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iPath2.0: interactive pathway explorer

Takuji Yamada, Ivica Letunic, Shujiro Okuda, Minoru Kanehisa, Peer Bork
2011 Nucleic Acids Research  
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

Maria Cecília D. Costa, Thijs Slijkhuis, Wilco Ligterink, Henk W.M. Hilhorst, Dick de Ridder, Harm Nijveen
2016 F1000Research  
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

Christine Chichester, Tobias Kuhn
2017 Data Science  
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

Man-Jun Yang, Zhi-Xue Cheng, Ming Jiang, Zao-Hai Zeng, Bo Peng, Xuan-Xian Peng, Hui Li
2018 Virulence  
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)

Mao Feng, Haitham Ramadan, Bin Han, Yu Fang, Jianke Li
2014 BMC Genomics  
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

S. Bovo, G. Mazzoni, D. G. Calò, G. Galimberti, F. Fanelli, M. Mezzullo, G. Schiavo, E. Scotti, A. Manisi, A. B. Samoré, F. Bertolini, P. Trevisi (+4 others)
2015 Journal of Animal Science  
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

Paul Abraham, Richard J. Giannone, Rachel M. Adams, Udaya Kalluri, Gerald A. Tuskan, Robert L. Hettich
2012 Molecular & Cellular Proteomics  
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

Qiaohui Zeng, Jianguo Jiang, Jingjing Wang, Qiuchan Zhou, Xuewu Zhang
2019 Marine Drugs  
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)

Xiaoming Song, Ying Li, Xilin Hou
2013 BMC Genomics  
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

Ulrik Plesner Jacobsen, Henrik Bjørn Nielsen, Falk Hildebrand, Jeroen Raes, Thomas Sicheritz-Ponten, Irene Kouskoumvekaki, Gianni Panagiotou
2012 The ISME Journal  
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

Aoife Joyce, Umer Z. Ijaz, Corine Nzeteu, Aoife Vaughan, Sally L. Shirran, Catherine H. Botting, Christopher Quince, Vincent O'Flaherty, Florence Abram
2018 Frontiers in Microbiology  
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

Derek J Stefanik, Tristan J Lubinski, Brian R Granger, Allyson L Byrd, Adam M Reitzel, Lukas DeFilippo, Allison Lorenc, John R Finnerty
2014 BMC Genomics  
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

M. Nieves Calvo-Vidal, Nahuel Zamponi, Jan Krumsiek, Max A. Stockslager, Maria V. Revuelta, Jude M. Phillip, Rossella Marullo, Ekaterina Tikhonova, Nikita Kotlov, Jayeshkumar Patel, Shao Ning Yang, Lucy Yang (+8 others)
2021 Cancer Research  
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

Erica M Forsberg, Tao Huan, Duane Rinehart, H Paul Benton, Benedikt Warth, Brian Hilmers, Gary Siuzdak
2018 Nature Protocols  
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

Héctor Argüello, Jordi Estellé, Sara Zaldívar-López, Ángeles Jiménez-Marín, Ana Carvajal, Mª Asunción López-Bascón, Fiona Crispie, Orla O'Sullivan, Paul D. Cotter, Feliciano Priego-Capote, Luis Morera, Juan J. Garrido
2018 Scientific Reports  
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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