GOSemSim statistics

info info

Citations per year

info

Popular tool citations

chevron_left GO semantic similarity analysis chevron_right
info

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?

Protocols

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

Versioning


No version available

Documentation


Maintainer


  • person_outline Guangchuang Yu

Publication for GOSemSim

GOSemSim citations

 (69)
library_books

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

2018
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 […]

library_books

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

2018
PeerJ
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 […]

library_books

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

2017
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 […]

library_books

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

2017
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 […]

library_books

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

2017
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 […]

library_books

Optimizing prognosis related key miRNA target interactions responsible for cancer metastasis

2017
Oncotarget
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 […]


Want to access the full list of citations?
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)

GOSemSim reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GOSemSim