Bioinformatics models in drug abuse and Neuro-AIDS: Using and developing databases

TitleBioinformatics models in drug abuse and Neuro-AIDS: Using and developing databases
Publication TypeJournal Article
Year of Publication2006
AuthorsShapshak, P, Duncan, R, Turchan-Cholewo, J, Nath, A, Minagar, A, Kangueane, P, Davis, W, Chiappelli, F, Elkomy, FF, Seth, R, Kazic, T
Date Published02/2006
KeywordsCocaine, External, Gene Expression, HIV-1 gp120, HIV-1 tat, Neuro-AIDS, neuron, public international database, The Agora

The magnitude of the problems of drug abuse and Neuro-AIDS warrants the development of novel approaches for testing hypotheses in diagnosis and treatment ranging from cell culture models to developing databases. In this study, cultured neurons were treated with/without HIV-TAT, ENV, or cocaine in a 2x2x2 expression study design. RNA was purified, labeled, and expression data were produced and analyzed using ANOVA. Thus, we identified 35 genes that were significantly expressed across treatment conditions. A diagram is presented showing examples of molecular relationships involving a significantly expressed gene in the current study (SOX2). Also, we use this information to discuss examples of gene expression interactions as a means to portray significance and complexity of gene expression studies in Drug Abuse and Neuro-AIDS. Furthermore, we discuss here that critical interactions remain undetected, which may be unravelled by developing robust database systems containing large datasets and gleaned information from collaborating scientists . Hence, we are developing a public domain database we named The Agora database , that will served as a shared infrastructure to query, deposit, and review information related to drug abuse and dementias including Neuro-AIDS. A workflow of this database is also outlined in this paper.