메뉴 건너뛰기




Volumn 6, Issue 1, 2007, Pages 51-59

Combining hierarchical and associative gene ontology relations with textual evidence in estimating gene and gene product similarity

Author keywords

BLAST; Gene ontology; Gene product similarity; GoPubMed; Ontology alignment

Indexed keywords

BIOMEDICAL ENGINEERING; GENES; HIERARCHICAL SYSTEMS; ONTOLOGY;

EID: 33947124631     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2007.891886     Document Type: Article
Times cited : (15)

References (38)
  • 2
    • 0023989064 scopus 로고
    • Improved tools for biological sequence analysis
    • W. R. Pearson and D. J. Lipman, "Improved tools for biological sequence analysis," Proc. Nat. Acad. Sci., vol. 85, pp. 2444-2448, 1988.
    • (1988) Proc. Nat. Acad. Sci , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 3
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • T. Smith and M. S. Waterman, "Identification of common molecular subsequences," J. Mol. Biol., vol. 147, pp. 195-197, 1981.
    • (1981) J. Mol. Biol , vol.147 , pp. 195-197
    • Smith, T.1    Waterman, M.S.2
  • 4
    • 23944520674 scopus 로고    scopus 로고
    • Gene ontology automatic annotation using a domain based gene product similarity measure
    • M. Popescu, J. M. Keller, and J. A. Mitchell, "Gene ontology automatic annotation using a domain based gene product similarity measure," in Proc. 14th IEEE Int. Conf. Fuzzy Systems, 2005, pp. 108-111.
    • (2005) Proc. 14th IEEE Int. Conf. Fuzzy Systems , pp. 108-111
    • Popescu, M.1    Keller, J.M.2    Mitchell, J.A.3
  • 5
    • 0043163729 scopus 로고    scopus 로고
    • The computational analysis of scientific literature to define and recognize gene expression clusters
    • S. Raychaudhuri, J. T. Chang, F. Imam, and R. B. Altman, "The computational analysis of scientific literature to define and recognize gene expression clusters," Nucl. Acids Res., vol. 31, no. 15, pp. 4553-4560, 2003.
    • (2003) Nucl. Acids Res , vol.31 , Issue.15 , pp. 4553-4560
    • Raychaudhuri, S.1    Chang, J.T.2    Imam, F.3    Altman, R.B.4
  • 6
    • 0037480738 scopus 로고    scopus 로고
    • Investigating semantic similarity measures across the Gene Ontology: The relationship between sequence and annotation
    • P. W. Lord, R. D. Stevens, A. Brass, and C. A. Goble, "Investigating semantic similarity measures across the Gene Ontology: The relationship between sequence and annotation," Bioinformatics, vol. 19, no. 10, pp. 1275-1283, 2002.
    • (2002) Bioinformatics , vol.19 , Issue.10 , pp. 1275-1283
    • Lord, P.W.1    Stevens, R.D.2    Brass, A.3    Goble, C.A.4
  • 8
    • 33947181015 scopus 로고    scopus 로고
    • F. M. Couto, M. J. Silva, and P. Coutinho, Implementation of a functional semantic similarity measure between gene-products Dept. Informatics, Univ. Lisbon, Lisbon, Portugal, 2003 [Online]. Available: http://www.di.fc.ul.pt/tech- reports/03-29.pdf, Technical Report
    • F. M. Couto, M. J. Silva, and P. Coutinho, Implementation of a functional semantic similarity measure between gene-products Dept. Informatics, Univ. Lisbon, Lisbon, Portugal, 2003 [Online]. Available: http://www.di.fc.ul.pt/tech- reports/03-29.pdf, Technical Report
  • 12
    • 1842650939 scopus 로고    scopus 로고
    • Exploiting hierarchical domain structure to compute similarity
    • P. Ganesan, H. Garcia-Molina, and J. Widom, "Exploiting hierarchical domain structure to compute similarity," ACM Trans. Inf. Syst., vol. 21, no. 1, pp. 64-93, 2003.
    • (2003) ACM Trans. Inf. Syst , vol.21 , Issue.1 , pp. 64-93
    • Ganesan, P.1    Garcia-Molina, H.2    Widom, J.3
  • 13
    • 15944407681 scopus 로고    scopus 로고
