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iPath2.0: interactive pathway explorer
2011
Nucleic Acids Research
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overview of protein functions in a genome or metagenome. iPath2.0 0 s main interface is an interactive Flash-based viewer, which allows users to easily navigate and explore the complex pathway maps. ...
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. ...
USER INTERFACE AND BASIC FUNCTIONS iPath2.0 0 s main interface allows users to easily navigate and explore the complex pathway maps. ...
doi:10.1093/nar/gkr313
pmid:21546551
pmcid:PMC3125749
fatcat:zwcg7kpng5af5our65ihzpuace
CyLineUp: A Cytoscape app for visualizing data in network small multiples
2016
F1000Research
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Yamada T, Letunic I, Okuda S, et al.: iPath2.0: interactive pathway explorer. Nucleic Acids Res. 2011; 39(Web Server issue): W412-5. PubMed Abstract | Publisher Full Text | Free Full Text 4. ...
Shannon P, Markiel A, Ozier O, et al.: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11): 2498-504. ...
The data were generated to explore the temporal changes induced by ABA in germinated A. thaliana seeds 9 . ...
doi:10.12688/f1000research.8402.1
pmid:27347378
pmcid:PMC4909101
fatcat:pesrsvfezvfwfe7c7urfuzpcim
Valorizing omics visualization for discovery
2017
Data Science
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The user needs to explore the data interactively in order to assess a wide range of questions. ...
Customized maps generated by iPath2.0 [52] allow users to ingest their own data in the context of genomics or metagenomics projects. ...
doi:10.3233/ds-170009
dblp:journals/datasci/Chichester17
fatcat:a5hdcgrwn5c3jkmeo3nhqt5tpa
Boosted TCA cycle enhances survival of zebrafish to Vibrio alginolyticus infection
2018
Virulence
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In the present study, we established a V. alginolyticus-zebrafish interaction model by which we explored how zebrafish survived from V. alginolyticus infection. ...
Pattern recognition analysis identified the TCA cycle as the most impacted pathway. ...
Comparative metabolic pathway analysis between the death group and the survival group was performed using iPath2.0 [24] . ...
doi:10.1080/21505594.2017.1423188
pmid:29338666
pmcid:PMC5955478
fatcat:t2u6r77t75ct5boewpabdmid3e
Hemolymph proteome changes during worker brood development match the biological divergences between western honey bees (Apis mellifera) and eastern honey bees (Apis cerana)
2014
BMC Genomics
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This also provides a starting point for future research on the specific hemolymph proteins or pathways related to the differential phenotypes or physiology. ...
Significantly, different protein expression patterns and metabolic pathways were observed in 74 proteins (166 spots) that were differentially abundant between the two bee species. ...
metabolic pathways using iPath2.0 [24] . ...
doi:10.1186/1471-2164-15-563
pmid:24996860
pmcid:PMC4111844
fatcat:3rfc6cqc6balzk3nxefkhxm2le
Deconstructing the pig sex metabolome: Targeted metabolomics in heavy pigs revealed sexual dimorphisms in plasma biomarkers and metabolic pathways1
2015
Journal of Animal Science
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Then, the interactive Pathways Explorer iPATH2.0 (Yamada et al., 2011) was used to obtain an overview of the KEGG pathways that included selected metabolites. ...
Metabolomic Pathway and Enrichment Analyses Comparing the Two Sexes An overview of the metabolic KEGG pathways obtained with iPATH2.0 that included the metabolites with KEGG accession numbers (n = 60) ...
doi:10.2527/jas.2015-9528
pmid:26641177
fatcat:uckr4oaeazajll5gxjuacy2pvm
Putting the Pieces Together: High-performance LC-MS/MS Provides Network-, Pathway-, and Protein-level Perspectives inPopulus
2012
Molecular & Cellular Proteomics
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and implementation of current state-of-the-art instrumentation afforded the most detailed look into the predicted proteome space of Populus, offering varying proteome perspectives: 1) network-wide, 2) pathway-specific ...
For a network-wide perspective of Populus metabolism, we employed the use of iPath2.0 23 (http://pathways.embl.de) to navigate and explore the predicted KEGG metabolic pathways (Supplemental Figure 3 ...
using iPath2.0. ...
doi:10.1074/mcp.m112.022996
pmid:23073815
pmcid:PMC3536892
fatcat:mzjoxvfgivgfnbeousvegwk73e
N-Terminal Acetylation and C-Terminal Amidation of Spirulina platensis-Derived Hexapeptide: Anti-Photoaging Activity and Proteomic Analysis
2019
Marine Drugs
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Network analysis indicated that these differential proteins were mapped into an interaction network composed of two core sub-networks. ...
Employing isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics, 60 differential proteins were identified, and major metabolic pathways were determined. ...
