GSEABase protocols

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GSEABase specifications

Information


Unique identifier OMICS_29378
Name GSEABase
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.42.0
Stability Stable
Requirements
AnnotationDbi, methods, testthat, R(>=2.6.0), GO.db, org.Hs.eg.db, Rgraphviz, hgu95av2.db, Biobase(>=2.17.8), XML, BiocGenerics(>=0.13.8), ReportingTools, annotate(>=1.45.3), graph(>=1.37.2)
Maintained Yes

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Additional information


https://bioconductor.org/packages/release/bioc/vignettes/GSEABase/inst/doc/GSEABase.pdf

GSEABase in pipelines

 (6)
2017
PMCID: 5217192
PMID: 28057021
DOI: 10.1186/s13041-016-0282-7

[…] to investigate the ontology of differentially expressed genes, enriched expression of go terms were assessed and confirmed with the hypergeometric test [], using the bioconductor package gostats/gseabase. these programs determine which go terms identified from lists of affected genes are statistically over— or under-represented, compared to the go terms represented in the microarray […]

2017
PMCID: 5646955
PMID: 28731140
DOI: 10.3892/mmr.2017.7058

[…] sites and differentially methylated regions were identified. gene ontology (go) and kyoto encyclopedia of genes and genomes (kegg) pathway enrichment analyses were performed via go stats and gseabase packages respectively. finally, the pathview package was used to construct the network of enriched pathways. a total of 198 degs (106 up- and 92 downregulated) were obtained. a total of 602 […]

2016
PMCID: 5114730
PMID: 27855694
DOI: 10.1186/s13045-016-0350-6

[…] under number gse85193., gene ontology enrichment analysis was carried out by the bioconductor package “topgo,” and kegg pathway enrichment analysis was conducted by the bioconductor package “gseabase” (http://www.r-project.org/; http://www.bioconductor.org/packages/release/bioc/html/gseabase.html). terms were accepted if they were hit more than one gene, and fisher’s exact test p value […]

2015
PMCID: 4600298
PMID: 26453029
DOI: 10.1186/s12866-015-0532-3

[…] enrichment analyses for sets of proteins using hypergeometric tests and the benjamini and hochberg false discovery rate multiple testing correction (p-value < 0.05) implemented in the r packages gseabase and gostats. go term categories containing singleton entries were excluded. go categories and enrichment datasets were visualized using the r package ggplot2 []. for time-point analyses, go […]

2015
PMCID: 4665839
PMID: 26788155
DOI: 10.3892/ol.2015.3751

[…] miranda v5 () (http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5) and targetscan 5.1 () (http://www.targetscan.org)., go analysis was performed with gseabase package from r statistical platform (http://www.r-project.org/). genes were categorized based on biological process (bp), molecular function (mf) and cellular component (cc). genmapp v2.1 […]


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GSEABase in publications

 (35)
PMCID: 5861998
PMID: 29478923
DOI: 10.1016/j.devcel.2018.01.022

[…] venn diagrams (c) for elevated and reduced transcript levels using limma v3.30.13 (). the five largest venn fields were analyzed for enriched biological processes (bp) using gostats v2.40.0 () and gseabase (). gene-specific bp term associations were previously generated using blast2go (, , ). parental, regulatory and component relationships between enriched bp were visualized as ‘perturbation […]

PMCID: 5836829
PMID: 29504896
DOI: 10.1186/s12864-018-4471-x

[…] pathways database was used to find pathways in which the differentially expressed genes are involved []. the gsea (gene set enrichment analysis) analysis was performed using the software package r gseabase of bioconductor []., in this study, we reproduced the lifespan extending effect of fucoxanthin in drosophila, which was published earlier []. treatment with 1 μm of fucoxanthin led […]

PMCID: 5765654
PMID: 29325559
DOI: 10.1186/s12915-017-0457-4

[…] a false discovery rate cut-off set to 0.05. we retained only go term enrichment results if at least five genes in the genome matched the go term. all analyses were performed using the r packages gseabase and gostats []., all complete genome assemblies and corresponding genome annotations were uploaded to the european nucleotide archive under accession numbers prjeb15648, prjeb20900, […]

PMCID: 5753922
PMID: 29317802
DOI: 10.1177/1177932217747256

[…] pathogen-host coexpression experiments to predict more phi for specific domains. our r script does not seek to compete with other approaches, such as gsea, or other r packages, such as limma or gseabase,; rather, we wrote an r script code to identify plausible pathogen genes involved in pathogenesis, particularly those with high expression variability. furthermore, using their functional […]

PMCID: 5687707
PMID: 29140992
DOI: 10.1371/journal.pone.0187735

[…] annotation analysis of all clusters was performed using a hyper geometric gene set enrichment test in r. the bioconductor packages biomart [], org.ss.eg.db: genome wide annotation for pig [], gseabase [], and gostats [] were used for the pathway enrichment and gene ontology (go) analyses. in this process, overrepresented gene sets were defined by the kyoto encyclopedia of genes […]


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