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
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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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    • "When available, COG assignment was performed using the Batch Web CD-Search online tool ( 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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    ABSTRACT: The gut microbiota (GM) consists of resident commensals and transient microbes conveyed by the diet but little is known about the role of the latter on GM homeostasis. Here we show, by a conjunction of quantitative metagenomics, in silico genome reconstruction and metabolic modeling, that consumption of a fermented milk product containing dairy starters and Bifidobacterium animalis potentiates colonic short chain fatty acids production and decreases abundance of a pathobiont Bilophila wadsworthia compared to a milk product in subjects with irritable bowel syndrome (IBS, n = 28). The GM changes parallel improvement of IBS state, suggesting a role of the fermented milk bacteria in gut homeostasis. Our data challenge the view that microbes ingested with food have little impact on the human GM functioning and rather provide support for beneficial health effects.
    Scientific Reports 09/2014; 4:6328. DOI:10.1038/srep06328 · 5.58 Impact Factor
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    • "To visualize the functional differences of hemolymph between the two bee species, differentially abundant proteins (Additional file 1: Table S1) were mapped to KEGG-derived metabolic pathways using iPath2.0 [24]. Only those honey bee proteins with assigned functions (i.e. "
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    ABSTRACT: Background Hemolymph plays key roles in honey bee molecule transport, immune defense, and in monitoring the physiological condition. There is a lack of knowledge regarding how the proteome achieves these biological missions for both the western and eastern honey bees (Apis mellifera and Apis cerana). A time-resolved proteome was compared using two-dimensional electrophoresis-based proteomics to reveal the mechanistic differences by analysis of hemolymph proteome changes between the worker bees of two bee species during the larval to pupal stages. Results The brood body weight of Apis mellifera was significantly heavier than that of Apis cerana at each developmental stage. Significantly, different protein expression patterns and metabolic pathways were observed in 74 proteins (166 spots) that were differentially abundant between the two bee species. The function of hemolymph in energy storage, odor communication, and antioxidation is of equal importance for the western and eastern bees, indicated by the enhanced expression of different protein species. However, stronger expression of protein folding, cytoskeletal and developmental proteins, and more highly activated energy producing pathways in western bees suggests that the different bee species have developed unique strategies to match their specific physiology using hemolymph to deliver nutrients and in immune defense. Conclusions Our disparate findings constitute a proof-of-concept of molecular details that the ecologically shaped different physiological conditions of different bee species match with the hemolymph proteome during the brood stage. This also provides a starting point for future research on the specific hemolymph proteins or pathways related to the differential phenotypes or physiology. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-563) contains supplementary material, which is available to authorized users.
    BMC Genomics 07/2014; 15(1):563. DOI:10.1186/1471-2164-15-563 · 3.99 Impact Factor
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