GeneSetDB statistics
GeneSetDB specifications
Information
| Unique identifier | OMICS_03953 |
|---|---|
| Name | GeneSetDB |
| Interface | Web user interface |
| Restrictions to use | None |
| Computer skills | Basic |
| Stability | Stable |
| Maintained | Yes |
Publication for GeneSetDB
GeneSetDB: A comprehensive meta-database, statistical and visualisation framework for gene set analysis.
GeneSetDB citations
(10)Module Analysis Captures Pancancer Genetically and Epigenetically Deregulated Cancer Driver Genes for Smoking and Antiviral Response
[…] 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 […]
Easy and efficient ensemble gene set testing with EGSEA
[…] 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 […]
Tumor protein 53 mutations are enriched in diffuse large B cell lymphoma with irregular CD19 marker expression
[…] 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) […]
RNA immunoprecipitation identifies novel targets of DAZL in human foetal ovary
[…] 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 […]
Combining multiple tools outperforms individual methods in gene set enrichment analyses
[…] 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 […]
Novel structural co expression analysis linking the NPM1 associated ribosomal biogenesis network to chronic myelogenous leukemia
[…] protein synthesis and cell growth in cml., in addition to the ribosome, the normal- and cml-specific npm1-doublets were in fact associated with a total of 20, 25 and 2 functional annotations of the genesetdb (go), reactome pathway database, and msigdb (kegg), respectively (fisher’s exact test, bonferroni adjusted p < 0.05) (). their association with cml would also be worth exploring […]
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