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GNEA specifications

Information


Unique identifier OMICS_17715
Name GNEA
Alternative name Gene Network Enrichment Analysis
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Gene Network Enrichment Analysis

GNEA in publications

 (8)
PMCID: 5735295
PMID: 29270355
DOI: 10.1016/j.lrr.2017.12.001

[…] (log-rank method, km) and cox proportional hazards (cox-ph) survival analyses were performed in ibm spss statistics 21, and all tests were bootstrapped 1000 times unless otherwise specified. gene network enrichment analysis was performed in string-db (http://string-db.org/) and the results imported into cytoscape for easier visualization. the linear support vector machine (lsvm) […]

PMCID: 5407620
PMID: 28448511
DOI: 10.1371/journal.pone.0176172

[…] cluster using tools such as enrichr []. other methods such as gene set enrichment analysis [] finds processes/gene lists which significantly correlate with a phenotype of interest. methods such as gene network enrichment analysis [] finds high transcriptionally affected sub network in a ppi network and looks for significant overlap with a biological process and gives biological processes […]

PMCID: 5133374
PMID: 27811935
DOI: 10.1038/emm.2016.97

[…] as interactome analysis using the metacore database from thomson reuters (ver. 6.11, build 41105, genego, thomson reuters, new york, ny, usa). the metacore pathway analysis tool was used to perform gene network enrichment analysis; the metacore interactome tool was used for the identification of transcriptional regulators of deg-enriched pathways. the transcriptional regulators of degs […]

PMCID: 3868055
PMID: 24062244
DOI: 10.2337/db13-1012

[…] table 3), including several of the proteins also validated by immunoblotting (compare with )., to further assess the strength of connectivity between the most abundant proteins, we used gene network enrichment analysis (,) to test for significant protein interactions based on yeast two-hybrid systems data. we identified the 14–3-3 protein ζ, encoded by ywhaz, interacting with krt18 […]

PMCID: 3278831
PMID: 22372958
DOI: 10.1186/1471-2105-12-S13-S15

[…] these contributions help us avoid some of the potential caveats present within microarray experiments., we are certainly not the first to integrate gene-expression data with gene-gene relationships. gnea [] is one such example. gnea uses a global protein-protein interaction network, finds subnetworks that correspond to regions of significantly differentially expressed genes; these subnetworks […]


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GNEA institution(s)
Department of Biomedical Engineering, Boston University, Boston, MA, USA; Department of Cardiology, Children’s Hospital, Boston, MA, USA; Children’s Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology, Boston, MA, USA; Harvard-Partners Center for Genetics and Genomics, Boston, MA, USA; Center of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Center for Advanced Genomic Technology, Boston University, Boston, MA, USA
GNEA funding source(s)
This work was supported by National Science Foundation grant number ITR-048715 and National Human Genome Research Institute grant number R01 HG003367-01A1, the National Institute of General Medical Sciences grant number K25-GM67825, the National Institute of Diabetes and Digestive and Kidney Diseases DGAP grant number TO1DK60837-01A1, and by the National Institutes of Health National Center for Biomedical Computing grant number 5U54LM008748–02.

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