메뉴 건너뛰기




Volumn 7, Issue , 2006, Pages

A literature-based similarity metric for biological processes

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL NETWORKS; BIOLOGICAL PROCESS; FUNCTIONAL MODULES; GENOME ANNOTATION; INTEGRATIVE ANALYSIS; LITERATURE ANALYSIS; SCIENTIFIC LITERATURE; SIMILARITY METRICS;

EID: 33749432121     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-363     Document Type: Article
Times cited : (12)

References (52)
  • 2
    • 0035830505 scopus 로고    scopus 로고
    • A biological atlas of functional maps
    • Vidal M: A biological atlas of functional maps. Cell 2001, 104:333-339.
    • (2001) Cell , vol.104 , pp. 333-339
    • Vidal, M.1
  • 3
    • 2642566695 scopus 로고    scopus 로고
    • A probabilistic view of gene function
    • Fraser AG, Marcotte EM: A probabilistic view of gene function. Nat Genet 2004, 36:559-564.
    • (2004) Nat Genet , vol.36 , pp. 559-564
    • Fraser, A.G.1    Marcotte, E.M.2
  • 6
    • 1542357674 scopus 로고    scopus 로고
    • Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data
    • Tanay A, Sharan R, Kupiec M, Shamir R: Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc Natl Acad Sci U S A 2004, 101:2981-2986.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 2981-2986
    • Tanay, A.1    Sharan, R.2    Kupiec, M.3    Shamir, R.4
  • 7
    • 24344498648 scopus 로고    scopus 로고
    • A network of transcriptionally coordinated functional modules in Soccharomyces cerevisiae
    • Petti AA, Church GM: A network of transcriptionally coordinated functional modules in Soccharomyces cerevisiae. Genome Res 2005, 15:1298-1306.
    • (2005) Genome Res , vol.15 , pp. 1298-1306
    • Petti, A.A.1    Church, G.M.2
  • 9
    • 24644470505 scopus 로고    scopus 로고
    • Ontological analysis of gene expression data: Current tools, limitations, and open problems
    • Khatri P, Draghici S: Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 2005, 21:3587-3595.
    • (2005) Bioinformatics , vol.21 , pp. 3587-3595
    • Khatri, P.1    Draghici, S.2
  • 10
    • 0037480738 scopus 로고    scopus 로고
    • Investigating semantic similarity measures across the Gene Ontology: The relationship between sequence and annotation
    • Lord PW, Stevens RD, Brass A, Goble CA: Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 2003, 19:1275-1283.
    • (2003) Bioinformatics , vol.19 , pp. 1275-1283
    • Lord, P.W.1    Stevens, R.D.2    Brass, A.3    Goble, C.A.4
  • 11
    • 0038478096 scopus 로고    scopus 로고
    • Semantic similarity measures as tools for exploring the gene ontology
    • Lord PW, Stevens RD, Brass A, Goble CA: Semantic similarity measures as tools for exploring the gene ontology. Pac Symp Biocomput 2003:601-612.
    • (2003) Pac Symp Biocomput , pp. 601-612
    • Lord, P.W.1    Stevens, R.D.2    Brass, A.3    Goble, C.A.4
  • 13
    • 25444482341 scopus 로고    scopus 로고
    • Theme discovery from gene lists for identification and viewing of multiple functional groups
    • Pehkonen P, Wong G, Toronen P: Theme discovery from gene lists for identification and viewing of multiple functional groups. BMC Bioinformatics 2005, 6:162.
    • (2005) BMC Bioinformatics , vol.6 , pp. 162
    • Pehkonen, P.1    Wong, G.2    Toronen, P.3
  • 15
    • 33646358998 scopus 로고    scopus 로고
    • Prediction of yeast protein-protein interaction network: Insights from the Gene Ontology and annotations
    • Wu X, Zhu L, Guo J, Zhang DY, Lin K: Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations. Nucleic Acids Res 2006, 34:2137-2150.
    • (2006) Nucleic Acids Res , vol.34 , pp. 2137-2150
    • Wu, X.1    Zhu, L.2    Guo, J.3    Zhang, D.Y.4    Lin, K.5
  • 16
  • 17
    • 33644856110 scopus 로고    scopus 로고
    • Improving missing value estimation in microarray data with gene ontology
    • Tuikkala J, Elo L, Nevalainen OS, Aittokallio T: Improving missing value estimation in microarray data with gene ontology. Bioinformatics 2006, 22:566-572.
    • (2006) Bioinformatics , vol.22 , pp. 566-572
    • Tuikkala, J.1    Elo, L.2    Nevalainen, O.S.3    Aittokallio, T.4
