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Protocols

iPath specifications

Information


Unique identifier OMICS_07437
Name iPath
Alternative name interactive Pathways Explorer
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline iPath Team

Publications for interactive Pathways Explorer

iPath citations

 (44)
library_books

Taxon Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient

2018
Front Microbiol
PMCID: 5943556
PMID: 29774016
DOI: 10.3389/fmicb.2018.00869

[…] ndance matrices were adapted for the Mothur software. At the third step, metabolic abundance was analyzed using MG-RAST metabolite annotations. The metabolic differential abundance was surveyed using iPATH (Yamada et al., ); this tool offers the visualization of shared and specific pathways between pairs of samples. […]

library_books

Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti

2018
PLoS Genet
PMCID: 5929573
PMID: 29672509
DOI: 10.1371/journal.pgen.1007357

[…] geom_histogram function of ggplot2, and the GC skew was calculated using the analysis of sequence heterogeneity sliding window plots online webserver []. The metabolic model was visualized using the iPath v2.0 webserver []. The logo of the transposon insertion site specificity was generated by first extracting the nucleotides surrounding all unique insertion sites in one replicate of the wild typ […]

library_books

Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass

2018
Front Microbiol
PMCID: 5871674
PMID: 29619022
DOI: 10.3389/fmicb.2018.00540

[…] aproteomics.html. In this pipeline, the enzyme commission (EC) numbers corresponding to the identified proteins are retrieved when available, MinPath () is used to construct parsimonious pathways and iPath2.0 () is employed for pathway visualization. Krona plots were constructed using the Krona template () and Circos plots using the Circos online tool developed by . […]

library_books

Population‐specific transcriptional differences associated with freeze tolerance in a terrestrial worm

2018
Ecol Evol
PMCID: 5901168
PMID: 29686857
DOI: 10.1002/ece3.3602

[…] n an unbiased set of annotation terms per gene to be used for both strains. The combined annotation also yielded a total of 1,136 unique enzyme codes which could be mapped to metabolic pathways using IPATH to determine the completeness of metabolic pathways represented in the transcriptome (Letunic, Yamada, Kanehisa, & Bork, ). This is visualized as red edges in Fig. , suggesting that most of the […]

library_books

Boosted TCA cycle enhances survival of zebrafish to Vibrio alginolyticus infection

2018
PMCID: 5955478
PMID: 29338666
DOI: 10.1080/21505594.2017.1423188

[…] d Prism v5.01 (GraphPad, La Jolla, CA, USA) were used to draw the histogram the scatter plot. Comparative metabolic pathway analysis between the death group and the survival group was performed using iPath2.0 []. […]

call_split

The effect of Clostridium butyricum on symptoms and fecal microbiota in diarrhea dominant irritable bowel syndrome: a randomized, double blind, placebo controlled trial

2018
Sci Rep
PMCID: 5813237
PMID: 29445178
DOI: 10.1038/s41598-018-21241-z
call_split See protocol

[…] Effect Size) was conducted to indicate the significant factors between the groups. The STAMP analysis was used to assess function richness between groups. The whole metabolic pathways were mapped by iPath2.0 (http://pathways.embl.de). […]

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iPath institution(s)
EMBL, Heidelberg, Germany

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