메뉴 건너뛰기




Volumn 25, Issue 1, 2006, Pages 1-8

From sequences to a functional unit

Author keywords

Component proteins; Composite proteins; Drug discovery; Family; Functional annotation; Gene fusion; Subfamily; Superfamily

Indexed keywords

GENE PRODUCT; PROTEIN;

EID: 33645792606     PISSN: 10948341     EISSN: 15312267     Source Type: Journal    
DOI: 10.1152/physiolgenomics.00166.2005     Document Type: Review
Times cited : (1)

References (52)
  • 4
    • 0033119399 scopus 로고    scopus 로고
    • Errors in genome annotation
    • Brenner SE. Errors in genome annotation. Trends Genet 15: 132-133, 1999.
    • (1999) Trends Genet , vol.15 , pp. 132-133
    • Brenner, S.E.1
  • 5
    • 0030983386 scopus 로고    scopus 로고
    • Population statistics of protein structures: Lessons from structural classifications
    • Brenner SE, Clothia C, and Hubbard TJ. Population statistics of protein structures: lessons from structural classifications. Curr Opin Struct Biol 7: 369-376, 1997.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 369-376
    • Brenner, S.E.1    Clothia, C.2    Hubbard, T.J.3
  • 6
    • 2642524299 scopus 로고    scopus 로고
    • Gene Ontology Annotation Database - An integrated resource of GO annotations to the UniProt Knowledgebase
    • Camon E, Barrell D, Lee V, Dimmer E and Apweiler R. Gene Ontology Annotation Database - an integrated resource of GO annotations to the UniProt Knowledgebase. In Silico Biol 4: 5-6, 2004.
    • (2004) In Silico Biol , vol.4 , pp. 5-6
    • Camon, E.1    Barrell, D.2    Lee, V.3    Dimmer, E.4    Apweiler, R.5
  • 7
    • 0029587166 scopus 로고
    • A method to predict functional residues in proteins
    • Casari G, Sander C, and Valencia A. A method to predict functional residues in proteins. Nat Struct Biol 2: 171-178, 1995.
    • (1995) Nat Struct Biol , vol.2 , pp. 171-178
    • Casari, G.1    Sander, C.2    Valencia, A.3
  • 8
    • 0027122748 scopus 로고
    • Proteins. One thousand families for the molecular biologist
    • Chothia C. Proteins. One thousand families for the molecular biologist. Nature 357: 543-544, 1992.
    • (1992) Nature , vol.357 , pp. 543-544
    • Chothia, C.1
  • 9
    • 0036795417 scopus 로고    scopus 로고
    • Crystallization and preliminary X-ray diffraction analysis of recombinant hydrolase domain of 10-formyltetrahydrofolate dehydrogenase
    • Chumanevich AA, Davies C, and Krupenko SA. Crystallization and preliminary X-ray diffraction analysis of recombinant hydrolase domain of 10-formyltetrahydrofolate dehydrogenase. Acta Crystallogr D58: 1841-1842, 2002.
    • (2002) Acta Crystallogr , vol.D58 , pp. 1841-1842
    • Chumanevich, A.A.1    Davies, C.2    Krupenko, S.A.3
  • 10
    • 0034163439 scopus 로고    scopus 로고
    • Horizontal gene transfer and the origin of species: Lessons from bacteria
    • De la Cruz F and Davies J. Horizontal gene transfer and the origin of species: lessons from bacteria. Trends Microbiol 8: 128-133, 2000.
    • (2000) Trends Microbiol , vol.8 , pp. 128-133
    • De La Cruz, F.1    Davies, J.2
  • 11
    • 0027364941 scopus 로고
    • Evolutionary mobile modules in proteins
    • Doolittle RF and Bork P. Evolutionary mobile modules in proteins. Sci Am 269: 50-56, 1993.
    • (1993) Sci Am , vol.269 , pp. 50-56
    • Doolittle, R.F.1    Bork, P.2
  • 12
    • 0033523989 scopus 로고    scopus 로고
    • Protein interaction maps for complete genomes based on gene fusion events
    • Enright AJ, Iliopoulos I, Kyrpides NC, and Ouzounis CA. Protein interaction maps for complete genomes based on gene fusion events. Nature 402: 86-90, 1999.
    • (1999) Nature , vol.402 , pp. 86-90
    • Enright, A.J.1    Iliopoulos, I.2    Kyrpides, N.C.3    Ouzounis, C.A.4
