-investigate-the-transcriptome-dynamics-following-fsh-decline-in-bovine-granulosa-cells
#4
David A Landry, Marc-André Sirard
In recent years, exciting progress was made to improve the embryo outcome after ovarian stimulation in domestic animals. The practice of follicle-stimulating hormone (FSH) withdrawal, which is defined as the period of time between the last injection of FSH and oocyte retrieval, resulted in embryo yields significantly superior. Since then, specific changes in the transcriptome of granulosa cells were associated with the increase and also the decline in oocyte developmental competence following the FSH decline...
April 14, 2018: Biology of Reproduction
https://www.readbyqxmd.com/read/29664904/surprisal-analysis-of-genome-wide-transcript-profiling-identifies-differentially-expressed-genes-and-pathways-associated-with-four-growth-conditions-in-the-microalga-chlamydomonas
#5
Kenny A Bogaert, Sheeba S Manoharan-Basil, Emilie Perez, Raphael D Levine, Francoise Remacle, Claire Remacle
The usual cultivation mode of the green microalga Chlamydomonas is liquid medium and light. However, the microalga can also be grown on agar plates and in darkness. Our aim is to analyze and compare gene expression of cells cultivated in these different conditions. For that purpose, RNA-seq data are obtained from Chlamydomonas samples of two different labs grown in four environmental conditions (agar@light, agar@dark, liquid@light, liquid@dark). The RNA seq data are analyzed by surprisal analysis, which allows the simultaneous meta-analysis of all the samples...
2018: PloS One
https://www.readbyqxmd.com/read/29664137/msh-homeobox-1-polymorphisms-and-the-risk-of-non-syndromic-orofacial-clefts-a-meta-analysis
#6
Min Gu, Yan Zhang, Hualian Liu, Jue Liu, Danxia Zhu, Xu Yang
MSH homebox 1 (MSX1) is a susceptibility gene for non-syndromic orofacial clefts (NSOCs). Here, a meta-analysis was conducted to assess their associations. A systematic search of PubMed to 1 September 2017, was performed to retrieve all eligible studies. Odds ratios (ORs) were used to calculate the associations. The stability of the results was evaluated by sensitivity analysis. Publication bias was assessed using Begg's funnel plots and the Egger test. In silico Msx1 expression during early mouse craniofacial development was evaluated by the Gene Expression Omnibus...
April 17, 2018: European Journal of Oral Sciences
https://www.readbyqxmd.com/read/29662637/the-wilms-tumor-gene-1-is-a-prognostic-factor-in-myelodysplastic-syndrome-a-meta-analysis
#7
Yanan Jiang, Lin Liu, Jinhuan Wang, Zeng Cao, Zhigang Zhao
Previous studies have suggested that Wilms' tumor gene-1 (WT1) may be related to a decrease in both relapse-free survival (RFS) and overall survival (OS) for patients with myelodysplastic syndrome (MDS). Therefore, we conducted a meta-analysis on the utility of WT1 as a prognostic indicator of MDS. Published reports were searched in the following databases: Cochrane Library, PubMed, Embase, and Web of Science. The meta-analysis was conducted using the Cochrane Collaboration RevMan 5.2 software. Six publications with 450 total patients met the inclusion criteria and were subjected to further examination...
March 23, 2018: Oncotarget
https://www.readbyqxmd.com/read/29656435/a-multi-omic-study-reveals-btg2-as-a-reliable-prognostic-marker-for-early-stage-non-small-cell-lung-cancer
#8
Sipeng Shen, Ruyang Zhang, Yichen Guo, Elizabeth Loehrer, Yongyue Wei, Ying Zhu, Qianyu Yuan, Sebastian Moran, Thomas Fleischer, Maria Moksnes Bjaanaes, Anna Karlsson, Maria Planck, Johan Staaf, Åslaug Helland, Manel Esteller, Li Su, Feng Chen, David C Christiani
B-cell translocation gene 2 (BTG2) is a tumor suppressor protein and is known to be downregulated in several types of cancer. In this study, we investigated a potential role for BTG2 in early-stage non-small cell lung cancer (NSCLC) survival. We analysed BTG2 methylation data from 1,230 early-stage NSCLC patients from five international cohorts, as well as gene expression data from 3,038 lung cancer cases from multiple cohorts. Three CpG probes (cg01798157, cg06373167, cg23371584) that detected BTG2 hypermethylation in tumor tissues were associated with lower overall survival...
