GNEA

[…] (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) […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]