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Volumn 2012, Issue , 2012, Pages

A topology-based metric for measuring term similarity in the gene ontology

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EID: 84862297314     PISSN: 16878027     EISSN: 16878035     Source Type: Journal    
DOI: 10.1155/2012/975783     Document Type: Article
Times cited : (47)

References (68)
  • 1
    • 27644434408 scopus 로고    scopus 로고
    • Phydbac gene function predictor: A gene annotation tool based on genomic context analysis
    • Enault F., Suhre K., Claverie J. M., Phydbac gene function predictor: a gene annotation tool based on genomic context analysis BMC Bioinformatics 2005 6 247
    • (2005) BMC Bioinformatics , vol.6 , pp. 247
    • Enault, F.1    Suhre, K.2    Claverie, J.M.3
  • 2
    • 0037480738 scopus 로고    scopus 로고
    • Investigating semantic similarity measures across the gene ontology: The relationship between sequence and annotation
    • DOI 10.1093/bioinformatics/btg153
    • Lord P. W., Stevens R. D., Brass A., Goble C. A., Investigating semantic similarity measures across the gene ontology: the relationship between sequence and annotation Bioinformatics 2003 19 10 1275 1283 (Pubitemid 36850221)
    • (2003) Bioinformatics , vol.19 , Issue.10 , pp. 1275-1283
    • Lord, P.W.1    Stevens, R.D.2    Brass, A.3    Goble, C.A.4
  • 4
    • 27544472676 scopus 로고    scopus 로고
    • Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary
    • DOI 10.1093/bioinformatics/bti430
    • Mao X., Cai T., Olyarchuk J. G., Wei L., Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary Bioinformatics 2005 21 19 3787 3793 (Pubitemid 41535528)
    • (2005) Bioinformatics , vol.21 , Issue.19 , pp. 3787-3793
    • Mao, X.1    Cai, T.2    Olyarchuk, J.G.3    Wei, L.4
  • 5
    • 48449104617 scopus 로고    scopus 로고
    • GOEAST: A web-based software toolkit for gene ontology enrichment analysis
    • Zheng Q., Wang X. J., GOEAST: a web-based software toolkit for gene ontology enrichment analysis Nucleic acids research 2008 36 W358 363
    • (2008) Nucleic Acids Research , vol.36 , pp. 358-363
    • Zheng, Q.1    Wang, X.J.2
  • 6
    • 75849158230 scopus 로고    scopus 로고
    • The gene ontology in 2010: Extensions and refinements
    • GO-Consortium, The gene ontology in 2010: extensions and refinements Nucleic Acids Research 2009 38 1 D331 D335
    • (2009) Nucleic Acids Research , vol.38 , Issue.1
    • Go-Consortium1
  • 7
    • 33644875286 scopus 로고    scopus 로고
    • The gene ontology (GO) project in 2006
    • GO-Consortium, The gene ontology (GO) project in 2006 Nucleic Acids Research 2006 34 D322 D326
    • (2006) Nucleic Acids Research , vol.34
    • Go-Consortium1
  • 11
    • 2642524299 scopus 로고    scopus 로고
    • The Gene Ontology Annotation (GOA) database - An integrated resource of GO annotations to the UniProt knowledgebase
    • Camon E., Barrell D., Lee V., Dimmer E., Apweiler R., The gene ontology annotation (GOA) databasean integrated resource of GO annotations to the UniProt knowledgebase In Silico Biology 2004 4 1 5 6 (Pubitemid 38714506)
    • (2004) Silico Biology , vol.4 , Issue.1 , pp. 5-6
    • Camon, E.1    Barrell, D.2    Lee, V.3    Dimmer, E.4    Apweiler, R.5
  • 14
    • 67449096981 scopus 로고    scopus 로고
    • The gene ontologyproviding a functional role in proteomic studies
    • Dimmer E. C., Huntley R. P., Barrell D. G., The gene ontologyproviding a functional role in proteomic studies Proteomics 2008 8 supplement 23-24 2 11
    • (2008) Proteomics , vol.8 , Issue.SUPPL. 23-24 , pp. 2-11
    • Dimmer, E.C.1    Huntley, R.P.2    Barrell, D.G.3
  • 15
    • 27144560185 scopus 로고    scopus 로고
    • Are the current ontologies in biology good ontologies?
