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Merging microarray studies to identify a common gene expression signature to several structural heart diseases

Olga Fajarda, Sara Duarte-Pereira, Raquel M. Silva, José Luís Oliveira
2020 BioData Mining  
We identified a gene expression signature common to different cardiac diseases and supported our findings by showing their involvement in the pathophysiology of the heart.  ...  Nine publicly available microarray datasets from studies of different heart diseases were merged to form a dataset composed of 689 samples and 8354 features.  ...  Results To identify a GES common in heart disease by merging microarray studies, we used a methodology composed of several steps. The first step consisted of identifying the studies to merge.  ... 
doi:10.1186/s13040-020-00217-8 pmid:32670412 pmcid:PMC7346458 fatcat:dhy2ok3sunbophe7wh3b4ln3mi

Integrative analysis of the mouse embryonic transcriptome

Amar V. Singh, Kenneth B. Knudsen, Thomas B. Knudsen
2007 Bioinformation  
The fields of developmental biology and teratology are now confronted with the need for automated access to a reference library of gene-expression signatures that benchmark programmed (genetic) and adaptive  ...  Using BDSM data integration tools, a gene-expression signature for 346 genes was resolved that accurately classified samples by organ system and developmental sequence.  ...  common transcriptional program' in multiple cancers. [8] In developmentteratogenesis, a preliminary meta-analysis across microarray studies in the mouse embryo returned a gene-expression signature of 512  ... 
doi:10.6026/97320630001406 pmid:17597930 pmcid:PMC1896055 fatcat:i6t44i3usragte77uettirn3du

Constructing and characterizing a bioactive small molecule and microRNA association network for Alzheimer's disease

F. Meng, E. Dai, X. Yu, Y. Zhang, X. Chen, X. Liu, S. Wang, L. Wang, W. Jiang
2013 Journal of the Royal Society Interface  
Differential expression analysis To obtain the CDGs, we conducted meta-analysis to merge the nine case-control microarray studies related to AD.  ...  To this end, we focused on the common gene expression signatures across AD patients with different conditions, such as AD severity and brain regions.  ... 
doi:10.1098/rsif.2013.1057 pmid:24352679 pmcid:PMC3899875 fatcat:qe3h367tordfxianxawndvtjgi

Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions

Michael K Skinner, Manikkam Mohan, Md M Haque, Bin Zhang, Marina I Savenkova
2012 Genome Biology  
A cluster analysis identified gene modules with coordinated gene expression and each had unique gene networks regulating tissue-specific gene expression and function.  ...  The microarrays from 11 different tissues were compared with a gene bionetwork analysis.  ...  This gene co-expression clustering/network analysis (GCENA) has been increasingly used to identify gene subnetworks for prioritizing gene targets associated with a variety of common human diseases such  ... 
doi:10.1186/gb-2012-13-10-r91 pmid:23034163 pmcid:PMC3491419 fatcat:2b7jj4p32nexbcxfv2q3a4bv54

Expectations, validity, and reality in gene expression profiling

Kyoungmi Kim, Stanislav O. Zakharkin, David B. Allison
2010 Journal of Clinical Epidemiology  
cancer, heart disease, and metabolic disorders.  ...  Objective: To provide a critical overview of gene expression profiling methodology and discuss areas of future development.  ...  EXPECTATIONS OF GENE EXPRESSION PROFILING STUDIES DNA microarray experiments are typically designed to achieve one or several of the following objectives: (1) to identify individual genes (transcripts  ... 
doi:10.1016/j.jclinepi.2010.02.018 pmid:20579843 pmcid:PMC2910173 fatcat:2e5kmg63pbezdpoevwcxofkkfi

Blood-Based Gene Expression Profiles Models for Classification of Subsyndromal Symptomatic Depression and Major Depressive Disorder

