iPath: Interactive exploration of biochemical pathways and networks

EMBL, Meyerhofstrasse 1, Heidelberg, Germany.
Trends in Biochemical Sciences (Impact Factor: 13.52). 04/2008; 33(3):101-3. DOI: 10.1016/j.tibs.2008.01.001
Source: PubMed

ABSTRACT iPath is an open-access online tool ( 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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    • "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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    ABSTRACT: Little is known about the role of transcriptomic changes in driving phenotypic evolution in natural populations, particularly in response to anthropogenic environmental change. Previous analyses of Daphnia genotypes separated by centuries of evolution in a lake using methods in resurrection ecology revealed striking genetic and phenotypic shifts that were highly correlated with anthropogenic environmental change, specifically phosphorus (P)-driven nutrient-enrichment (i.e., eutrophication). Here, we compared the transcriptomes of two ancient (~700-yr-old) and two modern (~10-yr-old) genotypes in historic (low P) and contemporary (high P) environmental conditions using microarrays. We found considerable transcriptomic variation between ‘ancient’ and ‘modern’ genotypes in both treatments, with stressful (low P) conditions eliciting differential expression (DE) of a larger number of genes. Further, more genes were DE between ‘ancient’ and ‘modern’ genotypes than within these groups. Expression patterns of individual genes differed greatly among genotypes, suggesting that different transcriptomic responses can result in similar phenotypes. While this confounded patterns between ‘ancient’ and ‘modern’ genotypes at the gene level, patterns were discernible at the functional level: annotation of DE genes revealed particular enrichment of genes involved in metabolic pathways in response to P-treatments. Analyses of gene families suggested significant DE in pathways already known to be important in dealing with P-limitation in Daphnia as well as in other organisms. Such observations on genotypes of a single natural population, separated by thousands of generations of evolution in contrasting environmental conditions before and during anthropogenic environmental changes highlight the important role of transcriptional mechanisms in the evolutionary responses of populations.This article is protected by copyright. All rights reserved.
    Molecular Ecology 11/2014; 24(1). DOI:10.1111/mec.13009 · 6.49 Impact Factor
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    • "To verify the completeness of the assembly, sequences were further classified by pathway using the KEGG KAAS tool (, and the representation of annotated metabolic pathways was compared graphically to the metabolic map inferred from the complete genome sequence of the sea anemone Nematostella vectensis using iPath2 (Moriya et al. 2007; Letunic et al. 2008) (, Fig. S1, Supporting information). "
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    ABSTRACT: Recent evidence suggests that corals can acclimatize or adapt to local stress factors through differential regulation of their gene expression. Profiling gene expression in corals from diverse environments can elucidate the physiological processes that may be responsible for maximizing coral fitness in their natural habitat and lead to a better understanding of the coral's capacity to survive the effects of global climate change. In an accompanying paper, we show that Porites astreoides from thermally different reef habitats exhibit distinct physiological responses when exposed to 6 weeks of chronic temperature stress in a common garden experiment. Here, we describe expression profiles obtained from the same corals for a panel of 9 previously reported and 10 novel candidate stress response genes identified in a pilot RNA-Seq experiment. The strongest expression change was observed in a novel candidate gene potentially involved in calcification, SLC26, a member of the solute carrier family 26 anion exchangers, which was down-regulated by 92-fold in bleached corals relative to controls. The most notable signature of divergence between coral populations was constitutive up-regulation of metabolic genes in corals from the warmer inshore location, including the gluconeogenesis enzymes pyruvate carboxylase and phosphoenolpyruvate carboxykinase and the lipid beta-oxidation enzyme acyl-CoA dehydrogenase. Our observations highlight several molecular pathways that were not previously implicated in the coral stress response and suggest that host management of energy budgets might play an adaptive role in holobiont thermotolerance.
    Molecular Ecology 07/2013; 16(16). DOI:10.1111/mec.12390 · 6.49 Impact Factor
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    • "Metabolic complementation of Lactococcus and Leuconostoc To evaluate to what extent Lactococcus and Leuconostoc strains can metabolically complement each other, the COG categories of the L. lactis TIFN1–7 pan-genome and TIFN8 Leuconostoc genome were mapped on the iPath (Letunic et al., 2008) for the general metabolism separately, and the maps were superimposed (Supplementary Figure 7). The COGs related to a variety of metabolic pathways were either detected in L. lactis pan-genome or in Leuconostoc TIFN8 genome, suggesting a complementation for each other (Supplementary Table 7). "
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    ABSTRACT: Maintenance of a high degree of biodiversity in homogeneous environments is poorly understood. A complex cheese starter culture with a long history of use was characterized as a model system to study simple microbial communities. Eight distinct genetic lineages were identified, encompassing two species: Lactococcus lactis and Leuconostoc mesenteroides. The genetic lineages were found to be collections of strains with variable plasmid content and phage sensitivities. Kill-the-winner hypothesis explaining the suppression of the fittest strains by density-dependent phage predation was operational at the strain level. This prevents the eradication of entire genetic lineages from the community during propagation regimes (back-slopping), stabilizing the genetic heterogeneity in the starter culture against environmental uncertainty.The ISME Journal advance online publication, 4 July 2013; doi:10.1038/ismej.2013.108.
    The ISME Journal 07/2013; 7(11). DOI:10.1038/ismej.2013.108 · 9.27 Impact Factor
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