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Publication for PiNGO
Module based functional pathway enrichment analysis of a protein protein interaction network to study the effects of intestinal microbiota depletion in mice
[…] 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. […]
Pivotal role of the muscle contraction pathway in cryptorchidism and evidence for genomic connections with cardiomyopathy pathways in RASopathies
[…] 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 […]
CytoITMprobe: a network information flow plugin for Cytoscape
[…] 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 […]
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