A-DaGO-Fun: An adaptable Gene Ontology semantic similarity-based functional analysis tool

Bioinformatics

Volumn 32, Issue 3, 2016, Pages 477-479

  Mazandu, Gaston K ^a,b,c   Chimusa, Emile R ^a   Mbiyavanga, Mamana ^a   Mulder, Nicola J ^a  

^a UNIVERSITY OF CAPE TOWN   (South Africa)

^b AFRICAN INSTITUTE FOR MATHEMATICAL SCIENCES   (South Africa)

^c Cape Coast Regional library Ghana Library Authority   (Ghana)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

BIOLOGY; FACTUAL DATABASE; GENE; GENE ONTOLOGY; GENETICS; HUMAN; MOLECULAR GENETICS; PROCEDURES; SEMANTICS; SOFTWARE;

COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; GENE ONTOLOGY; GENES; HUMANS; MOLECULAR SEQUENCE ANNOTATION; PROTEINS; SEMANTICS; SOFTWARE;

EID: 84962264480     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv590     Document Type: Article

References (14)

1. Caniza H, et al. (2014). GOssTo: a user-friendly stand-Alone and web tool for calculating semantic similarities on the gene ontology. Bioinformatics. 30, 2235-2236.
2. Du Z, et al. (2009). G-SESAME: web tools for GO-Term-based gene similarity analysis and knowledge discovery. Nucleic Acids Res. 37, D345-D349.
3. Fröhlich H, et al. (2007). GOSim-An R-package for computation of information theoretic GO similarities between terms and gene products. BMC Bioinformatics. 8, 166.
4. GO-Consortium. (2012). The gene ontology: enhancements for 2011. Nucleic Acids Res. 40, D559-D564.
5. Harispe S, et al. (2013). The Semantic Measures library and Toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies. Bioinformatics. 30, 740-742.
6. Huntley R.P, et al. (2014). The GOA database: gene ontology annotation updates for 2015. Nucleic Acids Res. 43, D1057-D1063.
7. Jeong J.C, and Chen X.W. (2014). A new semantic functional similarity over gene ontology. IEEE/ACM Trans. Comput. Biol. Bioinform. 12, 322-334.
8. Li B, et al. (2010). Effectively integrating information content and structural relationship to improve the go-based similarity measure between proteins. ArXiv e-prints, 1001.0958.
9. Mazandu G.K, and Mulder N.J. (2013). DaGO-Fun: tool for gene ontologybased functional analysis using term information content measures. BMC Bioinformatics. 14, 284.
10. Mazandu G.K, and Mulder N.J. (2013). Information content-based gene ontology semantic similarity approaches: toward a unified framework theory. BioMed Res. Int, 2013, Article ID 292063.
11. Mazandu G.K, and Mulder N.J. (2014). Information content-based gene ontology functional similarity measures: which one to use for a given biological data type? PLoS One. 9, e113859.
12. Wang J.Z, et al. (2007). A new method to measure the semantic similarity of GO terms. Bioinformatics. 23, 1274-1281.
13. Yu G, et al. (2010). GOSemSim: an R package for measuring semantic similarity among go terms and gene products. Bioinformatics. 26, 976-978.
14. Zhang P, et al. (2006). Gene functional similarity search tool (GFSST). BMC Bioinformatics. 7, 135.