jActiveModules protocols

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jActiveModules specifications

Information


Unique identifier OMICS_08331
Name jActiveModules
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
Version 3.1
Stability Stable
Requirements
Cytoscape
Maintained Yes

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Documentation


Publication for jActiveModules

jActiveModules in pipelines

 (3)
2015
PMCID: 4530213
PMID: 26273637
DOI: 10.1155/2015/619730

[…] differential expression was computed by the linear models and empirical bayes methods []. and then the p values of each gene were obtained., from the gene network of obesity and t2d, we used the jactivemodules [] and multiple gene expression profiles to find the active gene modules showing significant changes in expression in disease/normal conditions. the jactivemodules (version 1.8) […]

2014
PMCID: 4152332
PMID: 25180703
DOI: 10.1371/journal.pone.0106646

[…] in the original proteomic analysis. the values for specific nodes and edges are shown in for both the global network and the subnetworks. (a, b, c, d and e) shows the subnetworks generated by jactivemodules for each comparison. the majority of the proteins presenting with a fold change interact with glut4 (p19357; 7–26 proteins) and 14-3-3 protein zeta/delta (p63102; 4-14 proteins) […]

2013
PMCID: 3663784
PMID: 23432934
DOI: 10.1186/1471-2105-14-59

[…] recover topological characteristics present in the original active subnetwork than the single parameter approach? therefore, we do not further analyze the characteristics of networks generated by jactivemodules or the maximum likelihood approach., we use the cytoscape plugin networkanalyzer [] to analyze global characteristics of the networks generated from the full parameter and single […]


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jActiveModules in publications

 (51)
PMCID: 5857180
PMID: 29556568
DOI: 10.1016/j.bbrep.2018.01.001

[…] analysis, multiple-testing corrections on p-value and generating annotations using geo2r software (www.ncbi.nlm.nih.gov/geo/geo2r). were performed using imported expression data into the network, jactivemodules 3.1 detected active expression sub-networks , ., the database for annotation, visualization and integrated discovery, david (https://david.ncifcrf.gov) is one of the most efficient […]

PMCID: 5719419
PMID: 29215067
DOI: 10.1038/s41598-017-17505-9

[…] and active modules (highly connected subnetworks that have relatively higher levels of combined protein quantity compared to other potential subnetworks) were identified using the cytoscape plugin jactivemodules. network statistics including the degree (total number of associations) of a node or protein in the network and its total number of associations were computed using cytoscape default […]

PMCID: 5638204
PMID: 29023450
DOI: 10.1371/journal.pcbi.1005580

[…] disorders [, ], multiple cancers [] and many others [, ]. some of the first methods developed to take advantage of gene and protein interaction networks, such as dmgwas, dapple, nimmi, ipinbpa, jactivemodules [–], directly relied on the network annotations to iteratively search for neighbourhoods of associated genes while greedily exploring the network. more recently, several methods […]

PMCID: 5626145
PMID: 28767591
DOI: 10.1097/MD.0000000000007673

[…] using clusterprofiler package. a protein–protein interaction (ppi) network of selected degs was constructed based on the human protein reference database. active modules were explored using the jactivemodules plug-in in the cytoscape network modeling package., in total, 537 degs in ra samples were identified, including 241 upregulated and 296 downregulated genes. a total of 24,451 ppi pairs […]

PMCID: 5533795
PMID: 28754978
DOI: 10.1038/s41598-017-07189-6

[…] networks. the greedy searching strategy based on mutual information was employed to find the most succinct network maintaining the highest accumulated t-score for each diagnostic network using the jactivemodules plugin in cytoscape. mutual information is computed by equation , where a and c each denotes the nodes, x and y each represents the t-scores of a and c, p(x, y) is the probability […]


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jActiveModules institution(s)
Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Institute for Systems Biology, Seattle, WA, USA

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