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Volumn 17, Issue 4, 2000, Pages 283-293

Accurate prediction of protein functional class from sequence in the Mycobacterium tuberculosis and Escherichia coll genomes using data mining

Author keywords

Bioinformatics; Clustering; ILP; Machine learning

Indexed keywords


EID: 0000875752     PISSN: 0749503X     EISSN: None     Source Type: Journal    
DOI: 10.1002/1097-0061(200012)17:4<283::aid-yea52>3.0.co;2-f     Document Type: Article
Times cited : (56)

References (57)
  • 1
    • 0034708480 scopus 로고    scopus 로고
    • The genome sequence of Drosophilia melaiiogaster
    • Adams MD et al. 2000. The genome sequence of Drosophilia melaiiogaster. Science 287: 2185-2195.
    • (2000) Science , vol.287 , pp. 2185-2195
    • Adams, M.D.1
  • 3
    • 0034598746 scopus 로고    scopus 로고
    • Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling
    • Alizadeh A et al. 2000. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403: 503-511.
    • (2000) Nature , vol.403 , pp. 503-511
    • Alizadeh, A.1
  • 4
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF el al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 5
    • 0033957834 scopus 로고    scopus 로고
    • The SWISS-PROT protein sequence database and its supplement TrEMBL
    • Bairoch A, Apweiler R. 2000. The SWISS-PROT protein sequence database and its supplement TrEMBL. Nucleic Acids Res 28: 45-48.
    • (2000) Nucleic Acids Res , vol.28 , pp. 45-48
    • Bairoch, A.1    Apweiler, R.2
  • 6
    • 0032784646 scopus 로고    scopus 로고
    • Proteomics: Quantitative and physical mapping of cellular proteins
    • Blackstock WP, Weir MP. 1999. Proteomics: quantitative and physical mapping of cellular proteins. Tibtech 17: 121-127.
    • (1999) Tibtech , vol.17 , pp. 121-127
    • Blackstock, W.P.1    Weir, M.P.2
  • 7
    • 15444350252 scopus 로고    scopus 로고
    • The complete genome sequence of Escherichia coll K-12
    • Blattner FR et al. 1997. The complete genome sequence of Escherichia coll K-12. Science 277: 1453-1461.
    • (1997) Science , vol.277 , pp. 1453-1461
    • Blattner, F.R.1
  • 8
    • 0032491377 scopus 로고    scopus 로고
    • Predicting function: From genes to genomes and back
    • Bork P, Dandekar T, Diaz-Lazcoz Y et al. 1998. Predicting function: from genes to genomes and back. J Mol Biol 283: 707-725.
    • (1998) J Mol Biol , vol.283 , pp. 707-725
    • Bork, P.1    Dandekar, T.2    Diaz-Lazcoz, Y.3
  • 9
    • 0033119399 scopus 로고    scopus 로고
    • Errors in gene annotation
    • Brenner E. 1999. Errors in gene annotation. Trends Genet 15: 132-133.
    • (1999) Trends Genet , vol.15 , pp. 132-133
    • Brenner, E.1
  • 10
    • 0033528999 scopus 로고    scopus 로고
    • Functional genomics: Learning to think about gene expression data
    • Brent R. 1999. Functional genomics: learning to think about gene expression data. Curr Biol 9: R338-R341.
    • (1999) Curr Biol , vol.9
    • Brent, R.1
  • 11
    • 84984932472 scopus 로고    scopus 로고
    • Exploring the new world of the genome with DNA microarrays
    • Brown PO, Botstein D. 1999. Exploring the new world of the genome with DNA microarrays. Nature Genet 21: 33-37.
    • (1999) Nature Genet , vol.21 , pp. 33-37
    • Brown, P.O.1    Botstein, D.2
  • 12
    • 0031302034 scopus 로고    scopus 로고
    • 1997 ushers in an era of yeast functional genomics
    • Bussey H. 1997. 1997 ushers in an era of yeast functional genomics. Yeast 13: 1501-1503.
    • (1997) Yeast , vol.13 , pp. 1501-1503
    • Bussey, H.1
  • 13
    • 1942422934 scopus 로고
    • Model uncertainty: Data mining and statistical inference
    • Chatfield C. 1995. Model uncertainty: data mining and statistical inference. J R Slat Soc Ser A Stat Soc 158: 419-466.