  • 19
    • 0038017587 scopus 로고    scopus 로고
    • Mining microarray expression data by literature profiling
    • RESEARCH0055
    • Chaussabel D, Sher A: Mining microarray expression data by literature profiling. Genome Biol 2002, 3:RESEARCH0055.
    • (2002) Genome Biol , vol.3
    • Chaussabel, D.1    Sher, A.2
  • 21
    • 12744279636 scopus 로고    scopus 로고
    • Gene clustering by latent semantic indexing of MEDLINE abstracts
    • Homayouni R, Heinrich K, Wei L, Berry MW: Gene clustering by latent semantic indexing of MEDLINE abstracts. Bioinformatics 2005, 21:104-115.
    • (2005) Bioinformatics , vol.21 , pp. 104-115
    • Homayouni, R.1    Heinrich, K.2    Wei, L.3    Berry, M.W.4
  • 22
    • 0034565168 scopus 로고    scopus 로고
    • Genes, themes and microarrays: Using information retrieval for large-scale gene analysis
    • Shatkay H, Edwards S, Wilbur WJ, Boguski M: Genes, themes and microarrays: using information retrieval for large-scale gene analysis. Proc Int Conf Intell Syst Mol Biol 2000, 8:317-328.
    • (2000) Proc Int Conf Intell Syst Mol Biol , vol.8 , pp. 317-328
    • Shatkay, H.1    Edwards, S.2    Wilbur, W.J.3    Boguski, M.4
  • 25
    • 24644464205 scopus 로고    scopus 로고
    • Study of coordinative gene expression at the biological process level
    • Yu T, Sun W, Yuan S, Li KC: Study of coordinative gene expression at the biological process level. Bioinformatics 2005, 21:3651-3657.
    • (2005) Bioinformatics , vol.21 , pp. 3651-3657
    • Yu, T.1    Sun, W.2    Yuan, S.3    Li, K.C.4
  • 26
    • 15944407681 scopus 로고    scopus 로고
    • Non-lexical approaches to identifying associative relations in the gene ontology
    • Bodenreider O, Aubry M, Burgun A: Non-lexical approaches to identifying associative relations in the gene ontology. Pac Symp Biocomput 2005:91-102.
    • (2005) Pac Symp Biocomput , pp. 91-102
    • Bodenreider, O.1    Aubry, M.2    Burgun, A.3
  • 31
    • 84874665828 scopus 로고    scopus 로고
    • PubMed
    • PubMed [http://www.pubmed.org]
  • 32
    • 84874644670 scopus 로고    scopus 로고
    • Project Web Page
    • Project Web Page [http://www.cnb.csic.es/~monica/Similarity/]
  • 33
    • 0005180705 scopus 로고    scopus 로고
    • An Information-Theoretic Definition of Similarity
    • In July 24-27; Madison, Wisconsin, USA Morgan Kaufmann Publishers Inc
    • Lin D: An Information-Theoretic Definition of Similarity. In Fifteenth International Conference on Machine Learning; July 24-27; Madison, Wisconsin, USA Morgan Kaufmann Publishers Inc; 1998:296-304.
    • (1998) Fifteenth International Conference on Machine Learning , pp. 296-304
    • Lin, D.1
  • 34
    • 0345306178 scopus 로고    scopus 로고
    • Chitin scar breaks in aged Saccharomyces cerevisiae
    • Powell CD, Quain DE, Smart KA: Chitin scar breaks in aged Saccharomyces cerevisiae. Microbiology 2003, 149:3129-3137.
    • (2003) Microbiology , vol.149 , pp. 3129-3137
    • Powell, C.D.1    Quain, D.E.2    Smart, K.A.3
  • 35
    • 0038518286 scopus 로고    scopus 로고
    • Assembly of cytochrome c oxidase within the mitochondrion
    • Carr HS, Winge DR: Assembly of cytochrome c oxidase within the mitochondrion. Acc Chem Res 2003, 36:309-316.
    • (2003) Acc Chem Res , vol.36 , pp. 309-316
    • Carr, H.S.1    Winge, D.R.2
  • 36
    • 1242294474 scopus 로고    scopus 로고
    • Cox17 is functional when tethered to the mitochondrial inner membrane
    • Maxfield AB, Heaton DN, Winge DR: Cox17 is functional when tethered to the mitochondrial inner membrane. J Biol Chem 2004, 279:5072-5080.
    • (2004) J Biol Chem , vol.279 , pp. 5072-5080
    • Maxfield, A.B.1    Heaton, D.N.2    Winge, D.R.3
  • 37
    • 0034046342 scopus 로고    scopus 로고
    • Mitochondria-to-nuclear signaling is regulated by the subcellular localization of the transcription factors Rtg1p and Rtg3p
    • Sekito T, Thornton J, Butow RA: Mitochondria-to-nuclear signaling is regulated by the subcellular localization of the transcription factors Rtg1p and Rtg3p. Mol Biol Cell 2000, 11:2103-2115.
