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PiNGO specifications

Information


Unique identifier OMICS_02281
Name PiNGO
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for PiNGO

PiNGO citations

 (3)
library_books

Module based functional pathway enrichment analysis of a protein protein interaction network to study the effects of intestinal microbiota depletion in mice

2014
PMCID: 4055453
PMID: 24718810
DOI: 10.3892/mmr.2014.2137

[…] off value for the connectivity degree of nodes (proteins in the network) >2. Gene Ontology (GO) functional annotation and enrichment analysis of genes in the resulting modules was performed using the PiNGO plugin in Cytoscape () with a threshold P<0.05 based on a hypergeometric test. […]

library_books

Pivotal role of the muscle contraction pathway in cryptorchidism and evidence for genomic connections with cardiomyopathy pathways in RASopathies

2013
BMC Med Genomics
PMCID: 3626861
PMID: 23410028
DOI: 10.1186/1755-8794-6-5

[…] A new cohort of 43 candidate genes (Additional file : Table S7) was predicted by PiNGO 1.11 [], which is a Cytoscape plug-in (see Methods) []. The question we tried to address was which first-neighbor genes significantly interact with the original cohort of 179 literature-collecte […]

library_books

CytoITMprobe: a network information flow plugin for Cytoscape

2012
BMC Res Notes
PMCID: 3514294
PMID: 22587372
DOI: 10.1186/1756-0500-5-237

[…] that provide complementary functionality. For instance, output ITMs can be related to terms from controlled vocabularies such as Gene Ontology [] using functional enrichment analysis plugins such as PinGO [] or our own recently released CytoSaddleSum[]. The graph-theoretic structure of ITM subnetworks can be analyzed using a variety of algorithms such as MCODE [] or GraphletCounter [,].The archit […]

Citations

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PiNGO institution(s)
Department of Bioengineering, University of California San Diego, La Jolla, CA, USA

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