    • DOI 10.1038/nbt0905-1095, PII N09051095
    • Soldatova L. N., King R. D., Are the current ontologies in biology good ontologies? Nature Biotechnology 2005 23 9 1095 1098 (Pubitemid 41486390)
    • (2005) Nature Biotechnology , vol.23 , Issue.9 , pp. 1095-1098
    • Soldatova, L.N.1    King, R.D.2
  • 16
    • 15944381986 scopus 로고    scopus 로고
    • Beyond similarity-based methods to associate genes for the inference of function
    • PII S1478528203023183
    • Shon J., Park J. Y., Wei L., Beyond similarity-based methods to associate genes for the inference of function Drug Discovery Today 2003 1 3 89 96 (Pubitemid 40430705)
    • (2003) Drug Discovery Today: BIOSILICO , vol.1 , Issue.3 , pp. 89-96
    • Shon, J.1    Park, J.Y.2    Wei, L.3
  • 27
    • 77951942707 scopus 로고    scopus 로고
    • GOSemSim: An R package for measuring semantic similarity among GO terms and gene products
    • Yu G., Li F., Qin Y., Bo X., Wu Y., Wang S., GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics 2010 26 7 976 978
    • (2010) Bioinformatics , vol.26 , Issue.7 , pp. 976-978
    • Yu, G.1    Li, F.2    Qin, Y.3    Bo, X.4    Wu, Y.5    Wang, S.6
  • 28
    • 34447294237 scopus 로고    scopus 로고
    • A new method to measure the semantic similarity of GO terms
    • DOI 10.1093/bioinformatics/btm087
    • Wang J. Z., Du Z., Payattakool R., Yu P. S., Chen C. F., A new method to measure the semantic similarity of GO terms Bioinformatics 2007 23 10 1274 1281 (Pubitemid 47050544)
    • (2007) Bioinformatics , vol.23 , Issue.10 , pp. 1274-1281
    • Wang, J.Z.1    Du, Z.2    Payattakool, R.3    Yu, P.S.4    Chen, C.-F.5
  • 29
    • 0002016474 scopus 로고    scopus 로고
    • Semantic Similarity in a Taxonomy: An Information-Based Measure and its Application to Problems of Ambiguity in Natural Language
    • Resnik P., Semantic similarity in a taxonomy: an information-based measure and its application to problems of ambiguity in natural language Journal of Artificial Intelligence Research 1999 11 95 130 (Pubitemid 129628761)
    • (1999) Journal of Artificial Intelligence Research , vol.11 , pp. 95-130
    • Resnik, P.1
  • 33
    • 84860362791 scopus 로고    scopus 로고
    • Using the underlying biological organization of the MTB functional network for protein function prediction
    • Mazandu G. K., Mulder N. J., Using the underlying biological organization of the MTB functional network for protein function prediction Infection, Genetics and Evolution 2011 12 5 922 932
    • (2011) Infection, Genetics and Evolution , vol.12 , Issue.5 , pp. 922-932
    • Mazandu, G.K.1    Mulder, N.J.2
  • 35
    • 20444365683 scopus 로고    scopus 로고
    • GOToolBox: Functional analysis of gene datasets based on gene ontology
    • Martin D., Brun C., Remy E., Mouren P., Thieffry D., Jacq B., GOToolBox: functional analysis of gene datasets based on gene ontology Genome Biology 2004 5 12 R101
    • (2004) Genome Biology , vol.5 , Issue.12 , pp. 101
    • Martin, D.1    Brun, C.2    Remy, E.3    Mouren, P.4    Thieffry, D.5    Jacq, B.6
  • 37
    • 84891725921 scopus 로고    scopus 로고
    • A shortest-path graph kernel for estimating gene product semantic similarity
    • Alvarez M., Qi X., Yan C., A shortest-path graph kernel for estimating gene product semantic similarity Journal of Biomedical Semantics 2011 2 3 1 9
    • (2011) Journal of Biomedical Semantics , vol.2 , Issue.3 , pp. 1-9
    • Alvarez, M.1    Qi, X.2    Yan, C.3
  • 39
    • 58149411184 scopus 로고