Zhenghui Yi, Zezhi Li, Shunying Yu, Chengmei Yuan, Wu Hong, Zuowei Wang, Jian Cui, Tieliu Shi, Yiru Fang, Xiang Yang Zhang
2012 PLoS ONE  
Several studies have suggested that SSD is a transitory phenomena in the depression spectrum and is thus considered a subtype of depression.  ...  Then, 123 gene signatures were identified with significantly differential expression level between SSD and MDD.  ...  Acknowledgments The authors are very grateful to all participants. We thank Drs. Yingyan Hu, and Lan Cao for help with sample collection, and Dr. Liwei Liao for data analysis. Author Contributions  ... 
doi:10.1371/journal.pone.0031283 pmid:22348066 pmcid:PMC3278427 fatcat:7lpszv5alveq3cq7ytjti2b5fi

Gene expression analysis in RA: towards personalized medicine

A N Burska, K Roget, M Blits, L Soto Gomez, F van de Loo, L D Hazelwood, C L Verweij, A Rowe, G N Goulielmos, L G M van Baarsen, F Ponchel
2014 The Pharmacogenomics Journal  
In a specially designed study, gene profiling was applied to identify gene signatures corresponding to different stages of RA comparing synovial biopsies from early RA (disease duration o12 months, untreated  ...  Considering that the costs of obtaining data for gene expression microarray tend to be very expensive and could be reduced by merging existing data sets, data sharing, therefore, appears essential to allow  ... 
doi:10.1038/tpj.2013.48 pmid:24589910 pmcid:PMC3992869 fatcat:d6oyxbnlfvdkfohlx4qxuweysa

Bioinformatics methods in drug repurposing for Alzheimer's disease

John C. Siavelis, Marilena M. Bourdakou, Emmanouil I. Athanasiadis, George M. Spyrou, Konstantina S. Nikita
2015 Briefings in Bioinformatics  
In this study, we have used gene signatures, where upand down-regulated gene lists summarize a cell's gene expression perturbation from a drug or disease.  ...  differential gene expression and four drug repurposing tools.  ...  Methods Data We sought Alzheimer-related microarray studies in Gene Expression Omnibus (GEO)-a transcriptional data repository [16] .  ... 
doi:10.1093/bib/bbv048 pmid:26197808 fatcat:rhs2zohea5du3hzggo63gglne4

Unique MicroRNA Profile in End-stage Heart Failure Indicates Alterations in Specific Cardiovascular Signaling Networks

Sathyamangla V. Naga Prasad, Zhong-Hui Duan, Manveen K. Gupta, Venkata Suresh K. Surampudi, Stefano Volinia, George A. Calin, Chang-Gong Liu, Ashwin Kotwal, Christine S. Moravec, Randall C. Starling, Dianne M. Perez, Subha Sen (+4 others)
2009 Journal of Biological Chemistry  
A heart failure gene expression data base was used to analyze changes in expression patterns for these target nodal molecules.  ...  The goal of this study was to comprehensively test for alterations in miRNA expression using human heart failure samples with an aim to build signaling pathway networks using predicted targets for the  ...  Cardiac Microarray Expression Data Base-To test for changes in expression in the target gene sets, microarray data from cardio-genomics data base for normal and idiopathic heart failure were used.  ... 
doi:10.1074/jbc.m109.036541 pmid:19641226 pmcid:PMC2785678 fatcat:c7jst4zruvhr3hbnxt4fptw2qe

Impaired Cardiovascular Function Caused by Different Stressors Elicits a Common Pathological and Transcriptional Response in Zebrafish Embryos

Jing Chen
2013 Zebrafish  
Zebrafish embryos have been widely used to study the genes and processes needed for normal vertebrate heart development.  ...  We hypothesized that unrelated chemicals can trigger a common pathological response leading to the same end-stage heart failure.  ...  Acknowledgments We thank Craig A.  ... 
doi:10.1089/zeb.2013.0875 pmid:23837677 pmcid:PMC3760051 fatcat:nnbt7xzxqbfrjns3cmvyif56ia

Workshop report: Identifying opportunities for global integration of toxicogenomics databases, 26–27 June 2013, Research Triangle Park, NC, USA

