iPath2.0: interactive pathway explorer

By Takuji Yamada, Ivica Letunic, Shujiro Okuda, Minoru Kanehisa, Peer Bork. Nucleic Acids Res., 2011

322 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/91d8b3f836ae3796a6f8b492e5847a4336a5573b

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Citations in the corpus

Pathview Web: user friendly pathway visualization and data integration (2017, methodology): “A number of options / tools exist for pathway visualization (10–15), each with its unique focus and strength.”
Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions (2013, methodology): “(iPath2) [40] was used to map the functional genes involved in”
Rhizosphere microbiome assemblage is affected by plant development (2013, background): “The interactive pathways explorer 2 (iPATH2) (Yamada et al., 2011) was used to map the functional transcripts that were differentially expressed between early and late plant development (Supplementary Figure S2).”
Advances and Challenges in Metatranscriptomic Analysis (2019, methodology): “Once annotations are performed, enzymatic functions may also be mapped to known metabolic pathways, using tools like MinPath (Ye and Doak, 2009) or iPath (Yamada et al., 2011).”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, background): “…Murrell, 2012 IM Browser http://proteome.wayne.edu/PIMdb.html Pacifico et al., 2006 IPath http://pathways.embl.de Yamada et al., 2011 JNets http://www.manchester.ac.uk/bioinformatics/jnets Macpherson et al., 2009 KGML-ED http://kgml-ed.ipk-gatersleben.de Klukas &…”
Identification of genetic elements in metabolism by high-throughput mouse phenotyping (2018, unknown): “The Interactive Path-ways Explorer v2 web-based tool 50 was used to visualize the strong metabolic phenotype genes on a map representing global metabolism in mice.”
SMART: recent updates, new developments and status in 2015 (2014, methodology): “SMART’s integration of biological pathways data was greatly expanded in the current version, and is now synchronized with version 2 of the interactive Pathways Explorer (iPath2) (13).”
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways (2015, background): “0 [16], WikiPathways [17], Biographer [18], and the BioCyc pathway viewer [19].”