April 15, 2018: Molecular Oncology
https://www.readbyqxmd.com/read/29650561/meta-analysis-of-airway-epithelia-gene-expression-in-asthma
#9
Yi-Hsuan Tsai, Joel S Parker, Ivana V Yang, Samir N P Kelada
Differential gene expression in the airway epithelium of asthmatics vs. controls has been reported in several studies. However, there is no consensus on which genes are reproducibly affected in asthma. We sought to identify a consensus list of differentially expressed genes (DEGs) using a meta-analysis approach.We identified eight studies with data that met defined inclusion criteria. In total, these studies were comprised of 355 cases and 193 controls and involved sampling of either bronchial or nasal epithelium...
April 12, 2018: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
https://www.readbyqxmd.com/read/29625265/network-based-meta-analysis-in-the-identification-of-biomarkers-for-papillary-thyroid-cancer
#10
Hengqiang Zhao, Hehe Li
Papillary thyroid carcinoma (PTC) has been increasing across the world with incomplete understanding of its pathogenesis. We aimed to investigate gene alterations and biomarkers contributing to PTC development. A total of five eligible microarray datasets including 94 PTC and 81 normal thyroid samples were included to identify gene expression signatures. Using integrative meta-analysis of expression data (INMEX) program, we identified a total of 2699 differentially expressed genes (DEGs) (1333 overexpressed and 1366 underexpressed genes) in PTC relative to normal thyroid samples...
April 3, 2018: Gene
https://www.readbyqxmd.com/read/29618496/cell-centred-meta-analysis-reveals-baseline-predictors-of-anti-tnf%C3%AE-non-response-in-biopsy-and-blood-of-patients-with-ibd
#11
Renaud Gaujoux, Elina Starosvetsky, Naama Maimon, Francesco Vallania, Haggai Bar-Yoseph, Sigal Pressman, Roni Weisshof, Idan Goren, Keren Rabinowitz, Matti Waterman, Henit Yanai, Iris Dotan, Edmond Sabo, Yehuda Chowers, Purvesh Khatri, Shai S Shen-Orr
OBJECTIVE: Although anti-tumour necrosis factor alpha (anti-TNFα) therapies represent a major breakthrough in IBD therapy, their cost-benefit ratio is hampered by an overall 30% non-response rate, adverse side effects and high costs. Thus, finding predictive biomarkers of non-response prior to commencing anti-TNFα therapy is of high value. DESIGN: We analysed publicly available whole-genome expression profiles of colon biopsies obtained from multiple cohorts of patients with IBD using a combined computational deconvolution-meta-analysis paradigm which allows to estimate immune cell contribution to the measured expression and capture differential regulatory programmes otherwise masked due to variation in cellular composition...
April 4, 2018: Gut
https://www.readbyqxmd.com/read/29618007/subphenotype-meta-analysis-of-testicular-cancer-genome-wide-association-study-data-suggests-a-role-for-rbfox-family-genes-in-cryptorchidism-susceptibility
#12
Yanping Wang, Dione R Gray, Alan K Robbins, Erin L Crowgey, Stephen J Chanock, Mark H Greene, Katherine A McGlynn, Katherine Nathanson, Clare Turnbull, Zhaoming Wang, Marcella Devoto, Julia Spencer Barthold
STUDY QUESTION: Can subphenotype analysis of genome-wide association study (GWAS) data from subjects with testicular germ cell tumor (TGCT) provide insight into cryptorchidism (undescended testis, UDT) susceptibility? SUMMARY ANSWER: Suggestive intragenic GWAS signals common to UDT, TGCT case-case and TGCT case-control analyses occur in genes encoding RBFOX RNA-binding proteins (RBPs) and their neurodevelopmental targets. WHAT IS KNOWN ALREADY: UDT is a strong risk factor for TGCT, but while genetic risk factors for TGCT are well-known, genetic susceptibility to UDT is poorly understood and appears to be more complex...
