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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 citations

 (6)
library_books

Easy and efficient ensemble gene set testing with EGSEA

2017
F1000Res
PMCID: 5747338
PMID: 29333246
DOI: 10.5256/f1000research.13583.r27972

[…] 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 […]

library_books

Tumor protein 53 mutations are enriched in diffuse large B cell lymphoma with irregular CD19 marker expression

2017
Sci Rep
PMCID: 5431468
PMID: 28484276
DOI: 10.1038/s41598-017-01800-6

[…] 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 […]

call_split

RNA immunoprecipitation identifies novel targets of DAZL in human foetal ovary

2017
PMCID: 5943682
PMID: 28364521
DOI: 10.1093/molehr/gax004
call_split See protocol

[…] 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. […]

library_books

MelanomaDB: A Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease Associated Molecular Pathways

2013
PMCID: 3712543
PMID: 23875173
DOI: 10.3389/fonc.2013.00184

[…] 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 […]

library_books

Vasohibin 1 is identified as a master regulator of endothelial cell apoptosis using gene network analysis

2013
BMC Genomics
PMCID: 3570387
PMID: 23324451
DOI: 10.1186/1471-2164-14-23

[…] ), 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). […]

call_split

The Transcriptional Targets of Mutant FOXL2 in Granulosa Cell Tumours

2012
PLoS One
PMCID: 3460904
PMID: 23029457
DOI: 10.1371/journal.pone.0046270
call_split See protocol

[…] 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). […]

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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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