By iPath2.0 (http://pathways.embl.de/ipath2.cgi#) analysis, the global view of the pathways involved in differential proteins is presented in Figure 4E . ...
doi:10.3390/md17090520
fatcat:5kdlrhkzmjhizd6ysxi7xvksmq
Genome-wide analysis of the AP2/ERF transcription factor superfamily in Chinese cabbage (Brassica rapa ssp. pekinensis)
2013
BMC Genomics
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Orthologous gene interaction networks were constructed, and included seven CBF and four AP2 genes, primarily involved in cold regulatory pathways and ovule development, respectively. ...
The identification, classification, phylogenetic reconstruction, conserved motifs, chromosome distribution, functional annotation, expression patterns, and interaction networks of the AP2/ERF transcription ...
The functional pathways involving AP2/ERF superfamily were constructed by iPath2.0 software (http://pathways. embl.de/) [72] . ...
doi:10.1186/1471-2164-14-573
pmid:23972083
pmcid:PMC3765354
fatcat:uqbjs2qy2fgxbiu64bkeplt5bu
The chemical interactome space between the human host and the genetically defined gut metabotypes
2012
The ISME Journal
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To capture a snapshot of the highly conserved among healthy individuals metabolic network, we visualized the metabolic reactions with frequency 470% using iPath2.0 (http://pathways. embl.de/). ...
between the chemical signatures that characterize the organism-level metabolic status and host cellular pathways. ...
doi:10.1038/ismej.2012.141
pmid:23178670
pmcid:PMC3603391
fatcat:adwpam5hqbfh3lbnlmrhvc5ac4
Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass
2018
Frontiers in Microbiology
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Taken together, this study highlights the functional importance of Clostridia during the anaerobic digestion of grass and thus research avenues allowing members of this taxon to thrive should be explored ...
iPath2.0 (Yamada et al., 2011) is employed for pathway visualization. ...
Thus, in an effort to optimize the process of grass AD, research avenues aiming at tailoring bioreactor environmental conditions to Clostridia should be explored. ...
doi:10.3389/fmicb.2018.00540
pmid:29619022
pmcid:PMC5871674
fatcat:qqv6j2jtlvfidpulonbb66o4ra
Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian
2014
BMC Genomics
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In this species, it is possible to compare alternate developmental pathways leading from a larva to either a free-living polyp or a vermiform parasite that inhabits the mesoglea of a ctenophore host. ...
Based on gene ontology and metabolic pathway analyses and gene family surveys (bHLH-PAS, deiodinases, Fox genes, LIM homeodomains, minicollagens, nuclear receptors, Sox genes, and Wnts), the transcriptome ...
Enzymes were then formatted, and cross-referenced to an edge list file from the interactive tree of life to produce a file (Additional file 13), which was uploaded to the iPath2.0 program for visualization ...
doi:10.1186/1471-2164-15-71
pmid:24467778
pmcid:PMC3909931
fatcat:joet4qqtmrasrlzxnwk4qluga4
Oncogenic HSP90 facilitates metabolic alterations in aggressive B-cell lymphomas
2021
Cancer Research
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In cancer cells, HSP90 also becomes a nucleating site for the stabilization of multiprotein complexes including signaling pathways and transcription complexes. ...
Here we describe the role of this HSP90 form, referred to as oncogenic HSP90, in the regulation of cytosolic metabolic pathways in proliferating B-cell lymphoma cells. ...
Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P. iPath2.0: interactive pathway explorer. Nucleic Acids Res 2011;39:W412-5 33. Zhang B, Kirov S, Snoddy J. ...
doi:10.1158/0008-5472.can-21-2734
pmid:34479963
pmcid:PMC8530929
fatcat:pcyesgqndnh3zpk3bzbemh4674
Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online
2018
Nature Protocols
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We also describe unique visualization tools to assist in elucidation of statistically significant dysregulated metabolic pathways. ...
Additional multi-omics data can be uploaded and overlaid with previously identified pathways to enhance systems-wide analysis of the observed dysregulations. ...
; iPATH2.0 is an interactive tool for visualization of cellular pathways 14 ; MetExplore links metabolomics data within genome-scale metabolic networks 30 ; Metscape is a Cytoscape plug-in for visualizing ...
doi:10.1038/nprot.2017.151
pmid:29494574
pmcid:PMC5937130
fatcat:ojwld7dmhvcgdfci5pqb6hx7yu
Early Salmonella Typhimurium infection in pigs disrupts Microbiome composition and functionality principally at the ileum mucosa
2018
Scientific Reports
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In addition, Kegg orthology groups (KOs) were mapped to KEGG and visualized using the Interactive Pathway Explorer (iPath2.0) web-based tool 48 . Detection of metabolites by metabolomics. ...
Analysis of predicted metabolic routes in Interactive Pathways Explorer (Ipath2) showed an activation of valine, leucine and isoleucine metabolism, all of which result in the production of pantothenic ...
doi:10.1038/s41598-018-26083-3
pmid:29773876
pmcid:PMC5958136
fatcat:inhdm3gtlnfv7adoqhx2j6acji
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