Section: New Results

Data integration

Participants : Jacques Nicolas, Charles Bettembourg, Jérémie Bourdon, Jeanne Cambefort, Marie Chevallier, Guillaume Collet, Olivier Dameron, Damien Eveillard, Julie Laniau, Sylvain Prigent, Anne Siegel, Valentin Wucher.

Pan-genomic metabolic network of Ectocarpus siliculosus : We introduced the first metabolic network for the non-classical species E. Siliculosus, called EctoGEM. The reconstruction process includes draft reconstruction based on sequence and functional annotation analysis. It is followed by a combinatorial gap-filling process using the Meneco software based on answer set programming, a semantic analysis of the completion and a manual curation. This reconstruction enables a better understanding of organism biology and a reannotation of its genome. [J. Cambefort, G. Collet, O. Dameron, D. Eveillard, S. Prigent, A. Siegel] [22] , [11]

New insights on bacteria associated with brown algae As an application of our tools for the reconstruction of metabolic networks, we have contributed to the analysis of the genome of a bacteria which lives in symbiosis with brown algae by investigating candidates for metabolic exchanges between the bacteria and the algae. [G. Collet, J. Cambefort, A. Siegel] [19] [Online publication]

Modeling parsimonious putative regulatory networks We integrated heterogeneous information from two types of network predictions to determine a causal explanation for the observed gene co-expression. We modeled this integration as a combinatorial optimization problem. We demonstrated that this problem belongs to the NP-hard complexity class. We proposed an heuristic approach to have an approximate solution in a practical execution time. Our evaluation showed that the E.coli regulatory network resulting from the application of this method has higher accuracy than the putative one built with traditional tools. [A. Aravena, A. Siegel, D. Eveillard] [26] [Online publication]

Modeling of a gene network between mRNAs and miRNAs to predict gene functions involved in phenotypic plasticity in the pea aphid and non coding RNA in pea aphid During its PhD, V. Wucher has built the first network model of gene regulation by microRNAs in pea aphid. The thesis has studied the discrimination between embryos development towards either sexual or asexual reproduction types in the pea aphid Acyrthosiphon pisum, at the genomic level. The study of the post-transcriptional regulation network implies both the identification of regulated elements during embryogenesis and the identification of the interaction modules between microRNAs and mRNAs using formal concept analysis. It helps the understanding of regulation differences between sexual and asexual embryogenesis. Moreover, it is the first step towards the modeling of the entire set of genes regulations in pea aphid during embryogenesis. [V. Wucher, J. Nicolas, F. Legeai (Genscale team)] [13] , [39] , [30]

Using a large-scale knowledge database on reactions and regulations to exhibit key regulators A new formalism of regulated reactions combining biochemical transformations and regulatory effects was proposed to unify the different mechanisms contained in knowledge libraries. Based on a related causality graph, an algorithm was developed to propose a reasonable set of upstream regulators from lists of target molecules. Scores were added to candidates according to their ability to explain the greatest number of targets or only few specific ones. The method was validated on a real example related to glycolysis. [P. Blavy, A. Siegel] [18] [Online publication]

Semantic particularity measure for functional characterization of gene sets using gene ontology We propose a new approach to compute gene set particularities based on the information conveyed by Gene Ontology terms. A GO term informativeness can be computed using either its information content based on the term frequency in a corpus, or a function of the term's distance to the root. We demonstrated that the combination of semantic similarity and semantic particularity measures was able to identify genes with particular functions from among similar genes. This differentiation was not recognized using only a semantic similarity measure. [C. Bettembourg, O. Dameron] [17] [Online publication]

Integrating GALAXY workflows in a metadata management environment New tools are needed to enable the quick design and the intensive parallel execution of bioinformatics processes. Therefore, we proposed a new dataflow-oriented workflow management system dedicated to intensive bioinformatics tasks. We worked on the interoperatibility of bioinformatics workflows using a model-driven approach. Our results enable new import / export capabilities beetwen multiple workflow management environnements and insights to create a unique shared workflow model. [O. Dameron, F. Moreews (Genscale team), Y. Le Bras (GenOuest platform), C. Monjeaud (GenOuest platform), O. Collin (GenOuest platform)][36]