    • Features of similarity
    • Tversky A., Features of similarity Psychological Review 1977 84 4 327 352
    • (1977) Psychological Review , vol.84 , Issue.4 , pp. 327-352
    • Tversky, A.1
  • 40
    • 78149449890 scopus 로고    scopus 로고
    • An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology
    • Jain S., Bader G. D., An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology BMC Bioinformatics 2010 11 562
    • (2010) BMC Bioinformatics , vol.11 , pp. 562
    • Jain, S.1    Bader, G.D.2
  • 42
    • 0036088133 scopus 로고    scopus 로고
    • DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions
    • Xenarios I., Salwnski L., Duan X. J., DIP, the database of interacting proteins: a research tool for studying cellular networks of protein interactions Nucleic Acids Research 2002 30 1 303 305 (Pubitemid 34679570)
    • (2002) Nucleic Acids Research , vol.30 , Issue.1 , pp. 303-305
    • Xenarios, I.1    Salwinski, L.2    Duan, X.J.3    Higney, P.4    Kim, S.-M.5    Eisenberg, D.6
  • 45
    • 75549083295 scopus 로고    scopus 로고
    • Mint, the molecular interaction database: 2009 update
    • Ceol A., Aryamontri C. A., Licata L., Mint, the molecular interaction database: 2009 update Nucleic Acids Research 2010 38 supplement 1 D532 D539
    • (2010) Nucleic Acids Research , vol.38 , Issue.SUPPL. 1
    • Ceol, A.1    Aryamontri, C.A.2    Licata, L.3
  • 47
    • 84855569114 scopus 로고    scopus 로고
    • Generation and analysis of large-scale data-driven mycobacterium tuberculosis functional networks for drug target identification
    • Mazandu G. K., Mulder N. J., Generation and analysis of large-scale data-driven mycobacterium tuberculosis functional networks for drug target identification Advances in Bioinformatics 2011 2011 14
    • (2011) Advances in Bioinformatics , vol.2011 , pp. 14
    • Mazandu, G.K.1    Mulder, N.J.2
  • 48
    • 33845864703 scopus 로고    scopus 로고
    • Computational prediction of cancer-gene function
    • DOI 10.1038/nrc2036, PII NRC2036
    • Hu P., Bader G., Wigle D. A., Emili A., Computational prediction of cancer-gene function Nature Reviews Cancer 2007 7 1 23 34 (Pubitemid 46023413)
    • (2007) Nature Reviews Cancer , vol.7 , Issue.1 , pp. 23-34
    • Hu, P.1    Bader, G.2    Wigle, D.A.3    Emili, A.4
  • 49
    • 2942541277 scopus 로고    scopus 로고
    • Predicting co-complexed protein pairs using genomic and proteomic data integration
    • Zhang L. V., Wong S. L., King O. D., Roth F. P., Predicting co-complexed protein pairs using genomic and proteomic data integration BMC Bioinformatics 2004 5 38
    • (2004) BMC Bioinformatics , vol.5 , pp. 38
    • Zhang, L.V.1    Wong, S.L.2    King, O.D.3    Roth, F.P.4
  • 50
    • 33947328242 scopus 로고    scopus 로고
    • Choosing negative examples for the prediction of protein-protein interactions
    • Ben-Hur A., Noble W. S., Choosing negative examples for the prediction of protein-protein interactions BMC Bioinformatics 2006 7 supplement 1 S2
    • (2006) BMC Bioinformatics , vol.7 , Issue.SUPPL. 1 , pp. 2
    • Ben-Hur, A.1    Noble, W.S.2
  • 51
    • 27544491192 scopus 로고    scopus 로고
    • ROCR: Visualizing classifier performance in R
    • DOI 10.1093/bioinformatics/bti623
    • Sing T., Sander O., Beerenwinkel N., Lengauer T., ROCR: visualizing classifier performance in R Bioinformatics 2005 21 20 3940 3941 (Pubitemid 41535515)
    • (2005) Bioinformatics , vol.21 , Issue.20 , pp. 3940-3941
    • Sing, T.1    Sander, O.2    Beerenwinkel, N.3    Lengauer, T.4