    • (1995) J R Slat Soc ser A Stat Soc , vol.158 , pp. 419-466
    • Chatfield, C.1
  • 14
    • 0027696331 scopus 로고
    • Functional and teleological knowledge in the multimodelling approach for reasoning about physical systems: A case study in diagnosis
    • Chittaro L, Guida G, Tasso C, Toppano E. 1993. Functional and teleological knowledge in the multimodelling approach for reasoning about physical systems: a case study in diagnosis. IEEE Trans Syst Man Cyber 23: 1718-1751.
    • (1993) IEEE Trans Syst Man Cyber , vol.23 , pp. 1718-1751
    • Chittaro, L.1    Guida, G.2    Tasso, C.3    Toppano, E.4
  • 15
    • 0032508046 scopus 로고    scopus 로고
    • Deciphering the biology of Mycobacteriuni tuberculosis from the complete genome sequence
    • Cole ST et al. 1998. Deciphering the biology of Mycobacteriuni tuberculosis from the complete genome sequence. Nature 393: 537-544.
    • (1998) Nature , vol.393 , pp. 537-544
    • Cole, S.T.1
  • 16
    • 0032509302 scopus 로고    scopus 로고
    • Genome sequence of the nematode C. elegans: A platform for investigating biology
    • elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 2012-2018. Data: http://www.abcr.ac.uk/ deswww/Research/bio/ProteinFunclioiiJ.
    • (1998) Science , vol.282 , pp. 2012-2018
  • 18
    • 0030669030 scopus 로고    scopus 로고
    • Exploring the metabolic and genetic control of gene expression on a genomic scale
    • DeRisi JL, lyer VR, Brown PO. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686.
    • (1997) Science , vol.278 , pp. 680-686
    • Derisi, J.L.1    Lyer, V.R.2    Brown, P.O.3
  • 20
    • 0033102657 scopus 로고    scopus 로고
    • Functional genomics: From genes to new therapies
    • Dyer MR, Cohen D, Herrling P. 1999. Functional genomics: from genes to new therapies. Drug Discovery Today 4: 109-114.
    • (1999) Drug Discovery Today , vol.4 , pp. 109-114
    • Dyer, M.R.1    Cohen, D.2    Herrling, P.3
  • 21
    • 84866962930 scopus 로고    scopus 로고
    • EC_genc_list: http://genprotcc.mbl.edu : 80/start
  • 23
    • 10244239321 scopus 로고    scopus 로고
    • Life with 6000 genes
    • Goffeau A et al. 1996. Life with 6000 genes. Science 274: 546-567.
    • (1996) Science , vol.274 , pp. 546-567
    • Goffeau, A.1
  • 24
    • 0030660580 scopus 로고    scopus 로고
    • Gene families: The taxonomy of protein paralogs and chimeras
    • Henikoff S et al. 1997. Gene families: the taxonomy of protein paralogs and chimeras. Science 278: 609-614.
    • (1997) Science , vol.278 , pp. 609-614
    • Henikoff, S.1
  • 25
    • 0030725715 scopus 로고    scopus 로고
    • Functional genomics: It's all how you read it
    • Mieter P, Boguski N. 1997. Functional genomics: it's all how you read it. Science 278: 601-602.
    • (1997) Science , vol.278 , pp. 601-602
    • Mieter, P.1    Boguski, N.2
  • 27
    • 0001457344 scopus 로고    scopus 로고
    • Explanatory analysis of the metabolome using genetic programming of simple, interpretable rules
    • (in press).
    • Johnson HE, Gilbert RJ, Winson MK et al. 2000. Explanatory analysis of the metabolome using genetic programming of simple, interpretable rules. Genet Progr Evolvable Machines 1 (in press).
    • (2000) Genet Progr Evolvable Machines , vol.1
    • Johnson, H.E.1    Gilbert, R.J.2    Winson, M.K.3
  • 28
    • 0034160040 scopus 로고    scopus 로고
    • On the optimization of classes for the assignment of unidentified reading frames in functional genomics programmes: The need for machine learning
    • Kell DB, King RD. 2000. On the optimization of classes for the assignment of unidentified reading frames in functional genomics programmes: the need for machine learning. Trends Bioleclmol 18: 93-98.
    • (2000) Trends Bioleclmol , vol.18 , pp. 93-98
    • Kell, D.B.1    King, R.D.2
  • 29
    • 0026459988 scopus 로고
