GeneSetDB statistics

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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 in publications

 (10)
PMCID: 5828545
PMID: 29331675
DOI: 10.1016/j.ebiom.2017.11.028

[…] 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 […]

PMCID: 5747338
PMID: 29333246
DOI: 10.5256/f1000research.13583.r27972

[…] 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 […]

PMCID: 5431468
PMID: 28484276
DOI: 10.1038/s41598-017-01800-6

[…] 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) […]

PMCID: 5943682
PMID: 28364521
DOI: 10.1093/molehr/gax004

[…] 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 […]

PMCID: 5408797
PMID: 27694195
DOI: 10.1093/bioinformatics/btw623

[…] 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 […]


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GeneSetDB institution(s)
Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand

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