GNEA

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] , 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 […]

[…] 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 […]

[…] 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 […]