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GOSemSim specifications


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
AnnotationDbi, methods, utils, testthat, knitr, BiocInstaller, GO.db, org.Hs.eg.db, AnnotationHub, clusterProfiler, R(>=3.3.2), prettydoc, DOSE
Maintained Yes


No version available



  • person_outline Guangchuang Yu

Publication for GOSemSim

GOSemSim citations


Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation

BMC Genomics
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 […]


Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs

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 […]


EGFR feedback inhibition by Ran binding protein 6 is disrupted in cancer

Nat Commun
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 […]


Intracerebroventricular delivery of hematopoietic progenitors results in rapid and robust engraftment of microglia like cells

Sci Adv
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 […]


Interaction profiling of RNA binding ubiquitin ligases reveals a link between posttranscriptional regulation and the ubiquitin system

Sci Rep
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 […]


Optimizing prognosis related key miRNA target interactions responsible for cancer metastasis

PMCID: 5752539
PMID: 29312626
DOI: 10.18632/oncotarget.22724

[…] interaction network (ppi) is obtained from hprd. human kegg pathways from synapse (syn1741407) which shows the semantic similarity score >0.3 with a hallmark-associated go term using r package ‘gosemsim’, are considered to be associated with hallmarks of cancer. for each hallmark-associated kegg pathway, random-walk analysis of the protein interaction network with a restart probability […]

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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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