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GeneSetDB specifications

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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

 (10)
library_books

Module Analysis Captures Pancancer Genetically and Epigenetically Deregulated Cancer Driver Genes for Smoking and Antiviral Response

2017
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 […]

library_books

Easy and efficient ensemble gene set testing with EGSEA

2017
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 […]

library_books

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

2017
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) […]

library_books

RNA immunoprecipitation identifies novel targets of DAZL in human foetal ovary

2017
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 […]

library_books

Combining multiple tools outperforms individual methods in gene set enrichment analyses

2016
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 […]

library_books

Novel structural co expression analysis linking the NPM1 associated ribosomal biogenesis network to chronic myelogenous leukemia

2015
PMCID: 4513283
PMID: 26205693
DOI: 10.1038/srep10973

[…] 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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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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