    • Non-lexical approaches to identifying associative relations in the gene ontology
    • O. Bodenreider, M. Aubry, and A. Burgun, "Non-lexical approaches to identifying associative relations in the gene ontology," in Proc. Pac. Symp. Biocomputing, 2005, pp. 104-115.
    • (2005) Proc. Pac. Symp. Biocomputing , pp. 104-115
    • Bodenreider, O.1    Aubry, M.2    Burgun, A.3
  • 17
    • 0030633417 scopus 로고    scopus 로고
    • Automatic annotation for biological sequences by extraction of keywords from MEDLINE abstracts. Development of a prototype system
    • M. A. Andrade and A. Valencia, "Automatic annotation for biological sequences by extraction of keywords from MEDLINE abstracts. Development of a prototype system," in Proc. Annu. Int. Conf. Intelligent Systems for Molecular Biology, 1997, pp. 25-32.
    • (1997) Proc. Annu. Int. Conf. Intelligent Systems for Molecular Biology , pp. 25-32
    • Andrade, M.A.1    Valencia, A.2
  • 18
    • 0034020913 scopus 로고    scopus 로고
    • SAWTED: Structure assignment with text description-enhanced detection of remote homologues with automated SWISS-PROT annotation comparisons
    • R. M. MacCallum, L. A. Kelley, and M. J. Sternberg, "SAWTED: structure assignment with text description-enhanced detection of remote homologues with automated SWISS-PROT annotation comparisons," Bioinformatics, vol. 16, pp. 125-129, 2000.
    • (2000) Bioinformatics , vol.16 , pp. 125-129
    • MacCallum, R.M.1    Kelley, L.A.2    Sternberg, M.J.3
  • 20
    • 33947144740 scopus 로고    scopus 로고
    • Lexical Semantic Relatedness and Its Application in Natural Language Processing Department of Computer Science, University of Toronto, Technical report CSRG-390
    • A. Budanitsky, Lexical Semantic Relatedness and Its Application in Natural Language Processing Department of Computer Science, University of Toronto, Technical report CSRG-390, 1999.
    • (1999)
    • Budanitsky, A.1
  • 22
    • 0012430167 scopus 로고    scopus 로고
    • Semantic similarity based on corpus statistics and lexical taxonomy
    • presented at the, Research in Computational Linguistics, Taipei, Taiwan, R.O.C
    • J. Jiang and D. Conrath, "Semantic similarity based on corpus statistics and lexical taxonomy," presented at the Int. Conf. Research in Computational Linguistics, Taipei, Taiwan, R.O.C., 1997.
    • (1997) Int. Conf
    • Jiang, J.1    Conrath, D.2
  • 23
    • 34247260782 scopus 로고    scopus 로고
    • Maximizing semantic relatedness to perform word sense disambiguation Supercomputing Institute, Univ. Minnesota
    • Mar, Online, Available
    • T. Pedersen, S. Banerjee, and S. Patwardhan, Maximizing semantic relatedness to perform word sense disambiguation Supercomputing Institute, Univ. Minnesota, Res. Rep. UMSI 2005/25, Mar. 2005 [Online]. Available: http://www.msi.umn.edu/general/Reports/rpt-files/2005-25.pdf
    • (2005) Res. Rep. UMSI , vol.2005 , Issue.25
    • Pedersen, T.1    Banerjee, S.2    Patwardhan, S.3
  • 24
    • 0005180705 scopus 로고    scopus 로고
    • An information-theoretic definition of similarity
    • presented at the, Madison, WI
    • D. Lin, "An information-theoretic definition of similarity," presented at the 15th Int. Conf. Machine Learning, Madison, WI, 1998.
    • (1998) 15th Int. Conf. Machine Learning
    • Lin, D.1
  • 25
    • 0016572913 scopus 로고
    • A vector space model for automatic indexing
    • G. Salton, A. Wong, and C. S. Yang, "A vector space model for automatic indexing," Commun. Assoc. Comput. Mach., vol. 18, no. 11, pp. 613-620, 1975.
    • (1975) Commun. Assoc. Comput. Mach , vol.18 , Issue.11 , pp. 613-620
    • Salton, G.1    Wong, A.2    Yang, C.S.3
  • 27
    • 33747408363 scopus 로고    scopus 로고