March 29, 2018: Human Reproduction
https://www.readbyqxmd.com/read/29617692/prognostic-significance-of-lncrna-pvt1-and-its-potential-target-gene-network-in-human-cancers-a-comprehensive-inquiry-based-upon-21-cancer-types-and-9972-cases
#13
Rong-Quan He, Mei-Jiao Qin, Peng Lin, Yi-Huan Luo, Jie Ma, Hong Yang, Xiao-Hua Hu, Gang Chen
BACKGROUND/AIMS: Whether the level of long noncoding RNA plasmacytoma variant translocation 1 gene (lncRNA PVT1) expression influences the clinical development and outcome of human cancers has not been thoroughly elucidated to date. Inconsistencies still exist regarding the associations between PVT1 and the clinicopathological features, including patient survival data. Additionally, the regulatory mechanism of PVT1 among human cancers remains unclear. METHODS: we conducted a comprehensive inquiry to verify the implication of PVT1 expression in cancer patients by conducting a meta-analysis of 19 selected studies and The Cancer Genome Atlas (TCGA) database to examine the relationship between PVT1 expression and both the prognosis and clinicopathological features of cancer patients using STATA 12...
March 28, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29617535/association-of-methylation-signals-with-incident-coronary-heart-disease-in-an-epigenome-wide-assessment-of-circulating-tumor-necrosis-factor-%C3%AE
#14
Stella Aslibekyan, Golareh Agha, Elena Colicino, Anh N Do, Jari Lahti, Symen Ligthart, Riccardo E Marioni, Carola Marzi, Michael M Mendelson, Toshiko Tanaka, Matthias Wielscher, Devin M Absher, Luigi Ferrucci, Oscar H Franco, Christian Gieger, Harald Grallert, Dena Hernandez, Tianxiao Huan, Stella Iurato, Roby Joehanes, Allan C Just, Sonja Kunze, Honghuang Lin, Chunyu Liu, James B Meigs, Joyce B J van Meurs, Ann Zenobia Moore, Annette Peters, Holger Prokisch, Katri Räikkönen, Wolfgang Rathmann, Michael Roden, Katharina Schramm, Joel D Schwartz, John M Starr, André G Uitterlinden, Pantel Vokonas, Melanie Waldenberger, Chen Yao, Degui Zhi, Andrea A Baccarelli, Stefania Bandinelli, Ian J Deary, Abbas Dehghan, Johan Eriksson, Christian Herder, Marjo-Riitta Jarvelin, Daniel Levy, Donna K Arnett
Importance: Tumor necrosis factor α (TNF-α) is a proinflammatory cytokine with manifold consequences for mammalian pathophysiology, including cardiovascular disease. A deeper understanding of TNF-α biology may enhance treatment precision. Objective: To conduct an epigenome-wide analysis of blood-derived DNA methylation and TNF-α levels and to assess the clinical relevance of findings. Design, Setting, and Participants: This meta-analysis assessed epigenome-wide associations in circulating TNF-α concentrations from 5 cohort studies and 1 interventional trial, with replication in 3 additional cohort studies...
April 4, 2018: JAMA Cardiology
https://www.readbyqxmd.com/read/29617451/integrative-multi-platform-meta-analysis-of-gene-expression-profiles-in-pancreatic-ductal-adenocarcinoma-patients-for-identifying-novel-diagnostic-biomarkers
#15
Antonio Irigoyen, Cristina Jimenez-Luna, Manuel Benavides, Octavio Caba, Javier Gallego, Francisco Manuel Ortuño, Carmen Guillen-Ponce, Ignacio Rojas, Enrique Aranda, Carolina Torres, Jose Prados
Applying differentially expressed genes (DEGs) to identify feasible biomarkers in diseases can be a hard task when working with heterogeneous datasets. Expression data are strongly influenced by technology, sample preparation processes, and/or labeling methods. The proliferation of different microarray platforms for measuring gene expression increases the need to develop models able to compare their results, especially when different technologies can lead to signal values that vary greatly. Integrative meta-analysis can significantly improve the reliability and robustness of DEG detection...
