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Volumn 14, Issue 1, 2013, Pages

DaGO-Fun: Tool for Gene Ontology-based functional analysis using term information content measures

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL ANALYSIS; BIOLOGICAL APPLICATIONS; GENE ONTOLOGY ANNOTATIONS; INFORMATION CONTENT MEASURES; INFORMATION CONTENTS; SCIENTIFIC COMMUNITY; SEMANTIC SIMILARITY; SEMANTIC SIMILARITY MEASURES;

EID: 84884505519     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-284     Document Type: Article
Times cited : (31)

References (44)
  • 1
    • 0037480738 scopus 로고    scopus 로고
    • Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation
    • 10.1093/bioinformatics/btg153, 12835272
    • Lord PW, Stevens PW, Brass A, Goble CA. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 2003, 19(10):1275-1283. 10.1093/bioinformatics/btg153, 12835272.
    • (2003) Bioinformatics , vol.19 , Issue.10 , pp. 1275-1283
    • Lord, P.W.1    Stevens, P.W.2    Brass, A.3    Goble, C.A.4
  • 3
    • 33645468925 scopus 로고    scopus 로고
    • Gene functional similarity search tool (GFSST)
    • 10.1186/1471-2105-7-135, 1421445, 16536867
    • Zhang P, Jinghui Z, Huitao S, Russo J, Osborne B, Buetow K. Gene functional similarity search tool (GFSST). BMC Bioinformatics 2006, 7:135. 10.1186/1471-2105-7-135, 1421445, 16536867.
    • (2006) BMC Bioinformatics , vol.7 , pp. 135
    • Zhang, P.1    Jinghui, Z.2    Huitao, S.3    Russo, J.4    Osborne, B.5    Buetow, K.6
  • 4
    • 33748335463 scopus 로고    scopus 로고
    • A new measure for functional similarity of gene products based on Gene Ontology
    • 10.1186/1471-2105-7-302, 1559652, 16776819
    • Schlicker A, Domingues FS, Rahnenfuhrer J, Lengauer T. A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics 2006, 7:302. 10.1186/1471-2105-7-302, 1559652, 16776819.
    • (2006) BMC Bioinformatics , vol.7 , pp. 302
    • Schlicker, A.1    Domingues, F.S.2    Rahnenfuhrer, J.3    Lengauer, T.4
  • 5
    • 34447294237 scopus 로고    scopus 로고
    • A new method to measure the semantic similarity of GO terms
    • 10.1093/bioinformatics/btm087, 17344234
    • Wang JZ, Du Z, Payattakool R, Yu PS, Chen CF. A new method to measure the semantic similarity of GO terms. Bioinformatics 2007, 23(10):1274-1281. 10.1093/bioinformatics/btm087, 17344234.
    • (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
  • 6
    • 33847103869 scopus 로고    scopus 로고
    • Measuring semantic similarity between gene ontology terms
    • Couto F, Silva M, Coutinho P. Measuring semantic similarity between gene ontology terms. Data Knowl Eng 2007, 61(1):137-152.
    • (2007) Data Knowl Eng , vol.61 , Issue.1 , pp. 137-152
    • Couto, F.1    Silva, M.2    Coutinho, P.3
  • 8
    • 47149083877 scopus 로고    scopus 로고
    • Metrics for GO based protein semantic similarity: a systematic evaluation
    • 10.1186/1471-2105-9-S5-S4, 2638144, 19091027
    • Pesquita C, Faria D, Bastos H, Ferreira AEN, Falcão AO, Couto FM. Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinformatics 2008, 9(Suppl 5):S4. 10.1186/1471-2105-9-S5-S4, 2638144, 19091027.
    • (2008) BMC Bioinformatics , vol.9 , Issue.SUPPL 5
    • Pesquita, C.1    Faria, D.2    Bastos, H.3    Ferreira, A.E.N.4    Falcão, A.O.5    Couto, F.M.6
  • 10
    • 84873214187 scopus 로고    scopus 로고
    • Effectively integrating information content and structural relationship to improve the GO-based similarity measure between proteins.
    • ArXiv e-prints:1001.0958, 2010
    • Li B, Wang JZ, Feltus FA, Zhou J, Luo F. Effectively integrating information content and structural relationship to improve the GO-based similarity measure between proteins. ArXiv e-prints:1001.0958, 2010.
    • Li, B.1    Wang, J.Z.2    Feltus, F.A.3    Zhou, J.4    Luo, F.5
  • 12
    • 75849158230 scopus 로고    scopus 로고
    • The Gene Ontology in 2010: extensions and refinements
    • 2808930, 19920128, GO-Consortium
    • GO-Consortium The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res 2009, 38:D331-D335. 2808930, 19920128, GO-Consortium.
