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Number of citations per year for the bioinformatics software tool GNEA
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GNEA specifications

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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 citations

 (13)
library_books

Expression of a specific extracellular matrix signature is a favorable prognostic factor in acute myeloid leukemia

2017
PMCID: 5735295
PMID: 29270355
DOI: 10.1016/j.lrr.2017.12.001

[…] an-Meier (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) algorithm […]

library_books

Network Analysis Reveals Putative Genes Affecting Meat Quality in Angus Cattle

2017
Front Genet
PMCID: 5681485
PMID: 29163638
DOI: 10.3389/fgene.2017.00171

[…] s explaining a small portion of the variation in these complex traits, but they do not have large enough effects in order to reach significance. The danger of a false positive is overcome through the gene/network enrichment analysis where a true false positive gene would most likely be eliminated while genes with a real but small effect on the trait will be validate through their biological role i […]

library_books

Tracking disease progression by searching paths in a temporal network of biological processes

2017
PLoS One
PMCID: 5407620
PMID: 28448511
DOI: 10.1371/journal.pone.0176172

[…] ch 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 pertur […]

library_books

Network Pharmacology Studies on the Bioactive Compounds and Action Mechanisms of Natural Products for the Treatment of Diabetes Mellitus: A Review

2017
Front Pharmacol
PMCID: 5322182
PMID: 28280467
DOI: 10.3389/fphar.2017.00074

[…] , pancreatitis (), gout (), Alzheimer’s disease and DM and other metabolic disease (). For DM therapy, network pharmacology has been widely used in the mechanism studies.According to the study of , a gene network enrichment analysis (GNEA) was used to identify two sets of genes, IS-HD and NR-HD gene sets, which was associated with insulin signal and a network of nuclear receptors. They identified […]

library_books

Integrated computational approach to the analysis of RNA seq data reveals new transcriptional regulators of psoriasis

2016
PMCID: 5133374
PMID: 27811935
DOI: 10.1038/emm.2016.97

[…] To investigate the relationships between the DEGs, we performed gene network enrichment analysis using the MetaCore software. The top 10 signaling networks enriched with DEGs were mainly associated with different alterations in immune signaling present in the psor […]

library_books

Cellular and molecular determinants of all trans retinoic acid sensitivity in breast cancer: Luminal phenotype and RARα expression

2015
PMCID: 4520659
PMID: 25888236
DOI: 10.15252/emmm.201404670

[…] s and inactivates the retinoid (Thatcher et al, ; Topletz et al, ).To define the biochemical pathways regulated by ATRA and potentially involved in the anti-tumor action of the retinoid, we performed gene-network enrichment analysis of the microarray data, focusing on Luminal/ER+ tumors. Among the top 10 processes enriched (Supplementary Table ), the ER nuclear signal transduction pathway is of in […]


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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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