    • Drug design by machine learning - The use of inductive logic programming to model the structure-activity relationships of trimethoprim analogs binding to dihydrofolate-reductase
    • King RD, Muggleton S, Lewis RA, Sternberg M JE. 1992. Drug design by machine learning - the use of inductive logic programming to model the structure-activity relationships of trimethoprim analogs binding to dihydrofolate-reductase. Proc NatlAcadSci U S A 9: 11322-11326.
    • (1992) Proc NatlAcadSci U S A , vol.9 , pp. 11322-11326
    • King, R.D.1    Muggleton, S.2    Lewis, R.A.3    Sternberg, M.J.E.4
  • 30
    • 0030044168 scopus 로고    scopus 로고
    • Structure-activity relationships derived by machine learning: The use of atoms and their bond connectivities to predict mutagenicity by inductive logic programming
    • King RD, Muggleton SH, Srinivasan A, Sternberg MJE. 1996. Structure-activity relationships derived by machine learning: the use of atoms and their bond connectivities to predict mutagenicity by inductive logic programming. Proc Nat! Acad Sei USA 93: 438-442.
    • (1996) Proc Nat! Acad Sei USA , vol.93 , pp. 438-442
    • King, R.D.1    Muggleton, S.H.2    Srinivasan, A.3    Sternberg, M.J.E.4
  • 32
    • 10544256600 scopus 로고    scopus 로고
    • Expression monitoring by hybridization to high-density oligonucleotide arrays
    • Ellis Honvood: Chichester. Lockhart DJ, Dong HL, Byrne MC et al. 1996. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnol 14: 1675-1680.
    • (1996) Nature Biotechnol , vol.14 , pp. 1675-1680
    • Lockhart, D.J.1    Dong, H.L.2    Byrne, M.C.3
  • 33
    • 84866962931 scopus 로고    scopus 로고
    • A lagpie http://www-fp.mcs.anl.gov/ ~ gaasterland/genomc.html
    • Lagpie, A.1
  • 34
    • 21944442464 scopus 로고    scopus 로고
    • Levelwise search and borders of theories in knowledge discovery
    • Mannila H, Toivonen H. 1997. Levelwise search and borders of theories in knowledge discovery. Data Mining Knowledge Discovery 1: 241-258.
    • (1997) Data Mining Knowledge Discovery , vol.1 , pp. 241-258
    • Mannila, H.1    Toivonen, H.2
  • 37
    • 0000640432 scopus 로고
    • Inductive logic programming
    • Muggleton S. 1991. Inductive logic programming. New Gen Comput 8: 295-318.
    • (1991) New Gen Comput , vol.8 , pp. 295-318
    • Muggleton, S.1
  • 38
    • 0142253934 scopus 로고    scopus 로고
    • Knowledge discovery
    • Munakata T. 1999. Knowledge discovery. Comm ACM 41: 26-29.
    • (1999) Comm ACM , vol.41 , pp. 26-29
    • Munakata, T.1
  • 39
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Bio! 247: 536-540.
    • (1995) J Mol Bio! , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 41
    • 0030919411 scopus 로고    scopus 로고
    • Yeast as a navigational aid in genome analysis
    • Oliver SG. 1997. Yeast as a navigational aid in genome analysis. Microbiol UK 143: 1483-1487.
    • (1997) Microbiol UK , vol.143 , pp. 1483-1487
    • Oliver, S.G.1
  • 42
    • 0006617064 scopus 로고    scopus 로고
    • The yeast genome: Systematic analysis of DNA sequence and biological function
    • Copping LG, Dixon GK, Livingstone DJ (eds). Bios Scientific Publishing: Oxford
    • Oliver SG, Baganz F. 1998. The yeast genome: systematic analysis of DNA sequence and biological function. In Genomics: Commercial Opportunities from a Scientific Revolution, Copping LG, Dixon GK, Livingstone DJ (eds). Bios Scientific Publishing: Oxford; 37-51.
    • (1998) Genomics: Commercial Opportunities from A Scientific Revolution , pp. 37-51
    • Oliver, S.G.1    Baganz, F.2
  • 44
    • 0033933636 scopus 로고    scopus 로고
    • Cascaded multiple classifiers for secondary structure prediction
    • Ouali M, King RD. 2000. Cascaded multiple classifiers for secondary structure prediction. Protein Sei 9: 1162-1176.
