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Item The INIA Texas Gene Expression Database: An online tool for alcohol genomics(2012-04) Weyn-Vanhentenryck, Sebastien; Ponomarev, IgorAlcoholism is a serious condition that affects millions of people and costs billions of dollars each year in treatment, damages, and lost income. In addition, it carries a tremendous emotional burden. Alcoholism is caused by a combination of genetic and environmental factors, which have yet to be fully identified. Fortunately, alcoholism research, as well as research into other diseases with a genetic component, has greatly benefited from recent rapid developments in high-throughput genomic technologies and the development of relevant model organisms. This has been highly productive for progress in the field, but effective methods for identifying relevant data and for performing cross-dataset analyses have not been developed at the same pace. To help fulfill this need, I have developed the INIA (Integrative Neuroscience Initiative on Alcoholism) Texas Gene Expression Database (IT-GED), which is freely available at http://inia.icmb.utexas.edu. IT-GED is a web-based database which contains a compilation of the significantly expressed genes from each of several microarray datasets investigating the role of gene expression in the brain's regulation of alcohol consumption. The studies were performed both in model organisms (mouse and rat) and post-mortem humans. The data is presented via a user-friendly interface which provides advanced searching abilities for identifying genes of interest and tools for analysis of the data. These tools provide the ability to compare user data to every dataset in IT-GED in order to assess the significance of a group of genes across multiple datasets and the ability to generate visual networks of those genes in order to identify the ones that are likely the most functionally significant in the response to high alcohol consumption. IT-GED thus provides a means by which alcohol researchers can combine multiple sources of data to generate novel hypotheses concerning the genetic causes of alcoholism. The goal of IT-GED is to provide support for comparing and integrating results across gene expression studies of alcohol consumption and for generating novel hypotheses based on individual genes and gene-gene interactions by simplifying data access, providing various tools for analysis, and presenting users with an easy-to-use interface.Item Positively Correlated miRNA-miRNA Regulatory Networks in Mouse Frontal Cortex During Early Stages of Alcohol Dependence(2013-10) Nunez, Yury O.; Truitt, Jay M.; Gorini, Giorgio; Ponomareva, Olga N.; Blednov, Yuri A.; Harris, R. Adon; Mayfield, R. Dayne; Positively Correlated miRNA-miRNA Regulatory Networks in Mouse Frontal Cortex During Early Stages of Alcohol DependenceAlthough the study of gene regulation via the action of specific microRNAs (miRNAs) has experienced a boom in recent years, the analysis of genome-wide interaction networks among miRNAs and respective targeted mRNAs has lagged behind. MicroRNAs simultaneously target many transcripts and fine-tune the expression of genes through cooperative/combinatorial targeting. Therefore, they have a large regulatory potential that could widely impact development and progression of diseases, as well as contribute unpredicted collateral effects due to their natural, pathophysiological, or treatment-induced modulation. We support the viewpoint that whole mirnome-transcriptome interaction analysis is required to better understand the mechanisms and potential consequences of miRNA regulation and/or deregulation in relevant biological models. In this study, we tested the hypotheses that ethanol consumption induces changes in miRNA-mRNA interaction networks in the mouse frontal cortex and that some of the changes observed in the mouse are equivalent to changes in similar brain regions from human alcoholics. Results: miRNA-mRNA interaction networks responding to ethanol insult were identified by differential expression analysis and weighted gene coexpression network analysis (WGCNA). Important pathways (coexpressed modular networks detected by WGCNA) and hub genes central to the neuronal response to ethanol are highlighted, as well as key miRNAs that regulate these processes and therefore represent potential therapeutic targets for treating alcohol addiction. Importantly, we discovered a conserved signature of changing miRNAs between ethanol-treated mice and human alcoholics, which provides a valuable tool for future biomarker/diagnostic studies in humans. We report positively correlated miRNA-mRNA expression networks that suggest an adaptive, targeted miRNA response due to binge ethanol drinking. Conclusions: This study provides new evidence for the role of miRNA regulation in brain homeostasis and sheds new light on current understanding of the development of alcohol dependence. To our knowledge this is the first report that activated expression of miRNAs correlates with activated expression of mRNAs rather than with mRNA downregulation in an in vivo model. We speculate that early activation of miRNAs designed to limit the effects of alcohol-induced genes may be an essential adaptive response during disease progression.Item Positively correlated miRNA-mRNA regulatory networks in mouse frontal cortex during early stages of alcohol dependence(BMC Genomics, 2013-10-22) Nunez, Yury O.; Truitt, Jay M.; Gorini, Giorgio; Ponomareva, Olga N.; Blendnov; Harris, R. Adron; Mayfield, R. DayneBackground: Although the study of gene regulation via the action of specific microRNAs (miRNAs) has experienced a boom in recent years, the analysis of genome-wide interaction networks among miRNAs and respective targeted mRNAs has lagged behind. MicroRNAs simultaneously target many transcripts and fine-tune the expression of genes through cooperative/combinatorial targeting. Therefore, they have a large regulatory potential that could widely impact development and progression of diseases, as well as contribute unpredicted collateral effects due to their natural, pathophysiological, or treatment-induced modulation. We support the viewpoint that whole mirnome-transcriptome interaction analysis is required to better understand the mechanisms and potential consequences of miRNA regulation and/or deregulation in relevant biological models. In this study, we tested the hypotheses that ethanol consumption induces changes in miRNA-mRNA interaction networks in the mouse frontal cortex and that some of the changes observed in the mouse are equivalent to changes in similar brain regions from human alcoholics. Results: miRNA-mRNA interaction networks responding to ethanol insult were identified by differential expression analysis and weighted gene coexpression network analysis (WGCNA). Important pathways (coexpressed modular networks detected by WGCNA) and hub genes central to the neuronal response to ethanol are highlighted, as well as key miRNAs that regulate these processes and therefore represent potential therapeutic targets for treating alcohol addiction. Importantly, we discovered a conserved signature of changing miRNAs between ethanol-treated mice and human alcoholics, which provides a valuable tool for future biomarker/diagnostic studies in humans. We report positively correlated miRNA-mRNA expression networks that suggest an adaptive, targeted miRNA response due to binge ethanol drinking. Conclusions: This study provides new evidence for the role of miRNA regulation in brain homeostasis and sheds new light on current understanding of the development of alcohol dependence. To our knowledge this is the first report that activated expression of miRNAs correlates with activated expression of mRNAs rather than with mRNA downregulation in an in vivo model. We speculate that early activation of miRNAs designed to limit the effects of alcohol-induced genes may be an essential adaptive response during disease progression.Item Presentation: Ancestors of Us All: Recent Discoveries in Human Origins and Evolution(Environmental Science Institute, 2001-03-02) Kappelman, John; Environmental Science Institute