Dataset Information

MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization.

ABSTRACT:

Unlabelled

We present MetaRoute, an efficient search algorithm based on atom mapping rules and path weighting schemes that returns relevant or textbook-like routes between a source and a product metabolite within seconds for genome-scale networks. Its speed allows the algorithm to be used interactively through a web interface to visualize relevant routes and local networks for one or multiple organisms based on data from KEGG.

Availability

http://www-bs.informatik.uni-tuebingen.de/Services/MetaRoute.

Supplementary information

Supplementary details are available at http://www-bs.informatik.uni-tuebingen.de/Services/MetaRoute.

SUBMITTER: Blum T

PROVIDER: S-EPMC2530881 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization.

Blum Torsten T Kohlbacher Oliver O

Bioinformatics (Oxford, England) 20080716 18

<h4>Unlabelled</h4>We present MetaRoute, an efficient search algorithm based on atom mapping rules and path weighting schemes that returns relevant or textbook-like routes between a source and a product metabolite within seconds for genome-scale networks. Its speed allows the algorithm to be used interactively through a web interface to visualize relevant routes and local networks for one or multiple organisms based on data from KEGG.<h4>Availability</h4>http://www-bs.informatik.uni-tuebingen.de ...[more]

PMID: 18635573

Similar Datasets

Project description:Understanding of genotype-phenotype associations is important not only for furthering our knowledge on internal cellular processes, but also essential for providing the foundation necessary for genetic engineering of microorganisms for industrial use (e.g., production of bioenergy or biofuels). However, genotype-phenotype associations alone do not provide enough information to alter an organism's genome to either suppress or exhibit a phenotype. It is important to look at the phenotype-related genes in the context of the genome-scale network to understand how the genes interact with other genes in the organism. Identification of metabolic subsystems involved in the expression of the phenotype is one way of placing the phenotype-related genes in the context of the entire network. A metabolic system refers to a metabolic network subgraph; nodes are compounds and edges labels are the enzymes that catalyze the reaction. The metabolic subsystem could be part of a single metabolic pathway or span parts of multiple pathways. Arguably, comparative genome-scale metabolic network analysis is a promising strategy to identify these phenotype-related metabolic subsystems. Network Instance-Based Biased Subgraph Search (NIBBS) is a graph-theoretic method for genome-scale metabolic network comparative analysis that can identify metabolic systems that are statistically biased toward phenotype-expressing organismal networks. We set up experiments with target phenotypes like hydrogen production, TCA expression, and acid-tolerance. We show via extensive literature search that some of the resulting metabolic subsystems are indeed phenotype-related and formulate hypotheses for other systems in terms of their role in phenotype expression. NIBBS is also orders of magnitude faster than MULE, one of the most efficient maximal frequent subgraph mining algorithms that could be adjusted for this problem. Also, the set of phenotype-biased metabolic systems output by NIBBS comes very close to the set of phenotype-biased subgraphs output by an exact maximally-biased subgraph enumeration algorithm ( MBS-Enum ). The code (NIBBS and the module to visualize the identified subsystems) is available at http://freescience.org/cs/NIBBS.

Dataset Information

MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization.

Unlabelled

Availability

Supplementary information

Publications

MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets