GOlorize protocols

View GOlorize computational protocol

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GOlorize specifications

Information


Unique identifier OMICS_08983
Name GOlorize
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Beta
Requirements
Cytoscape
Maintained Yes

Versioning


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Maintainer


  • person_outline Benno Schwikowski <>

Publication for GOlorize

GOlorize in pipeline

2013
PMCID: 3730603
PMID: 23843398
DOI: 10.1098/rspb.2013.1381

[…] with network analyzer [], and jactivemodules v. 2.2 [] was used to analyse network characteristics. go analysis was conducted with the biological network gene ontology (bingo, v. 2.0) plugin [] and golorize tools [] used for statistical evaluation of groups of proteins with respect to the present annotations available in the gene ontology consortium (http://www.geneontology.org). go […]


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GOlorize in publications

 (10)
PMCID: 5928603
PMID: 29512785
DOI: 10.3892/mmr.2018.8668

[…] when the degree of cut-off was 2, the node score cut-off was 0.2, the k-core was 2, and the maximum depth was 100. go-associated analysis was performed on the module with the maximum score using golorize (version: 1.0.0.beta1) (). in addition, the top five go terms in the module were analyzed., the integrated regulatory network was constructed based on the degs, mirnas and tfs. mirnas […]

PMCID: 5915032
PMID: 29455577
DOI: 10.1080/15548627.2017.1415189

[…] q14457, q8neb9 and o75385), are targets of well-characterized post-translational modifications that lead to activation of autophagy. the resulting network includes 146 proteins and 530 interactions. golorize [] and bingo [] analyses identified 600 go biological process terms as enriched within this network, as well as 120 enriched cellular component terms and 67 molecular function terms (table […]

PMCID: 4614801
PMID: 26489668
DOI: 10.1038/srep15340

[…] enriched in each module determined by hypergeometric test with a p value was less than 0.05., significant gene ontology (go) categories (‘biological processes’) were enriched using cytoscape plugin golorize, with a fdr less than 0.05., how to cite this article: liu, n. et al. a functional module-based exploration between inflammation and cancer in esophagus. sci. rep. 5, 15340; doi: […]

PMCID: 4447275
PMID: 26020946
DOI: 10.1371/journal.pgen.1005155

[…] value in wild type cells, and font size to enrichment q-value. go categories were assigned to genes using the bingo application for cytoscape and coloring the go categories was performed using golorize application for cytoscape., a tcf21 functional knockout and reporter line, tcf21 lacz/+, was constructed by substituting the lacz gene into the first exon of the murine gene employing […]

PMCID: 3730603
PMID: 23843398
DOI: 10.1098/rspb.2013.1381

[…] with network analyzer [], and jactivemodules v. 2.2 [] was used to analyse network characteristics. go analysis was conducted with the biological network gene ontology (bingo, v. 2.0) plugin [] and golorize tools [] used for statistical evaluation of groups of proteins with respect to the present annotations available in the gene ontology consortium (http://www.geneontology.org). go […]


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GOlorize institution(s)
Systems Biology Unit, Institut Pasteur, Paris, France; Macromolecular Interaction Genetics, Institut Pasteur, Paris, France

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