Diana M. Hendrickx, Rebecca R. Boyles, Jos C. S. Kleinjans, Allen Dearry
2014 Archives of Toxicology  
Acknowledgments This report is based on the "Workshop on Identifying Opportunities for Global Integration of Toxicogenomics Databases", 26-27 June 2013, hosted at the National Institute of Environmental  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s)  ...  CMap (https://www.broadinstitute.org/cmap/) is a database that uses mRNA expression signatures from cultured human cells treated with bioactive small molecules to connect diseases, genes and drugs.  ... 
doi:10.1007/s00204-014-1387-3 pmid:25326818 pmcid:PMC4247478 fatcat:ibhun6x3gng5bb6pfswl23v5gu

Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns

Daniel Baron, Emeric Dubois, Audrey Bihouée, Raluca Teusan, Marja Steenman, Philippe Jourdon, Armelle Magot, Yann Péréon, Reiner Veitia, Frédérique Savagner, Gérard Ramstein, Rémi Houlgatte
2011 BMC Genomics  
We are grateful to Jean Léger for encouragement and assistance at the beginning of this work.  ...  The first author DB received funds from a grant (application number 12309) awarded by the "Association Française contre les Myopathies" (AFM).  ...  This comparison enables to identify: i) robust signatures of a pathology or a treatment across several independent studies. ii) sets of genes that may be similarly modulated in different disease states  ... 
doi:10.1186/1471-2164-12-113 pmid:21324190 pmcid:PMC3049149 fatcat:laqesn4j2nbmlja5ykvmth6gya

Survey of Network-Based Approaches to Research of Cardiovascular Diseases

Anida Sarajlić, Nataša Pržulj
2014 BioMed Research International  
Consequently, topology of biological networks has successfully been used for identifying genes, pathways, and modules that govern molecular actions underlying various complex diseases.  ...  that underlie diseases.  ...  Known causal congenital heart disease (CHD) genes and genes differentially expressed in this disease (named target genes) were mapped onto a PPI network with the aim of identifying gene modules relevant  ... 
doi:10.1155/2014/527029 pmid:24772427 pmcid:PMC3977459 fatcat:pu2qrjtgg5hm7j6htwcm3koi2u

Identification of potential crucial genes in atrial fibrillation: a bioinformatic analysis

Junguo Zhang, Xin Huang, Xiaojie Wang, Yanhui Gao, Li Liu, Ziyi Li, Xuejiao Chen, Jie Zeng, Zebing Ye, Guowei Li
2020 BMC Medical Genomics  
After merging all microarray data and adjusting batch effect, differentially expressed genes (DEGs) were identified.  ...  In the present study, we aim to identify potential crucial genes associated with AF through bioinformatic analyses of public datasets.  ...  GSEA was applied to test merged GEO dataset to identify functional gene sets correlated with heart.  ... 
doi:10.1186/s12920-020-00754-5 pmid:32682418 fatcat:3qtzsgz765hplllejv36qimpii

Whole Blood Gene Expression and Atrial Fibrillation: The Framingham Heart Study

Honghuang Lin, Xiaoyan Yin, Kathryn L. Lunetta, Josée Dupuis, David D. McManus, Steven A. Lubitz, Jared W. Magnani, Roby Joehanes, Peter J. Munson, Martin G. Larson, Daniel Levy, Patrick T. Ellinor (+2 others)
2014 PLoS ONE  
We integrated differential gene expression with gene-gene interaction information to identify several signaling pathways possibly involved in AFrelated transcriptional regulation.  ...  Conclusion: We examined associations of gene expression with AF in a large community-based cohort.  ...  As a proof-of-concept, we performed RT-PCR on 95 coronary heart disease-related genes in 429 samples selected for a pilot study [29] .  ... 
doi:10.1371/journal.pone.0096794 pmid:24805109 pmcid:PMC4013062 fatcat:atfckglgcjdvxm23cukqwg5xfu
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