    • (2000) Mol Biol Cell , vol.11 , pp. 2103-2115
    • Sekito, T.1    Thornton, J.2    Butow, R.A.3
  • 38
    • 20544432791 scopus 로고    scopus 로고
    • Cell wall integrity signaling in Saccharomyces cerevisiae
    • Levin DE: Cell wall integrity signaling in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 2005, 69:262-291.
    • (2005) Microbiol Mol Biol Rev , vol.69 , pp. 262-291
    • Levin, D.E.1
  • 39
    • 84874647917 scopus 로고    scopus 로고
    • SGD GO Term Finder
    • SGD GO Term Finder [http://db.yeastgenome.org/cgi-bin/GO/goTermFinder]
  • 40
    • 0037770197 scopus 로고    scopus 로고
    • Roles played by Ras subfamily proteins in the cell and developmental biology of microorganisms
    • Weeks G, Spiegelman GB: Roles played by Ras subfamily proteins in the cell and developmental biology of microorganisms. Cell Signal 2003, 15:901-909.
    • (2003) Cell Signal , vol.15 , pp. 901-909
    • Weeks, G.1    Spiegelman, G.B.2
  • 41
    • 0031664339 scopus 로고    scopus 로고
    • Roles of prenyl protein proteases in maturation of Saccharomyces cerevisiae a-factor
    • Boyartchuk VL, Rine J: Roles of prenyl protein proteases in maturation of Saccharomyces cerevisiae a-factor. Genetics 1998, 150:95-101.
    • (1998) Genetics , vol.150 , pp. 95-101
    • Boyartchuk, V.L.1    Rine, J.2
  • 42
    • 0141484562 scopus 로고    scopus 로고
    • Biological networks: The tinkerer as an engineer
    • Alon U: Biological networks: the tinkerer as an engineer. Science 2003, 301:1866-1867.
    • (2003) Science , vol.301 , pp. 1866-1867
    • Alon, U.1
  • 43
    • 0037174638 scopus 로고    scopus 로고
    • Systems biology. Life's complexity pyramid
    • Oltvai ZN, Barabasi AL: Systems biology. Life's complexity pyramid. Science 2002, 298:763-764.
    • (2002) Science , vol.298 , pp. 763-764
    • Oltvai, Z.N.1    Barabasi, A.L.2
  • 44
    • 84948481845 scopus 로고
    • An algorithm for suffix stripping
    • Porter MF: An algorithm for suffix stripping. Program 1980, 14:130-137.
    • (1980) Program , vol.14 , pp. 130-137
    • Porter, M.F.1
  • 45
    • 0034818212 scopus 로고    scopus 로고
    • Unsupervised learning by probabilistic latent semantic analysis
    • Hofmann T: Unsupervised learning by probabilistic latent semantic analysis. Mach Learn 2001, 42:177-196.
    • (2001) Mach Learn , vol.42 , pp. 177-196
    • Hofmann, T.1
  • 46
    • 0033592606 scopus 로고    scopus 로고
    • Learning the parts of objects by non-negativematrix factorization
    • Lee DD, Seung HS: Learning the parts of objects by non-negativematrix factorization. Nature 1999, 401:788-791.
    • (1999) Nature , vol.401 , pp. 788-791
    • Lee, D.D.1    Seung, H.S.2
  • 47
    • 0042826822 scopus 로고    scopus 로고
    • Independent component analysis: Algorithms and applications
    • Hyvarinen A, Oja E: Independent component analysis: algorithms and applications. Neural Networks 2000, 13:411-430.
    • (2000) Neural Networks , vol.13 , pp. 411-430
    • Hyvarinen, A.1    Oja, E.2
  • 50
    • 84937549955 scopus 로고
    • Scree Test for Number of Factors
    • Cattell RB: Scree Test for Number of Factors. Multivar Behav Res 1966, 1:245-276.
    • (1966) Multivar Behav Res , vol.1 , pp. 245-276
    • Cattell, R.B.1
  • 51
    • 0003033112 scopus 로고
    • Using information content to evaluate semantic similarity in a taxonomy
    • Resnik P: Using information content to evaluate semantic similarity in a taxonomy. Proc Int Joint Conference on Al, IJCAI-95 1995:448-453.
    • (1995) Proc Int Joint Conference on Al, IJCAI-95 , pp. 448-453
    • Resnik, P.1
  • 52
    • 0002016474 scopus 로고    scopus 로고
    • Semantic similarity in a taxonomy: Aninformation-based measure and its application to problems of ambiguity innatural language
    • Resnik P: Semantic similarity in a taxonomy: Aninformation-based measure and its application to problems of ambiguity innatural language. J Artif Intell Res 1999, 11:95-130.
    • (1999) J Artif Intell Res , vol.11 , pp. 95-130
    • Resnik, P.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.