Pathview protocols

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description
Pathview computational protocol

Pathview specifications

Information


Unique identifier OMICS_05212
Name Pathview
Alternative name Pathview Web
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.20.0
Stability Stable
Requirements
AnnotationDbi, methods, BiocGenerics, utils, R(>=2.10), RUnit, org.Hs.eg.db, graph, org.Mm.eg.db, Rgraphviz, KEGGgraph, XML, png, KEGGREST, gage
Maintained Yes

Versioning


Add your version

Documentation


Maintainer


  • person_outline Weijun Luo <>

Additional information


https://pathview.uncc.edu/

Information


Unique identifier OMICS_05212
Name Pathview
Alternative name Pathview Web
Interface Web user interface
Restrictions to use None
Input data Some (1) gene data cover any data that map to unique gene IDs including genes, transcripts, genomic loci, proteins, enzymes and their attributes; (2) compound data cover any data that map to unique compound IDs including compounds, metabolites, drugs, small molecules and their attributes.
Output data Graphs with user data mapped.
Programming languages R
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Weijun Luo <>

Additional information


https://pathview.uncc.edu/

Publications for Pathview

Pathview IN pipelines

 (4)
2018
PMCID: 5796909
PMID: 29434599
DOI: 10.3389/fimmu.2018.00080

[…] for kegg, go bp, cc, and mf terms using the conditional hypergeometric test implemented in the gostats r package (function: hypergtest) (42). annotated kegg pathway diagrams were drawn using the pathview r package (43). enrichment of medical subject heading (mesh) terms was evaluated using the hypergeometric test implemented in the meshr r package (function: meshhypergtest) (44). likewise, […]

2018
PMCID: 5813940
PMID: 29447215
DOI: 10.1371/journal.pone.0192606

[…] we also used the r package gage [99] to identify pathways that were perturbed in a single direction or generally dysregulated due to maternal diet, and visualized those pathways using the r package pathview [100]., we validated the differential expression of three genes with rt-qpcr in the hf daughters (mpo, anxa2, and chrna4), using gapdh as a normalizer. we extracted total rna from the liver […]

2017
PMCID: 5339665
PMID: 28326294
DOI: 10.3389/fcimb.2017.00066

[…] analysis based on kegg pathway database (http://www.genome.jp/kegg/) was done using the r package gage v2.22 (luo et al., 2009). pathway-level differential expression was visually checked using pathview (luo and brouwer, 2013). functional classification of gene products was predicted using blastp v2.5.0+ (altschul et al., 1997) by the clusters within the orthologous group (cog) database […]

2017
PMCID: 5487013
PMID: 28654683
DOI: 10.1371/journal.pone.0179613

[…] the wnt signaling pathway was further visualized using a pathway map and a gene-transcription factor interaction network. the pathway map was downloaded from kegg [31] and rendered with pathview [22] using gene expression data for days 1 to 4. the gene-transcription factor network was created by including all genes in the wnt pathway present in the filtered dataset […]

Pathview institution(s)
Department of Bioinformatics and Genomics, UNC Charlotte, Charlotte, NC, USA; UNC Charlotte Bioinformatics Service Division, North Carolina Research Campus, Kannapolis, NC, USA; Department of Computer Science, UNC Charlotte, Charlotte, NC, USA
Pathview funding source(s)
Supported by National Science Foundation [ABI-1565030]; UNC Charlotte CCI Faculty Innovation Award.

Pathview review

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Martin Abba

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Desktop
Nice R/Bioconductor package to visualize Differentially expressed genes and differentially methylated regions among KEGG based pathways just providing a gene Entrez ID list with their associated fold changes.