    • (2009) Nucleic Acids Res , vol.38
  • 13
    • 33644875286 scopus 로고    scopus 로고
    • The Gene Ontology (GO) project in 2006
    • 1347384, 16381878, GO-Consortium
    • GO-Consortium The Gene Ontology (GO) project in 2006. Nucleic Acids Res 2006, 34:D322-D326. 1347384, 16381878, GO-Consortium.
    • (2006) Nucleic Acids Res , vol.34
  • 14
    • 38549159946 scopus 로고    scopus 로고
    • FunSimMat: a comprehensive functional similarity database
    • Database issue, 2238903, 17932054
    • Schlicker A, Albrecht M. FunSimMat: a comprehensive functional similarity database. Nucleic Acids Res 2008, 36(Database issue):D434-D439. 2238903, 17932054.
    • (2008) Nucleic Acids Res , vol.36
    • Schlicker, A.1    Albrecht, M.2
  • 17
    • 33645821454 scopus 로고    scopus 로고
    • Assessing semantic similarity measures for the characterization of human regulatory pathways
    • 10.1093/bioinformatics/btl042, 16492685
    • Guo X, Liu R, Shriver C, Hu H, Liebman M. Assessing semantic similarity measures for the characterization of human regulatory pathways. Bioinformatics 2006, 22(8):967-973. 10.1093/bioinformatics/btl042, 16492685.
    • (2006) Bioinformatics , vol.22 , Issue.8 , pp. 967-973
    • Guo, X.1    Liu, R.2    Shriver, C.3    Hu, H.4    Liebman, M.5
  • 18
    • 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. J Art Intell Res 1999, 11:95-130.
    • (1999) J Art Intell Res , vol.11 , pp. 95-130
    • Resnik, P.1
  • 21
    • 84884726933 scopus 로고    scopus 로고
    • Information content-based Gene Ontology semantic similarity approaches: toward a unified framework theory
    • Ariticle ID 292063, 11 pages
    • Mazandu GK, Mulder NJ. Information content-based Gene Ontology semantic similarity approaches: toward a unified framework theory. BioMed Res Int 2013, 2013:Ariticle ID 292063, 11 pages.
    • (2013) BioMed Res Int , vol.2013
    • Mazandu, G.K.1    Mulder, N.J.2
  • 22
    • 84862297314 scopus 로고    scopus 로고
    • A topology-based metric for measuring term similarity in the Gene Ontology
    • Ariticle ID 975783, 17 pages
    • Mazandu GK, Mulder NJ. A topology-based metric for measuring term similarity in the Gene Ontology. Adv Bioinformatics 2012, 2012:Ariticle ID 975783, 17 pages.
    • (2012) Adv Bioinformatics , vol.2012
    • Mazandu, G.K.1    Mulder, N.J.2
  • 23
    • 67849110934 scopus 로고    scopus 로고
    • Fast gene ontology based clustering for microarray experiments
    • 10.1186/1756-0381-1-11, 2613876, 19025591
    • Ovaska K, Laakso M, Hautaniemi S. Fast gene ontology based clustering for microarray experiments. BioData Mining 2008, 1:11. 10.1186/1756-0381-1-11, 2613876, 19025591.
    • (2008) BioData Mining , vol.1 , pp. 11
    • Ovaska, K.1    Laakso, M.2    Hautaniemi, S.3
  • 24
    • 78149449890 scopus 로고    scopus 로고
    • An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology
    • 10.1186/1471-2105-11-562, 2998529, 21078182
    • Jain S, Bader GD. An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology. BMC Bioinformatics 2010, 11:562. 10.1186/1471-2105-11-562, 2998529, 21078182.
    • (2010) BMC Bioinformatics , vol.11 , pp. 562
    • Jain, S.1    Bader, G.D.2
  • 25
    • 77956497662 scopus 로고    scopus 로고
    • (2010) Improving disease gene prioritization using the semantic similarity of gene ontology terms
    • 10.1093/bioinformatics/btq384, 2935448, 20823322
    • Schlicker A, Lengauer T, Albrecht M. (2010) Improving disease gene prioritization using the semantic similarity of gene ontology terms. Bioinformatics 2010, 26(18):i561-i567. 10.1093/bioinformatics/btq384, 2935448, 20823322.
    • (2010) Bioinformatics , vol.26 , Issue.18
    • Schlicker, A.1    Lengauer, T.2    Albrecht, M.3
  • 26
    • 58149411184 scopus 로고
    • Features of similarity
    • Tversky A. Features of similarity. Psychol Rev 1977, 84(4):327-352.
    • (1977) Psychol Rev , vol.84 , Issue.4 , pp. 327-352
    • Tversky, A.1
  • 28
    • 79951480123 scopus 로고    scopus 로고
    • Vienna, Austria, [3-900051-07-0], R Development Core Team
