GOSemSim protocols

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GOSemSim specifications

Information


Unique identifier OMICS_10329
Name GOSemSim
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 2.6.2
Stability Stable
Requirements
AnnotationDbi, methods, utils, testthat, knitr, BiocInstaller, GO.db, org.Hs.eg.db, AnnotationHub, clusterProfiler, R(>=3.3.2), prettydoc, DOSE
Maintained Yes

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Maintainer


  • person_outline Guangchuang Yu <>

Publication for GOSemSim

GOSemSim in pipelines

 (2)
2018
PMCID: 5905132
PMID: 29665773
DOI: 10.1186/s12864-018-4649-2

[…] of them were significantly overlapped with the three co-expression modules identified by applying wgcna to the 20 cell-pooling samples (fig. ). gene ontology (go) enrichment analysis by topgo [] and gosemsim [] indicated that genes encoding for membrane proteins which participate in cell communication, signaling and oxidation-reduction processes for energy generation were strongly enriched […]

2016
PMCID: 5090062
PMID: 27805906
DOI: 10.1098/rsob.160224

[…] enrichment analysis. redundant go terms were removed, using revigo software []. the semantic similarity of the enriched go terms (p-value ≤ 0.05) of groups of mirnas targets was evaluated with the gosemsim package (1.28.1) []. to estimate the p-value of the given similarity score, we calculated the semantic similarity of randomly sampled set pairs of go terms of the same size; the p-value […]


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GOSemSim in publications

 (69)
PMCID: 5905132
PMID: 29665773
DOI: 10.1186/s12864-018-4649-2

[…] algorithm [] implemented in topgo [], with all genes encoding for proteins involved in the ppi network as background. pairwise functional similarities of discriminating modules were calculated using gosemsim [], by averaging similarities of the three go categories: cellular component (cc), biological process (bp), and molecular function (mf). hierarchical clustering with complete linkage […]

PMCID: 5807978
PMID: 29441236
DOI: 10.7717/peerj.4345

[…] assemblies, which can lead to false positive categories. we clustered significant go-categories for each cluster using semantic similarity between categories in the zebrafish genome according to the gosemsim-package in r () as a distance measurement. the distance matrix for go-categories was supplied to the hclust function in r and a cutoff of 0.8 was used to categories the go-categories […]

PMCID: 5725448
PMID: 29229958
DOI: 10.1038/s41467-017-02185-w

[…] uniprot_ids of the proteins identified in the mass spectrometry experiments. the enrichment results were filtered to reduce the number of redundant go classes, by using the “clusterprofiler” and “gosemsim” packages in r [,]. all code used to analyze the data and generate the plots is available at: https://github.com/squatrim/oldrini2017., ranbp6 crispr constructs were generated with guided […]

PMCID: 5721728
PMID: 29226242
DOI: 10.1126/sciadv.1701211

[…] μct, μbu_tx, and taμbu_tx cells, enrichment analysis was performed by gsea preranked on go biological processes (). significant enrichments were clustered on the basis of semantic similarities with gosemsim ()., all statistical tests were two-sided. for comparisons other than rna-seq results, student’s t test was used for two-group comparisons. for comparisons with more than two groups, one-way […]

PMCID: 5707401
PMID: 29185492
DOI: 10.1038/s41598-017-16695-6

[…] the interactions between rbuls and putative protein partners as biologically meaningful if the gene ontology (go) similarity between the putative interactors was high. we used the r package gosemsim to compute go similarities between rbuls and their interaction partners based on the wang’s index (wi) comparing their biological process (bp) go terms (state june 2017). wi was developed […]


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GOSemSim institution(s)
Beijing Institute of Radiation Medicine, Beijing, China; Department of Biochemistry and Molecular Biology, Anhui Medical University, Hefei, China
GOSemSim funding source(s)
National Key Technologies R&D Program for New Drugs (2009ZX09301-002); National Nature Science Foundation of China (30530650); National Science Fund for Distinguished Young Scholars (30625041)

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