2019-07-05T15:07:59Z (GMT) by De Sl Martina Kutmon
Abstract: Genome-scale metabolic models are important in understanding metabolism at the cellular level and play a key role in flux prediction and metabolic engineering projects. Recon, a stoichiometry based genome scale model for humans, provides a collection of genes, reactions and their corresponding metabolites as one comprehensive knowledge-base, based on literature and databases through manual curation. Combining genome scale metabolic models with omics data has been performed in several studies, however the focus on mathematical modeling meant that classical analyses which are part of omics data analysis pipelines (Pathway Enrichment and Network Analysis) have rarely been applied.
In order to improve the usefulness of these models for pathway and network analysis, several problems need to be addressed, e.g. inconsistencies in (or lack thereof) mappings between identifiers from different databases and incomplete stereochemistry of the involved metabolites. Nonetheless, Recon provides detailed information – such as cellular location, transport reactions and occurrence in tissue (types) – commonly missing from pathway knowledge bases.
During this Science Cafe, Chaitra and Denise will present part of their respective PhD projects, where they combine forces to overcome the issues raised above. First, Chaitra will explain how she visualizes omics data on “pathways” derived from genome scale models. This is followed by Denise, who will present their project idea for combining Recon3D (the latest genome scale metabolic model for Homo sapiens) with WikiPathways, aiming to aid both the bioinformatics and metabolic modeling communities and their respective projects.