PathVisio protocols

View PathVisio computational protocol

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PathVisio specifications

Information


Unique identifier OMICS_10374
Name PathVisio
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License Apache License version 2.0
Computer skills Medium
Version 3.0
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/PathVisio

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Publications for PathVisio

PathVisio in pipelines

 (2)
2017
PMCID: 5681904
PMID: 29163640
DOI: 10.3389/fgene.2017.00174

[…] method on the gene list annotated from the variants present in the vcf provided as input. metacore employs a hyper-geometric model to determine the significance of the enrichments. pathvisio also uses an over-representation analysis and it is based on methods adopted in the mappfinder tool () with settings designed for gene expression data. finally, ipa utilizes a method […]

2011
PMCID: 3030591
PMID: 21305041
DOI: 10.1371/journal.pone.0016516

[…] with p-value less than 0.01 were considered to be distinctly expressed. kegg analysis was based on the comparative results between our mapping genes and the updated kegg database , . genmapp 2.0 and pathvisio were respectively used to evaluate differentiated gene expression in a variety of biological pathways , ., the samples for qrt-pcr were derived from the human posterior um cell lines m17, […]


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PathVisio in publications

 (82)
PMCID: 5902856
PMID: 29661132
DOI: 10.1186/s12864-018-4651-8

[…] to each other using the edger tmm normalization method., all rna-seq data analysis was preformed using r (v3.2.4) and bioconductor (v3.3). the pathway maps of pl and lp synthesis were produced using pathvisio. the heatmap was drawn using r package pheatmap. all other figures were produced using sigmaplot for windows version 13.0., to examine expression of genes involved in pl and lp synthesis […]

PMCID: 5884322
PMID: 29438851
DOI: 10.1016/j.jprot.2018.02.015

[…] proteins was visualised using volcano plots using log2 (fold change) plotted against significance in r studio. pathway analysis of label free quantitative proteomic data was performed using pathvisio [] together with wikipathways [] to visualize and highlight altered pathways from identified proteins., in these experimental conditions we considered cys containing peptides […]

PMCID: 5907308
DOI: 10.1186/s13098-018-0315-8

[…] the kyoto encyclopedia of genes and genomes (kegg), and the signaling pathway mapping was performed using the automatic annotation server of the kegg. the signaling pathway map was realized using pathvisio program, a free available signaling pathway drawing software., results: the contigs were taken from the kegg database and their mapped transcription represents the signaling pathway […]

PMCID: 5884799
PMID: 29618802
DOI: 10.1038/s41598-018-24032-8

[…] of the molecules from the dataset comparisons to a main pathway through term clustering in cluego, the next iteration step involved analysis of pathway statistical inference and visualisation in pathvisio. the signalling pathway of ifn- γ was shown to be the most significant one either in cluego and pathvisio analyses. once the pathway was selected, it was then fully filled by the total […]

PMCID: 5813898
PMID: 29447151
DOI: 10.1371/journal.pcbi.1005740

[…] explosions resulting from multicomponent complexes and molecules with multiple states., sbgn is supported by a range of visualisation tools, including celldesigner [], sbgn-editor (sbgn-ed) [], pathvisio [] and sbgnviz []. sbgn diagrams are published in open repositories such as biomodels [] (for computational models) and reactome [] (for pathway data). to help scientists understand sbgn […]


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PathVisio institution(s)
Department of Bioinformatics, BiGCaT Maastricht University, Universiteitssingel, Maastricht, Netherlands

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