title: Systematic discovery of the grammar of translational inhibition by RNA hairpins.
abstract: Recent discovery of gene expression mechanisms has propelled molecular genetics to a state of rapid development, a state likely to persist due to continuing advances in understanding control systems of fundamental cellular processes. An algorithm for that advancement starts in this paper with a gene of interest and a characteristic function of that gene. The set of all genes with counteracting function is identified by pathway searches. Also associated with the first gene is the set of the genes which byproducts of its transcription might downregulate, identified relative to searches involving sequence alignments. Our focus is the intersection of the counteracting gene set and the downregulated gene set. The result is hypothesis generation. Examples of and predictions from this approach are given in the context of apoptosis. Also discussed is application of the algorithm to rational drug design from a new development platform.
authors.affiliation: Renaissance Computing Institute and School of Pharmacy, Campus Box 7360, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7360, USA. clark_jeffries@med.unc.edu
authors.forename: Clark
authors.initials: C
authors.lastname: Jeffries
authors.forename: Diana O
authors.initials: DO
authors.lastname: Perkins
authors.forename: Michael
authors.initials: M
authors.lastname: Jarstfer
mesh_terms: D000465:Algorithms; D020087:Alu Elements / Q000235:genetics; D017209:Apoptosis / Q000235:genetics; D019295:Computational Biology; D015195:Drug Design; D005786:Gene Expression Regulation / Q000235:genetics*; D020868:Gene Silencing; D006801:Humans; D035683:MicroRNAs / Q000235:genetics; D014176:Protein Biosynthesis / Q000235:genetics*; D016337:RNA, Catalytic / Q000235:genetics*; D016415:Sequence Alignment
chemical_list: D035683:MicroRNAs; D016337:RNA, Catalytic; C418481:hairpin ribozyme