    • (2000) Protein Sei , vol.9 , pp. 1162-1176
    • Ouali, M.1    King, R.D.2
  • 45
    • 0031576361 scopus 로고    scopus 로고
    • Intermediate sequences increase the detection of homology between sequences
    • Park J, Teichmann SA, Hubbard T, Chothia C. 1997. Intermediate sequences increase the detection of homology between sequences. J Mol Biol 273: 349-354.
    • (1997) J Mol Biol , vol.273 , pp. 349-354
    • Park, J.1    Teichmann, S.A.2    Hubbard, T.3    Chothia, C.4
  • 46
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson WR, Lipman DJ. 1988. Improved tools for biological sequence comparison. Proc Natl Acad Sei USA 85: 2444-2448.
    • (1988) Proc Natl Acad Sei USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 48
    • 33749197358 scopus 로고    scopus 로고
    • ProtParam_tpol: hUp:/www.expasy.ch/tooIs/protparam.html
    • ProtParam_tpol: hUp:/www.expasy.ch/tooIs/protparam.html
  • 49
    • 85101511266 scopus 로고    scopus 로고
    • Analysis and visualization of classifier performance: Comparison under imprecise class and cost distributions
    • Heckerman D, Mannila H, Pregibon D (eds). AAAI Press: Menlo Park, CA
    • Provost F, Fawcett T. 1997. Analysis and visualization of classifier performance: comparison under imprecise class and cost distributions. In Proceedings of KDD-97, Heckerman D, Mannila H, Pregibon D (eds). AAAI Press: Menlo Park, CA; 43-48.
    • (1997) Proceedings of KDD-97 , pp. 43-48
    • Provost, F.1    Fawcett, T.2
  • 51
    • 0000008691 scopus 로고    scopus 로고
    • Large-scale phenotypic analysis in microtitre plates of mutants with deleted open reading frames from yeast chromosome III: Key step between genomic sequencing and protein function
    • Crai AG, Joheisel DJ (eds). Academic Press: London
    • Rieger KJ, Orlowska G, Kaniak A, Coppee JY, Aljinovic G, Slonimski PP. 1999. Large-scale phenotypic analysis in microtitre plates of mutants with deleted open reading frames from yeast chromosome III: key step between genomic sequencing and protein function. In Methods in Microbiology 28 (Automation: Genomic and Functional Analysis), Crai AG, Joheisel DJ (eds). Academic Press: London; 205-227.
    • (1999) Methods in Microbiology 28 (Automation: Genomic and Functional Analysis) , pp. 205-227
    • Rieger, K.J.1    Orlowska, G.2    Kaniak, A.3    Coppee, J.Y.4    Aljinovic, G.5    Slonimski, P.P.6
  • 52
    • 0002374976 scopus 로고    scopus 로고
    • Neidhardt F el al. (eds). American Society for Microbiology: Washington DC
    • Riley M, Labedan B. 1996. E. coli gene products: physiological functions and common ancestries. In Escherichia coli and Salmonella: Cellular ami Molecular Biology, Neidhardt F el al. (eds). American Society for Microbiology: Washington DC; 2118-22002.
    • (1996) E. coli gene products: Physiological functions and common ancestries , pp. 2118-22002
    • Riley, M.1    Labedan, B.2
  • 53
    • 84866962928 scopus 로고    scopus 로고
    • SC_gene_list http://www.mips.biochem.mpg.de/proj/yeast/catalogues/index.html
  • 54
    • 0030660581 scopus 로고    scopus 로고
    • Genomic perspective on protein families
    • Tatusov RL, Koonin EV, Lipman DJA. 1997. Genomic perspective on protein families. Science 278: 631-637.
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.A.3
  • 55
    • 0032540981 scopus 로고    scopus 로고
    • Dynamic sequence databank searching with templates and multiple alignments
    • Taylor WR. 1998. Dynamic sequence databank searching with templates and multiple alignments. J Mol Biol 280: 375-406.
    • (1998) J Mol Biol , vol.280 , pp. 375-406
    • Taylor, W.R.1
  • 56
    • 84866954780 scopus 로고    scopus 로고
    • TB_genc_list http://www.sanger.ac.uk/Projects/M_tuberculosis/ gene_Iist_full.shtm


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.