  • 13
    • 0035159831 scopus 로고    scopus 로고
    • Fusion of the BCR and the fibroblast growth factor receptor-1 (FGFR1) genes as a result of t(8;22)(p11;q11) in a myeloproliferative disorder: The first fusion gene involving BCR but not ABL
    • Fioretos T, Panagopoulos I, Lassen C, Swedin A, Billstrom R, Isaksson M, Strombeck B, Olofsson T, Mitelman F, and Johansson B. Fusion of the BCR and the fibroblast growth factor receptor-1 (FGFR1) genes as a result of t(8;22)(p11;q11) in a myeloproliferative disorder: the first fusion gene involving BCR but not ABL. Genes Chromosomes Cancer 32: 302-310, 2001.
    • (2001) Genes Chromosomes Cancer , vol.32 , pp. 302-310
    • Fioretos, T.1    Panagopoulos, I.2    Lassen, C.3    Swedin, A.4    Billstrom, R.5    Isaksson, M.6    Strombeck, B.7    Olofsson, T.8    Mitelman, F.9    Johansson, B.10
  • 14
    • 0032229196 scopus 로고    scopus 로고
    • Sources of systematic error in functional annotation of genomes: Domain rearrangement, non-orthologous gene displacement and operon disruption
    • Galperin MY and Koonin EV. Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption. In Silico Biol 1: 55-67, 1998.
    • (1998) In Silico Biol , vol.1 , pp. 55-67
    • Galperin, M.Y.1    Koonin, E.V.2
  • 15
    • 0034923923 scopus 로고    scopus 로고
    • Divergent evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct suprafamilies
    • Gerlt JA and Babbitt PC. Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu Rev Biochem 70: 209-246, 2001.
    • (2001) Annu Rev Biochem , vol.70 , pp. 209-246
    • Gerlt, J.A.1    Babbitt, P.C.2
  • 17
    • 0037968852 scopus 로고    scopus 로고
    • Functional divergence in protein (family) sequence evolution
    • Gu X. Functional divergence in protein (family) sequence evolution. Genetica 118: 133-141, 2003.
    • (2003) Genetica , vol.118 , pp. 133-141
    • Gu, X.1
  • 18
    • 13444250007 scopus 로고    scopus 로고
    • ADDA: A domain database with global coverage of the protein universe
    • Heger A, Wilton CA, Sivakumar A, and Holm L. ADDA: a domain database with global coverage of the protein universe. Nucleic Acids Res 33: D188-D191, 2005.
    • (2005) Nucleic Acids Res , vol.33
    • Heger, A.1    Wilton, C.A.2    Sivakumar, A.3    Holm, L.4
  • 19
    • 1642445486 scopus 로고    scopus 로고
    • Sensitive pattern discovery with "fuzzy" alignments of distantly related proteins
    • Heger A and Holm L. Sensitive pattern discovery with "fuzzy" alignments of distantly related proteins. Bioinformatics 19, Suppl 1: I130 -I137, 2003.
    • (2003) Bioinformatics , vol.19 , Issue.1 SUPPL.
    • Heger, A.1    Holm, L.2
  • 20
    • 8444243745 scopus 로고    scopus 로고
    • Accurate detection of very sparse sequence motifs
    • Heger A, Lappe M, and Holm L. Accurate detection of very sparse sequence motifs. J Comput Biol 11: 843-857, 2004.
    • (2004) J Comput Biol , vol.11 , pp. 843-857
    • Heger, A.1    Lappe, M.2    Holm, L.3
  • 21
    • 0034767547 scopus 로고    scopus 로고
    • Annotation transfer for genomics: Measuring functional divergence in multi-domain proteins
    • Hegyi H and Gerstein M. Annotation transfer for genomics: measuring functional divergence in multi-domain proteins. Genome Res 11: 1632-1640, 2001.
    • (2001) Genome Res , vol.11 , pp. 1632-1640
    • Hegyi, H.1    Gerstein, M.2
  • 23
    • 4944225083 scopus 로고    scopus 로고
    • Remote homology detection: A motif based approach
    • Hur A and Burtlag D. Remote homology detection: a motif based approach. Bioinformatics 19, Suppl 1: 26-33, 2003.
    • (2003) Bioinformatics , vol.19 , Issue.1 SUPPL. , pp. 26-33
    • Hur, A.1    Burtlag, D.2
  • 25
