Browsing by Subject "microarray"

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The INIA Texas Gene Expression Database: An online tool for alcohol genomics
(2012-04) Weyn-Vanhentenryck, Sebastien; Ponomarev, Igor
Alcoholism 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.
Integrative analysis of high-throughput biological data: shrinkage correlation coefficient and comparative expression analysis
(2009-12) Yao, Jianchao; Roux, Stanley J.; Chen, Zengjian J.; Markey, Mia K.; Miranker, Daniel P.; Fu, Bo
The focus for this research is to develop and apply statistical methods to analyze and interpret high-throughput biological data. We developed a novel correlation coefficient, shrinkage correlation coefficient (SCC), that fully exploits the similarity between the replicated microarray experimental samples. The methodology considers both the number of replicates and the variance within each experimental group in clustering expression data, and provides a robust statistical estimation of the error of replicated microarray data. Applying SCC-based hierarchical clustering to the replicated microarray data obtained from germinating spores of the fern Ceratopteris richardii, we discovered two clusters of genes with shared expression patterns during spore germination. This computational approach is not only applicable to DNA microarray analysis but is also applicable to proteomics data or any other high-throughput analysis methodology. The suppression of APY1 and APY2 in mutants expressing an inducible RNAi system resulted in plants with a dwarf phenotype and disrupted auxin distribution, and we used these mutants to discover what genes changed expression during growth suppression. We evaluated the gene expression changes of apyrase-suppressed RNAi mutants that had been grown in the light and in the darkness, using the NimbleGen Arabidopsis thaliana 4-Plex microarray, respectively. We compared the two sets of large-scale expression data and identified genes whose expression significantly changed after apyrase suppression in light and darkness, respectively. Our results allowed us to highlight some of the genes likely to play major roles in mediating the growth changes that happen when plants drastically reduce their production of APY1 and APY2, some more associated with growth promotion and others, such as stress-induced genes, more associated with growth inhibition. There is a strong rationale for ranking all these genes as prime candidates for mediating the inhibitory growth effects of suppressing apyrase expression, thus the NimbleGen data will serve as a catalyst and valuable guide to the subsequent physiological and molecular experiments that will be needed to clarify the network of gene expression changes that accompany growth inhibition.
Social Odors Conveying Dominance and Reproductive information Induce Rapid Physiological and Neuromolecular Changes in a Cichlid Fish
(2015-02) Simoes, Jose M.; Barata, Eduardo N.; Harris, Rayna M.; O'Connell, Lauren A.; Hofmann, Hans A.; Oliveira, Rui F.; Harris, Rayna M.; O'Connell, Lauren A.; Hofmann, Hans A.
Social plasticity is a pervasive feature of animal behavior. Animals adjust the expression of their social behavior to the daily changes in social life and to transitions between life-history stages, and this ability has an impact in their Darwinian fitness. This behavioral plasticity may be achieved either by rewiring or by biochemically switching nodes of the neural network underlying social behavior in response to perceived social information. Independent of the proximate mechanisms, at the neuromolecular level social plasticity relies on the regulation of gene expression, such that different neurogenomic states emerge in response to different social stimuli and the switches between states are orchestrated by signaling pathways that interface the social environment and the genotype. Here, we test this hypothesis by characterizing the changes in the brain profile of gene expression in response to social odors in the Mozambique Tilapia, Oreochromis mossambicus. This species has a rich repertoire of social behaviors during which both visual and chemical information are conveyed to conspecifics. Specifically, dominant males increase their urination frequency during agonist encounters and during courtship to convey chemical information reflecting their dominance status. Results: We recorded electro-olfactograms to test the extent to which the olfactory epithelium can discriminate between olfactory information from dominant and subordinate males as well as from pre- and post-spawning females. We then performed a genome-scale gene expression analysis of the olfactory bulb and the olfactory cortex homolog in order to identify the neuromolecular systems involved in processing these social stimuli. Conclusions: Our results show that different olfactory stimuli from conspecifics' have a major impact in the brain transcriptome, with different chemical social cues eliciting specific patterns of gene expression in the brain. These results confirm the role of rapid changes in gene expression in the brain as a genomic mechanism underlying behavioral plasticity and reinforce the idea of an extensive transcriptional plasticity of cichlid genomes, especially in response to rapid changes in their social environment.