BayGO: Bayesian analysis of ontology term enrichment in microarray data

Abstract Background The search for enriched (aka over-represented or enhanced) ontology terms in a list of genes obtained from microarray experiments is becoming a standard procedure for a system-level analysis. This procedure tries to summarize the information focussing on classification designs such as Gene Ontology, KEGG pathways, and so on, instead of focussing on individual genes. Although it is well known in statistics that association and significance are distinct concepts, only the former approach has been used to deal with the ontology term enrichment problem. Results BayGO implements a Bayesian approach to search for enriched terms from microarray data. The R source-code is freely available at http://blasto.iq.usp.br/~tkoide/BayGO in three versions: Linux, which can be easily incorporated into pre-existent pipelines; Windows, to be controlled interactively; and as a web-tool. The software was validated using a bacterial heat shock response dataset, since this stress triggers known system-level responses. Conclusion The Bayesian model accounts for the fact that, eventually, not all the genes from a given category are observable in microarray data due to low intensity signal, quality filters, genes that were not spotted and so on. Moreover, BayGO allows one to measure the statistical association between generic ontology terms and differential expression, instead of working only with the common significance analysis.

Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon

Abstract Background Xylella fastidiosa, a Gram-negative fastidious bacterium, grows in the xylem of several plants causing diseases such as citrus variegated chlorosis. As the xylem sap contains low concentrations of amino acids and other compounds, X. fastidiosa needs to cope with nitrogen limitation in its natural habitat. Results In this work, we performed a whole-genome microarray analysis of the X. fastidiosa nitrogen starvation response. A time course experiment (2, 8 and 12 hours) of cultures grown in defined medium under nitrogen starvation revealed many differentially expressed genes, such as those related to transport, nitrogen assimilation, amino acid biosynthesis, transcriptional regulation, and many genes encoding hypothetical proteins. In addition, a decrease in the expression levels of many genes involved in carbon metabolism and energy generation pathways was also observed. Comparison of gene expression profiles between the wild type strain and the rpoN null mutant allowed the identification of genes directly or indirectly induced by nitrogen starvation in a σ54-dependent manner. A more complete picture of the σ54 regulon was achieved by combining the transcriptome data with an in silico search for potential σ54-dependent promoters, using a position weight matrix approach. One of these σ54-predicted binding sites, located upstream of the glnA gene (encoding glutamine synthetase), was validated by primer extension assays, confirming that this gene has a σ54-dependent promoter. Conclusions Together, these results show that nitrogen starvation causes intense changes in the X. fastidiosa transcriptome and some of these differentially expressed genes belong to the σ54 regulon.

Conceptual problem for noncommutative inflation and the new approach for nonrelativistic inflationary equation of state

In a previous paper, we connected the phenomenological noncommutative inflation of Alexander, Brandenberger and Magueijo [ Phys. Rev. D 67 081301 (2003)] and Koh and Brandenberger [ J. Cosmol. Astropart Phys. 2007 21 ()] with the formal representation theory of groups and algebras and analyzed minimal conditions that the deformed dispersion relation should satisfy in order to lead to a successful inflation. In that paper, we showed that elementary tools of algebra allow a group-like procedure in which even Hopf algebras (roughly the symmetries of noncommutative spaces) could lead to the equation of state of inflationary radiation. Nevertheless, in this paper, we show that there exists a conceptual problem with the kind of representation that leads to the fundamental equations of the model. The problem comes from an incompatibility between one of the minimal conditions for successful inflation (the momentum of individual photons being bounded from above) and the Fock-space structure of the representation which leads to the fundamental inflationary equations of state. We show that the Fock structure, although mathematically allowed, would lead to problems with the overall consistency of physics, like leading to a problematic scattering theory, for example. We suggest replacing the Fock space by one of two possible structures that we propose. One of them relates to the general theory of Hopf algebras (here explained at an elementary level) while the other is based on a representation theorem of von Neumann algebras (a generalization of the Clebsch-Gordan coefficients), a proposal already suggested by us to take into account interactions in the inflationary equation of state.