    • 0025765803 scopus 로고
    • SH2 and SH3 domains: Elements that control interactions of cytoplasmic signaling proteins
    • Koch CA, Anderson D, Moran MF, Ellis C, and Pawson T. SH2 and SH3 domains: elements that control interactions of cytoplasmic signaling proteins. Science 252: 668-674, 1991.
    • (1991) Science , vol.252 , pp. 668-674
    • Koch, C.A.1    Anderson, D.2    Moran, M.F.3    Ellis, C.4    Pawson, T.5
  • 26
    • 0033767381 scopus 로고    scopus 로고
    • Two genes become one: The genes encoding heterochromatin protein SU(VAR)3-9 and translation initiation factor subunit elF-2 are joined to a dicistronic unit in holometabolic insects
    • Kraussa V and Reutera G. Two genes become one: the genes encoding heterochromatin protein SU(VAR)3-9 and translation initiation factor subunit elF-2 are joined to a dicistronic unit in holometabolic insects. Genetics 156: 1157-1167, 2000.
    • (2000) Genetics , vol.156 , pp. 1157-1167
    • Kraussa, V.1    Reutera, G.2
  • 27
    • 3242810318 scopus 로고    scopus 로고
    • MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
    • Kumar S, Tamura K, and Nei M. MEGA3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5: 150-163, 2004.
    • (2004) Brief Bioinform , vol.5 , pp. 150-163
    • Kumar, S.1    Tamura, K.2    Nei, M.3
  • 28
    • 0036598066 scopus 로고    scopus 로고
    • Gene transfer in bacteria: Speciation without species?
    • Lawrence JG. Gene transfer in bacteria: speciation without species? Theor Popul Biol 61: 449-460, 2002.
    • (2002) Theor Popul Biol , vol.61 , pp. 449-460
    • Lawrence, J.G.1
  • 29
    • 19944402235 scopus 로고    scopus 로고
    • Who tangos with GOA? Use of Gene Ontology Annotation (GOA) for biological interpretation of "-omics" data and for validation of automatic annotation tools
    • Lee V, Camon E, Dimmer E, Barrell D, and Apweiler R. Who tangos with GOA? Use of Gene Ontology Annotation (GOA) for biological interpretation of "-omics" data and for validation of automatic annotation tools. In Silico Biol 5: 5-8, 2005.
    • (2005) In Silico Biol , vol.5 , pp. 5-8
    • Lee, V.1    Camon, E.2    Dimmer, E.3    Barrell, D.4    Apweiler, R.5
  • 30
    • 0036699189 scopus 로고    scopus 로고
    • Sequence clustering strategies improve homology recognitions while reducing search times
    • Li W, Jaroszewski L, and Godzik A. Sequence clustering strategies improve homology recognitions while reducing search times. Protein Eng 15: 643-649, 2002.
    • (2002) Protein Eng , vol.15 , pp. 643-649
    • Li, W.1    Jaroszewski, L.2    Godzik, A.3
  • 31
    • 0036358890 scopus 로고    scopus 로고
    • Physiological genomics of Escherichia coli protein families
    • Liang P, Labedan B, and Riley M. Physiological genomics of Escherichia coli protein families. Physiol Genomics 9: 15-26, 2002.
    • (2002) Physiol Genomics , vol.9 , pp. 15-26
    • Liang, P.1    Labedan, B.2    Riley, M.3
  • 33
    • 0242354129 scopus 로고    scopus 로고
    • The origin of new genes: Glimpses from the young and old
    • Long M, Betran E, Thornton K, and Wang W. The origin of new genes: glimpses from the young and old. Nat Genet 4: 865-875, 2003.
    • (2003) Nat Genet , vol.4 , pp. 865-875
    • Long, M.1    Betran, E.2    Thornton, K.3    Wang, W.4
  • 34
  • 36
    • 0036352010 scopus 로고    scopus 로고
    • Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors
    • Mirny LA and Gelfand MS. Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors. J Mol Biol 321: 7-20, 2002.
    • (2002) J Mol Biol , vol.321 , pp. 7-20
    • Mirny, L.A.1    Gelfand, M.S.2
  • 37
    • 0034883978 scopus 로고    scopus 로고
    • Divergence of function in sequence-related groups of Escherichia coli proteins
