Article

iPath: Interactive exploration of biochemical pathways and networks

EMBL, Meyerhofstrasse 1, Heidelberg, Germany.
Trends in Biochemical Sciences (Impact Factor: 11.23). 04/2008; 33(3):101-3. DOI: 10.1016/j.tibs.2008.01.001
Source: PubMed

ABSTRACT

iPath is an open-access online tool (http://pathways.embl.de) for visualizing and analyzing metabolic pathways. An interactive viewer provides straightforward navigation through various pathways and enables easy access to the underlying chemicals and enzymes. Customized pathway maps can be generated and annotated using various external data. For example, by merging human genome data with two important gut commensals, iPath can pinpoint the complementarity of the host-symbiont metabolic capacities.

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    • "GO annotations were then used in an enrichment analysis for biological processes, molecular function, and cellular components as implemented in GOrilla with a P-value threshold of 0.001 (Eden et al. 2009). Furthermore, we visualized metabolic pathways associated with shared differentially expressed genes through annotation with KEGG orthologs (Kyoto Encyclopedia of Genes and Genomes; Kanehisa et al. 2012) as implemented in iPath v2 (Letunic et al. 2008).Fig. 1. A. Primary enzymes involved in the oxidative phosphorylation pathway of the mitochondrial respiratory chain, which represents a nexus of H 2 S toxicity and detoxification. H 2 S is toxic because it blocks cytochrome c oxidase (COX; complex IV) of the respiratory chain. "
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    • "c pathways was prominent in both between - and within - population contrasts , but under HiP , metabolic pathways were upregulated in A rela - tive to M genotypes . Pathways that were differentially regulated in at least one of the between - population contrasts ( Appendix S2 , Supporting information ) were combined for visualiza - tion in iPath ( Letunic et al . 2008 ) . This was carried out separately for the HiP and LoP treatments to identify potential functional relevance of differential regulation in response to P - supply ( Fig . 2A : HiP ; Fig . 2B : LoP ) . These pathways are expected to be particularly impor - tant because they underlie differential regulation between A and M genotypes , whi"
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    • "When available, COG assignment was performed using the Batch Web CD-Search online tool (http://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi). Predicted functions were projected on KEGG metabolic pathways using the Ipath software55 and compared to essential genes identified in the model organism Bacillus subtilis56. When species-level taxonomy could not be assigned, higher taxonomic levels were assigned using MEGAN57. "
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