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GOstats specifications

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Unique identifier OMICS_14555
Name GOstats
Alternative name GO stats
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A gene universe and a list of selected genes from that universe
Output data p-value, odds ratio, expected gene count, and actual gene count for each term tested along with the vector of gene identifiers annotated at each term.
Output format HTML
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.46.0
Stability Stable
Requirements
methods, stats, RColorBrewer, BiocGenerics, stats4, R(>=2.10), RUnit, genefilter, multtest, org.Hs.eg.db, SparseM, xtable, graph, RBGL, Rgraphviz, geneplotter, ALL, GSEABase, Biobase(>=1.15.29), Category(>=2.43.2), AnnotationDbi(>=0.0.89), GO.db(>=1.13.0), annotate(>=1.13.2), AnnotationForge, hgu95av2.db(>=1.13.0)
Maintained Yes

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Maintainer


  • person_outline S. Falcon <>

Publication for GOstats

GOstats citations

 (506)
library_books

B cell activation and plasma cell differentiation are inhibited by de novo DNA methylation

2018
PMCID: 5953949
PMID: 29765016
DOI: 10.1038/s41467-018-04234-4

[…] only genes expressed at more than 1 fpkm in at least two samples were considered for differential analysis. gene ontology of differentially expressed genes was performed using the r/bioconductor gostats package (v.2.36.0) and considered dependencies and similarities in calculating go term p values, which were subsequently fdr corrected. gene set enrichment analysis (gsea) used the pre-ranked […]

library_books

Comparative analysis of distinctive transcriptome profiles with biochemical evidence in bisphenol S and benzo[a]pyrene exposed liver tissues of the olive flounder Paralichthys olivaceus

2018
PMCID: 5929548
PMID: 29715276
DOI: 10.1371/journal.pone.0196425

[…] analysis was employed in order to construct a heat map using mev v.7.4 (dana-farber cancer institute, boston, ma, usa) software. gene ontology (go) analysis of the contigs was performed using the gostats program (http://www.bioconductor.org/packages/3.3/bioc/html/gostats) and fisher’s exact test (p < 0.05), as implemented in the sequence annotation tool blast2go []., all the raw data […]

library_books

Long non coding RNAs involved in the regulatory network during porcine pre implantation embryonic development and iPSC induction

2018
PMCID: 5923264
PMID: 29703926
DOI: 10.1038/s41598-018-24863-5

[…] was greater than 1. the gene ontology (go) functional and kegg pathway enrichment analyses of differential expression genes and wgcna module genes were performed in r/bioconductor using the package: gostats, gsea to compute the statistics and goplot to visualize the function analysis. all the statistical significance described above was p-value., the porcine embryonic fibroblasts (pefs) […]

library_books

Detecting phenotype driven transitions in regulatory network structure

2018
PMCID: 5908977
PMID: 29707235
DOI: 10.1038/s41540-018-0052-5

[…] across all the modules. we also repeated each analysis using the top 100 core genes in order to test the dependence of the enrichment on the cutoff. go term enrichment was calculated using the gostats package in r, with the following parameters: the gene universe is defined to be the set of all possible target genes in the initial networks, and the p-value calculation is conditioned […]

library_books

p52 expression enhances lung cancer progression

2018
PMCID: 5904214
PMID: 29666445
DOI: 10.1038/s41598-018-24488-8

[…] affymetrix gene expression and transcriptome analysis consoles., functions enriched within p52-regulated genes were identified through a hypergeometric test with respect to go terms, using r package gostats (v1.7.4). for each go term, genes from the reference set of whole human genome protein-coding genes and the concerned set of p52-regulated genes were respectively identified, and a p-value […]

library_books

Dynamic transcriptomic analysis of Ischemic Injury in a Porcine Pre Clinical Model mimicking Donors Deceased after Circulatory Death

2018
PMCID: 5899088
PMID: 29654283
DOI: 10.1038/s41598-018-24282-6

[…] and ward linkage from the list of differentially expressed genes between ischemia and control., the detection of significantly overrepresented gene ontology categories was performed using the gostats package in bioconductor. the list of differentially expressed genes was divided in two parts: up-regulated and down-regulated genes. for each sublist, we performed a hypergeometrical […]


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GOstats institution(s)
Fred Hutchison Cancer Research Center, Program Computational Biology, Seattle, WA, USA

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