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, 39 (Web Server issue), W412-5

iPath2.0: Interactive Pathway Explorer

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iPath2.0: Interactive Pathway Explorer

Takuji Yamada et al. Nucleic Acids Res.

Abstract

iPath2.0 is a web-based tool (http://pathways.embl.de) for the visualization and analysis of cellular pathways. Its primary map summarizes the metabolism in biological systems as annotated to date. Nodes in the map correspond to various chemical compounds and edges represent series of enzymatic reactions. In two other maps, iPath2.0 provides an overview of secondary metabolite biosynthesis and a hand-picked selection of important regulatory pathways and other functional modules, allowing a more general overview of protein functions in a genome or metagenome. iPath2.0's main interface is an interactive Flash-based viewer, which allows users to easily navigate and explore the complex pathway maps. In addition to the default pre-computed overview maps, iPath offers several data mapping tools. Users can upload various types of data and completely customize all nodes and edges of iPath2.0's maps. These customized maps give users an intuitive overview of their own data, guiding the analysis of various genomics and metagenomics projects.

Figures

Figure 1.
Figure 1.
Enzymatic activity in the human gut microbiome: the nodes colored in red represent enzymes or proteins detected in metagenomic data derived from human fecal samples (12). Users can easily get an overview of complete metabolic and other pathways. In this example, enzymes in glycerolipid metabolism (center left) or proteins in protein export systems (center right) are overrepresented compared to other pathways in the data set. Line widths in the map are proportional to the level of overrepresentation.

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