  • 52
    • 84862298784 scopus 로고    scopus 로고
    • Semantic similarity analysis of protein data: Assessment with biological features and issues
    • Advance Access
    • Guzzi P. H., Mina M., Guerra C., Cannataro M., Semantic similarity analysis of protein data: assessment with biological features and issues Briefings in Bioinformatics 2012 Advance Access 17
    • (2012) Briefings in Bioinformatics , pp. 17
    • Guzzi, P.H.1    Mina, M.2    Guerra, C.3    Cannataro, M.4
  • 53
    • 79951480123 scopus 로고    scopus 로고
    • R Development Core Team, R Vienna, Austria R Foundation for Statistical Computing
    • R Development Core Team, R: A Language and Environment for Statistical Computing 2010 Vienna, Austria R Foundation for Statistical Computing
    • (2010) R: A Language and Environment for Statistical Computing
  • 54
    • 79961135005 scopus 로고    scopus 로고
    • R Development Core Team, R Vienna, Austria R Foundation for Statistical Computing
    • R Development Core Team, R: A Language and Environment for Statistical Computing 2011 Vienna, Austria R Foundation for Statistical Computing
    • (2011) R: A Language and Environment for Statistical Computing
  • 55
    • 49949096013 scopus 로고    scopus 로고
    • Gene ontology term overlap as a measure of gene functional similarity
    • Mistry M., Pavlidis P., Gene ontology term overlap as a measure of gene functional similarity BMC Bioinformatics 2008 9 327
    • (2008) BMC Bioinformatics , vol.9 , pp. 327
    • Mistry, M.1    Pavlidis, P.2
  • 57
    • 84872756107 scopus 로고    scopus 로고
    • CESSM: Collaborative Evaluation of Semantic Similarity Measures. JB2009: Challenges in Bioinformatics: 15, 2009
    • Pesquita C., Pessoa D., Faria D., Couto F.,. CESSM: Collaborative Evaluation of Semantic Similarity Measures. JB2009: Challenges in Bioinformatics: 15, 2009
    • Pesquita, C.1    Pessoa, D.2    Faria, D.3    Couto, F.4
  • 59
    • 75849153303 scopus 로고    scopus 로고
    • The universal protein resource (UniProt) in 2010
    • UniProt-Consortium, The universal protein resource (UniProt) in 2010 Nucleic Acids Research 2009 38 1 D142 D148
    • (2009) Nucleic Acids Research , vol.38 , Issue.1
    • Uniprot-Consortium1
  • 64
  • 65
    • 0025878149 scopus 로고
    • Amino acid substitution matrices from an information theoretic perspective
    • Altschul S. F., Amino acid substitution matrices from an information theoretic perspective Journal of Molecular Biology 1991 219 3 555 565
    • (1991) Journal of Molecular Biology , vol.219 , Issue.3 , pp. 555-565
    • Altschul, S.F.1
  • 66
    • 79955412523 scopus 로고    scopus 로고
    • Scoring protein relationships in functional interaction networks predicted from sequence data
    • Mazandu G. K., Mulder N. J., Scoring protein relationships in functional interaction networks predicted from sequence data PLoS ONE 2011 6 4
    • (2011) PLoS ONE , vol.6 , Issue.4
    • Mazandu, G.K.1    Mulder, N.J.2
  • 68
    • 78049250483 scopus 로고    scopus 로고
    • More than 1,001 problems with protein domain databases: Transmembrane regions, signal peptides and the issue of sequence homology
    • Wong W. C., Maurer-Stroh S., Eisenhaber F., More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology PLoS Computational Biology 2010 6 7 e1000867
    • (2010) PLoS Computational Biology , vol.6 , Issue.7 , pp. 1000867
    • Wong, W.C.1    Maurer-Stroh, S.2    Eisenhaber, F.3


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