GOstats protocols

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GOstats specifications

Information


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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  • person_outline S. Falcon <>

Publication for GOstats

GOstats in pipelines

 (73)
2018
PMCID: 5796182
PMID: 29329273
DOI: 10.3390/ijms19010234

[…] than 4., functional enrichment analysis is a method of cross-integration between biology and mathematics, which is the best choice to solve the massive data of gene chip. in this study, we used the gostats and kegg.db toolkit in the r language to perform functional enrichment analysis on the significantly differentially expressed genes and select the go entry with a count value greater […]

2018
PMCID: 5796909
PMID: 29434599
DOI: 10.3389/fimmu.2018.00080

[…] the benjamini–hochberg method ()., differentially expressed genes were analyzed to assess enrichment for kegg, go bp, cc, and mf terms using the conditional hypergeometric test implemented in the gostats r package (function: hypergtest) (). annotated kegg pathway diagrams were drawn using the pathview r package (). enrichment of medical subject heading (mesh) terms was evaluated using […]

2018
PMCID: 5806438
PMID: 29422031
DOI: 10.1186/s12864-018-4499-y

[…] and differentially expressed genes were identified with r [] and edger []. descriptive plots were generated, and gene ontology (go) analysis and hierarchical clustering were performed, with r and gostats []. comparison with a publicly available microarray dataset [] was done using paralogue and probe identifier information available via ensembl’s biomart […]

2018
PMCID: 5811047
PMID: 29390040
DOI: 10.1371/journal.ppat.1006858

[…] and kegg metabolic pathways to genes in the list of differentially expressed genes (degs) resulting from comparisons of infected and uninfected mouse was assessed with functions from the r package gostats []. for the applied conditional hypergeometric test for overrepresentation of go terms in each of the three ontologies (molecular function, biological process and cellular component) […]

2018
PMCID: 5878008
PMID: 29440499
DOI: 10.1073/pnas.1718263115

[…] this package and the clusterseq package (). the go enrichment analysis on grafting-specific genes was done with a customized r script (https://github.com/alexga/graftingscripts) using the package gostats ()., we thank niko geldner, dolf weijers, paul tarr, yka helariutta, ruth stadler, li-jia qu, and the nottingham arabidopsis stock centre for providing seeds. funding for this work […]


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GOstats in publications

 (482)
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 […]

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 […]

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) […]

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 […]

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 […]


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

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