2018: PloS One
https://www.readbyqxmd.com/read/29616113/clinical-significance-of-high-expression-of-mir-452-5p-in-lung-squamous-cell-carcinoma
#16
Xiao-Ning Gan, Ting-Qing Gan, Rong-Quan He, Jie Luo, Rui-Xue Tang, Han-Lin Wang, Hong Zhou, Hui Qing, Jie Ma, Xiao-Hua Hu, Gang Chen
The role of microRNA (miRNA)-452-5p in lung squamous cell carcinoma (LUSC) remains unclear. Therefore, the present systematic study was performed to investigate the clinical significance and the rudimentary mechanism of the function of miR-452-5p in LUSC. The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were utilized to confirm the expression level and clinical value of miR-452-5p in LUSC. Using online databases and bioinformatic software, gene ontology (GO), pathway and protein-protein interaction (PPI) analyses of miR-452-5p target genes were performed to examine the molecular mechanism of miR-452-5p...
May 2018: Oncology Letters
https://www.readbyqxmd.com/read/29616090/clinical-value-and-potential-pathways-of-mir-183-5p-in-bladder-cancer-a-study-based-on-mirna-seq-data-and-bioinformatics-analysis
#17
Jia-Min Gao, Lin-Zhen Huang, Zhi-Guang Huang, Rong-Quan He
The clinicopathological value and exploration of the potential molecular mechanism of microRNA-183-5p (miR-183-5p) have been investigated in various cancers; however, to the best of the author's knowledge, no similar research has been reported for bladder cancer. In the present study, it was revealed that the expression level of miR-183-5p was notably increased in bladder cancer tissues compared with adjacent non-cancerous tissues (P=0.001) and was markedly increased in the tissue samples of papillary, pathological T stage (T0-T2) and pathological stage (I-II) compared with tissue samples of their counterparts (P=0...
April 2018: Oncology Letters
https://www.readbyqxmd.com/read/29615643/computational-repositioning-and-preclinical-validation-of-mifepristone-for-human-vestibular-schwannoma
#18
Jessica E Sagers, Adam S Brown, Sasa Vasilijic, Rebecca M Lewis, Mehmet I Sahin, Lukas D Landegger, Roy H Perlis, Isaac S Kohane, D Bradley Welling, Chirag J Patel, Konstantina M Stankovic
The computational repositioning of existing drugs represents an appealing avenue for identifying effective compounds to treat diseases with no FDA-approved pharmacotherapies. Here we present the largest meta-analysis to date of differential gene expression in human vestibular schwannoma (VS), a debilitating intracranial tumor, and use these data to inform the first application of algorithm-based drug repositioning for this tumor class. We apply an open-source computational drug repositioning platform to gene expression data from 80 patient tumors and identify eight promising FDA-approved drugs with potential for repurposing in VS...
April 3, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29610217/sequence-based-analysis-of-lipid-related-metabolites-in-a-multiethnic-study
#19
Elena V Feofanova, Bing Yu, Ginger A Metcalf, Xiaoming Liu, Donna Muzny, Jennifer E Below, Lynne E Wagenknecht, Richard A Gibbs, Alanna C Morrison, Eric Boerwinkle
Small molecule lipid-related metabolites are important components of fatty acid and steroid metabolism, two important contributors to human health. This study investigated the extent to which rare and common genetic variants spanning the human genome influence the lipid-related metabolome. Sequence data from 1,552 European-Americans (EA) and 1,872 African-Americans (AA) were analyzed to examine the impact of common and rare variants on the levels of 102 circulating lipid-related metabolites measured by a combination of chromatography and mass spectroscopy...
April 2, 2018: Genetics
https://www.readbyqxmd.com/read/29606904/4q21-2q21-3-duplication-molecular-and-neuropsychological-aspects
#20
REVIEW
Ivan Y Iourov, Maria A Zelenova, Svetlana G Vorsanova, Victoria V Voinova, Yuri B Yurov
During the last decades, a large amount of newly described microduplications and microdeletions associated with intellectual disability (ID) and related neuropsychiatric diseases have been discovered. However, due to natural limitations, a significant part of them has not been the focus of multidisciplinary approaches. Here, we address previously undescribed chromosome 4q21.2q21.3 microduplication for gene prioritization, evaluation of cognitive abilities and estimation of genomic mechanisms for brain dysfunction by molecular cytogenetic (cytogenomic) and gene expression (meta-) analyses as well as for neuropsychological assessment...
April 2018: Current Genomics
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