    • R Development Core Team R: A Language and Environment for Statistical Computing 2010, Vienna, Austria, http://www.R-project.org. [3-900051-07-0], R Development Core Team.
    • (2010) R: A Language and Environment for Statistical Computing
  • 29
    • 79961135005 scopus 로고    scopus 로고
    • Vienna: R Foundation for Statistical Computing., [ISBN 3-900051-07-0]., R Development Core Team
    • R Development Core Team R: A Language and Environment for Statistical Computing 2011, Vienna: R Foundation for Statistical Computing., http://www.R-project.org. [ISBN 3-900051-07-0]., R Development Core Team.
    • (2011) R: A Language and Environment for Statistical Computing
  • 30
    • 77951942707 scopus 로고    scopus 로고
    • GOSemSim: an R package for measuring semantic similarity among GO terms and gene products
    • 10.1093/bioinformatics/btq064, 20179076
    • Yu G, Li F, Qin Y, Bo X, Wu Y, Wand S. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics 2010, 26(7):976-978. 10.1093/bioinformatics/btq064, 20179076.
    • (2010) Bioinformatics , vol.26 , Issue.7 , pp. 976-978
    • Yu, G.1    Li, F.2    Qin, Y.3    Bo, X.4    Wu, Y.5    Wand, S.6
  • 33
    • 67849104643 scopus 로고    scopus 로고
    • G-SESAME: web tools for GO-term-based gene similarity analysis and knowledge discovery
    • Du Z, Li L, Chen CF, Yu PS, Wang JW. G-SESAME: web tools for GO-term-based gene similarity analysis and knowledge discovery. Nucleic Acids Res 2009, 37(2):D345-D349.
    • (2009) Nucleic Acids Res , vol.37 , Issue.2
    • Du, Z.1    Li, L.2    Chen, C.F.3    Yu, P.S.4    Wang, J.W.5
  • 34
    • 78649946112 scopus 로고    scopus 로고
    • CESSM: Collaborative evaluation of semantic similarity measures
    • Pesquita C, Pessoa D, Faria D, Couto F. CESSM: Collaborative evaluation of semantic similarity measures. JB2009: Challenges Bioinformatics 2009, http://xldb.fc.ul.pt/xldb/publications/Pesquita:CESSMCollaborative:2009_document.pdf.
    • (2009) JB2009: Challenges Bioinformatics
    • Pesquita, C.1    Pessoa, D.2    Faria, D.3    Couto, F.4
  • 36
    • 75849153303 scopus 로고    scopus 로고
    • The Universal Protein resource (UniProt) in 2010
    • 2808944, 19843607, UniProt-Consortium
    • UniProt-Consortium The Universal Protein resource (UniProt) in 2010. Nucleic Acids Res 2010, 38:D142-D148. 2808944, 19843607, UniProt-Consortium.
    • (2010) Nucleic Acids Res , vol.38
  • 39
    • 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) database - An integrated resource of GO annotations to the UniProt knowledgebase. Silico Biol 2004, 4(1):5-6.
    • (2004) Silico Biol , vol.4 , Issue.1 , pp. 5-6
    • Camon, E.1    Barrell, D.2    Lee, V.3    Dimmer, E.4    Apweiler, R.5
  • 41
    • 58149187893 scopus 로고    scopus 로고
    • The GOA database in 2009-an integrated Gene Ontology Annotation resource
    • 10.1093/nar/gkn803, 2686469, 18957448
    • Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R. The GOA database in 2009-an integrated Gene Ontology Annotation resource. Nucleic Acids Res 2009, 37:D396-D403. 10.1093/nar/gkn803, 2686469, 18957448.
    • (2009) Nucleic Acids Res , vol.37
    • Barrell, D.1    Dimmer, E.2    Huntley, R.P.3    Binns, D.4    O'Donovan, C.5    Apweiler, R.6
  • 42
    • 84875404822 scopus 로고    scopus 로고
    • Binomial approximation to the generalized generalized hypergeometric distribution
    • Teerapabolarn K. Binomial approximation to the generalized generalized hypergeometric distribution. Int J Pure Appl Math 2013, 83(4):559-563.
    • (2013) Int J Pure Appl Math , vol.83 , Issue.4 , pp. 559-563
    • Teerapabolarn, K.1
  • 43
    • 84855569114 scopus 로고    scopus 로고
    • Generation and analysis of large-scale data-driven Mycobacterium tuberculosis functional networks for drug target identification
    • Article ID 801478
    • Mazandu GK, Mulder NJ. Generation and analysis of large-scale data-driven Mycobacterium tuberculosis functional networks for drug target identification. Adv Bioinformatics 2011, 2011:Article ID 801478.
    • (2011) Adv Bioinformatics , vol.2011
    • Mazandu, G.K.1    Mulder, N.J.2


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