GeneSetDB

[…] enrichment (GSE) analysis methods released through the Bioconductor project together with a steady increase in the number of gene set collections available through online databases such as MSigDB , GeneSetDB and KEGG . In an effort to unify these computational methods and knowledge-bases, the EGSEA R/Bioconductor package was developed. EGSEA, which stands for Ensemble of Gene Set Enrichment Ana […]

[…] ere 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 […]

[…] This 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. […]

[…] ified. Then, the molecular pathways these genes correspond to, along with any statistically significant pathway enrichment within the list of variant genes and targeting drugs, are retrieved from the GeneSetDB pathway analysis web tool (). A diagram showing tumor variant genes in the context of molecular pathways is generated using the KEGG, Reactome, and Biocarta pathways included in the R graphi […]

[…] ), and unless otherwise stated, multiple testing corrections were applied using the Benjamini and Hochberg method. Gene ontology/pathway enrichment analyses were carried out using Fatigo software [], GeneSetDB [], GATHER (http://gather.genome.duke.edu/) and IPA (Ingenuity systems, http://www.ingenuity.com). […]

[…] gulated genes for further functional analysis. Relationships between differentially regulated genes were explored further using the tools GATHER (Gene Annotation Tool to Help Explain Relationships) , GeneSetDB (http://genesetdb.auckland.ac.nz/haeremai.html, NZ) and Ingenuity Pathway Analysis software (http://www.ingenuity.com, Redwood, CA). […]