GeneSetDB

[…] ratio between edges inside/outside the subnetwork larger than ½., to assign biological meaning to these subnetworks of modules, we perform gene set enrichment analysis based on the databases genesetdb () and msigdb (). for the latter, we restrict the enrichment to hallmark (h), curated (c2), go (c5), oncogenic (c6) and immunologic signatures (c7) gene sets, which include the gene sets […]

[…] of an appropriate linear model for differential expression analysis, egsea builds gene signature specific indexes that link a wide range of mouse or human gene set collections obtained from msigdb, genesetdb and kegg to the gene expression data being investigated. egsea is then configured and the ensemble enrichment analysis run, returning an object that can be queried using several s4 methods […]

[…] used for pathway analyses. pathway analyses were performed using panther (www.pantherdb.org). a customized list of genes involved in differentiation of different cell lineages was downloaded from genesetdb (http://genesetdb.auckland.ac.nz/haeremai.html) (supplementary table ). the genesettest function from the “limma” package (https://bioconductor.org/packages/release/bioc/html/limma.html) […]

[…] was filtered further to include only ensembl genes with an hgnc gene symbol in the biomart database. relationships between significantly differentially expressed rnas were further explored using genesetdb () using all genes represented in the control and dazl immunoprecipitations as the universe., the r115g mutant dazl overexpression construct was generated by pcr of the r115g coding […]

[…] converted into entrez ids. kegg pathways () for mouse and human were downloaded using the gage package. to extend the capabilities of egsea, a third database of gene sets was downloaded from the genesetdb () http://genesetdb.auckland.ac.nz/sourcedb.html project. in total, more than 25 000 gene sets have been collated and stored as r objects within the egseadata package along with annotation […]