    • Nahum LA and Riley M. Divergence of function in sequence-related groups of Escherichia coli proteins. Genome Res 11: 1375-1381, 2001.
    • (2001) Genome Res , vol.11 , pp. 1375-1381
    • Nahum, L.A.1    Riley, M.2
  • 39
    • 0842346438 scopus 로고    scopus 로고
    • Specificity in signal transduction: From phosphotyrosine-SH2 domain interactions to complex cellular systems
    • Pawson T. Specificity in signal transduction: from phosphotyrosine-SH2 domain interactions to complex cellular systems. Cell 116: 191-203, 2004.
    • (2004) Cell , vol.116 , pp. 191-203
    • Pawson, T.1
  • 40
    • 0031684427 scopus 로고    scopus 로고
    • . Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm
    • Rigoutsos I and Floratos A. Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm. Bioinformatics 14: 55-67, 1998.
    • (1998) Bioinformatics , vol.14 , pp. 55-67
    • Rigoutsos, I.1    Floratos, A.2
  • 41
    • 0031584266 scopus 로고    scopus 로고
    • Protein evolution viewed through Escherichia coli protein sequences: Introducing the notion of a structural segment of homology, the module
    • Riley M and Labedan B. Protein evolution viewed through Escherichia coli protein sequences: introducing the notion of a structural segment of homology, the module. J Mol Biol 268: 857-868, 1997.
    • (1997) J Mol Biol , vol.268 , pp. 857-868
    • Riley, M.1    Labedan, B.2
  • 44
    • 0347125234 scopus 로고    scopus 로고
    • GenProtEC: An updated and improved analysis of functions of Escherichia coli K-12 proteins
    • Serres MH, Goswami S, and Riley M. GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins. Nucleic Acids Res 32: D300-D302, 2004.
    • (2004) Nucleic Acids Res , vol.32
    • Serres, M.H.1    Goswami, S.2    Riley, M.3
  • 45
    • 13844255774 scopus 로고    scopus 로고
    • Structural domains, protein modules, and sequence similarities enrich our understanding of the Shewanella oneidensis MR-1 proteome
    • Serres M and Riley M. Structural domains, protein modules, and sequence similarities enrich our understanding of the Shewanella oneidensis MR-1 proteome. OMICS 8: 306-321, 2004.
    • (2004) OMICS , vol.8 , pp. 306-321
    • Serres, M.1    Riley, M.2
  • 46
    • 0031604140 scopus 로고    scopus 로고
    • Phylogenetic inference in protein superfamilies: Analysis of the SH2 domains
    • Sjolander K. Phylogenetic inference in protein superfamilies: analysis of the SH2 domains. Proc Int Conf Intell Syst Mol Biol 6: 165-174, 1998.
    • (1998) Proc Int Conf Intell Syst Mol Biol , vol.6 , pp. 165-174
    • Sjolander, K.1
  • 49
    • 0141730411 scopus 로고    scopus 로고
    • Evolution thinks modular
    • Vespignani A. Evolution thinks modular. Nat Genet 35: 118-119, 2003.
    • (2003) Nat Genet , vol.35 , pp. 118-119
    • Vespignani, A.1
  • 50
    • 0037106541 scopus 로고    scopus 로고
    • Density of points clustering, application to transcriptomic data analysis
    • Wicker N, Dembele D, Raffelsbeger W, and Poch O. Density of points clustering, application to transcriptomic data analysis. Nucleic Acids Res 30: 3992-4000, 2002.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3992-4000
    • Wicker, N.1    Dembele, D.2    Raffelsbeger, W.3    Poch, O.4
  • 51
    • 0034897827 scopus 로고    scopus 로고
    • Secator: A program for inferring protein sub-families from phylogenetic trees
    • Wicker N, Perrin GR, Thierry JC, and Poch O. Secator: a program for inferring protein sub-families from phylogenetic trees. Mol Biol Evol 18: 1435-1441, 2001.
    • (2001) Mol Biol Evol , vol.18 , pp. 1435-1441
    • Wicker, N.1    Perrin, G.R.2    Thierry, J.C.3    Poch, O.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.