    • M. Popescu, J. M. Keller, and J. A. Mitchell, Fuzzy measures on the Gene Ontology for gene product similarity, IEEE/ACM Trans. Comput. Biol. Bioinf., 3, no. 3, pp. 263-274, 2006.
    • M. Popescu, J. M. Keller, and J. A. Mitchell, "Fuzzy measures on the Gene Ontology for gene product similarity," IEEE/ACM Trans. Comput. Biol. Bioinf., vol. 3, no. 3, pp. 263-274, 2006.
  • 28
    • 0000299560 scopus 로고
    • Rank and product-moment correlation
    • M. Kendall, "Rank and product-moment correlation," Biometrika, vol. 36, pp. 177-193, 1949.
    • (1949) Biometrika , vol.36 , pp. 177-193
    • Kendall, M.1
  • 30
    • 23144448699 scopus 로고    scopus 로고
    • GoPubMed: Exploring PubMed with the gene ontology
    • A. Doms and M. Schroeder, "GoPubMed: Exploring PubMed with the gene ontology," Nucl. Acids Res., vol. 33, pp. W783-W786, 2005.
    • (2005) Nucl. Acids Res , vol.33
    • Doms, A.1    Schroeder, M.2
  • 31
    • 33645118994 scopus 로고    scopus 로고
    • GoPubMed: Ontology based literature search applied to Gene Ontology and PubMed
    • presented at the, Bielefeld, Germany
    • Delfs, R. A. Doms, A. Kozlenkov, and M. Schroeder, "GoPubMed: Ontology based literature search applied to Gene Ontology and PubMed," presented at the German Bioinformatics Conf., Bielefeld, Germany, 2004.
    • (2004) German Bioinformatics Conf
    • Delfs, R.1    Doms, A.2    Kozlenkov, A.3    Schroeder, M.4
  • 32
    • 0004116125 scopus 로고
    • Implementation of the SMART information retrieval system Cornell Univ., Ithaca, NY
    • Tech. Rep. 85-686
    • C. Buckley, Implementation of the SMART information retrieval system Cornell Univ., Ithaca, NY, Tech. Rep. 85-686, 1985.
    • (1985)
    • Buckley, C.1
  • 34
    • 0007276238 scopus 로고
    • Global Optimization by Random Walk Sampling Methods
    • Amsterdam, The Netherlands: Thesis Publishers
    • E. H. Romeijn, Global Optimization by Random Walk Sampling Methods, ser. Tinbergen Institute Research Series. Amsterdam, The Netherlands: Thesis Publishers, 1992, vol. 32.
    • (1992) ser. Tinbergen Institute Research Series , vol.32
    • Romeijn, E.H.1
  • 35
    • 33646126091 scopus 로고    scopus 로고
    • Gene expression patterns in Rainbow Trout, Onorhynchus mykiss, exposed to a suite of model toxicants
    • S. E. Hook, A. D. Skillman, J. A. Small, and L. R. Schultz, "Gene expression patterns in Rainbow Trout, Onorhynchus mykiss, exposed to a suite of model toxicants," Aquatic Toxicol., vol. 77, no. 4, pp. 372-385, 2005.
    • (2005) Aquatic Toxicol , vol.77 , Issue.4 , pp. 372-385
    • Hook, S.E.1    Skillman, A.D.2    Small, J.A.3    Schultz, L.R.4
  • 36
    • 3142665525 scopus 로고    scopus 로고
    • GOstat: Find statistically overrepresented Gene Ontologies within group of genes
    • T. Beissbarth and T. Speed, "GOstat: find statistically overrepresented Gene Ontologies within group of genes," Bioinformatics, vol. 20, pp. 1464-1465, 2004.
    • (2004) Bioinformatics , vol.20 , pp. 1464-1465
    • Beissbarth, T.1    Speed, T.2
  • 38
    • 33947141021 scopus 로고    scopus 로고
    • B. Gopalan, C. Posse, A. Sanfilippo, M. Stenzel-Poore, S. Stevens, J. Castaño, N. Beagley, R. Riensche, B. Baddeley, R. Simon, and J. Pustejovsky, Aligning Ontologies and Integrating Textual Evidence for Pathway Analysis of Microarray data 2006, unpublished manuscript.
    • B. Gopalan, C. Posse, A. Sanfilippo, M. Stenzel-Poore, S. Stevens, J. Castaño, N. Beagley, R. Riensche, B. Baddeley, R. Simon, and J. Pustejovsky, Aligning Ontologies and Integrating Textual Evidence for Pathway Analysis of Microarray data 2006, unpublished manuscript.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.