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Volumn 22, Issue 5, 2012, Pages 594-601

Current challenges in genome annotation through structural biology and bioinformatics

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

EID: 84867747152     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2012.07.005     Document Type: Review
Times cited : (15)

References (71)
  • 2
    • 36448988254 scopus 로고    scopus 로고
    • Predicting protein function from sequence and structure
    • Lee D., Redfern O., Orengo C. Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol 2007, 8:995-1005.
    • (2007) Nat Rev Mol Cell Biol , vol.8 , pp. 995-1005
    • Lee, D.1    Redfern, O.2    Orengo, C.3
  • 3
    • 0033832615 scopus 로고    scopus 로고
    • Predicting protein function by genomic context: quantitative evaluation and qualitative inferences
    • Huynen M., Snel B., Lathe W., Bork P. Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res 2000, 10:1204-1210.
    • (2000) Genome Res , vol.10 , pp. 1204-1210
    • Huynen, M.1    Snel, B.2    Lathe, W.3    Bork, P.4
  • 4
    • 0037398732 scopus 로고    scopus 로고
    • Missing genes in metabolic pathways: a comparative genomics approach
    • Osterman A., Overbeek R. Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol 2003, 7:238-251.
    • (2003) Curr Opin Chem Biol , vol.7 , pp. 238-251
    • Osterman, A.1    Overbeek, R.2
  • 5
    • 55749094855 scopus 로고    scopus 로고
    • An integrated software system for analyzing ChIP-chip and ChIP-seq data
    • Ji H., Jiang H., Ma W., Johnson D.S., Myers R.M., Wong W.H. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 2008, 26:1293-1300.
    • (2008) Nat Biotechnol , vol.26 , pp. 1293-1300
    • Ji, H.1    Jiang, H.2    Ma, W.3    Johnson, D.S.4    Myers, R.M.5    Wong, W.H.6
  • 6
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: a revolutionary tool for transcriptomics
    • Wang Z., Gerstein M., Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63.
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 7
    • 2942572926 scopus 로고    scopus 로고
    • Quantifying the relationship between co-expression, co-regulation and gene function
    • Allocco D.J., Kohane I.S., Butte A.J. Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics 2004, 5:18.
    • (2004) BMC Bioinformatics , vol.5 , pp. 18
    • Allocco, D.J.1    Kohane, I.S.2    Butte, A.J.3
  • 8
    • 25444434087 scopus 로고    scopus 로고
    • AVID: an integrative framework for discovering functional relationships among proteins
    • Jiang T., Keating A.E. AVID: an integrative framework for discovering functional relationships among proteins. BMC Bioinformatics 2005, 6:136.
    • (2005) BMC Bioinformatics , vol.6 , pp. 136
    • Jiang, T.1    Keating, A.E.2
  • 10
    • 42449105845 scopus 로고    scopus 로고
    • In silico characterization of proteins: UniProt, InterPro and Integr8
    • Mulder N.J., Kersey P., Pruess M., Apweiler R. In silico characterization of proteins: UniProt, InterPro and Integr8. Mol Biotechnol 2008, 38:165-177.
    • (2008) Mol Biotechnol , vol.38 , pp. 165-177
    • Mulder, N.J.1    Kersey, P.2    Pruess, M.3    Apweiler, R.4
  • 13
    • 33846036096 scopus 로고    scopus 로고
    • The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
    • Berman H., Henrick K., Nakamura H., Markley J.L. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 2007, 35:D301-D303.
    • (2007) Nucleic Acids Res , vol.35
    • Berman, H.1    Henrick, K.2    Nakamura, H.3    Markley, J.L.4
  • 14
    • 34347394165 scopus 로고    scopus 로고
    • Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint
    • Marsden R.L., Lewis T.A., Orengo C.A. Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint. BMC Bioinformatics 2007, 8:86.
    • (2007) BMC Bioinformatics , vol.8 , pp. 86
    • Marsden, R.L.1    Lewis, T.A.2    Orengo, C.A.3
  • 15
    • 84984752764 scopus 로고    scopus 로고
    • Assignment of protein function in the postgenomic era
    • Saghatelian A., Cravatt B.F. Assignment of protein function in the postgenomic era. Nat Chem Biol 2005, 1:130-142.
    • (2005) Nat Chem Biol , vol.1 , pp. 130-142
    • Saghatelian, A.1    Cravatt, B.F.2
  • 16
    • 1542646982 scopus 로고    scopus 로고
    • Gene sharing, lens crystallins and speculations on an eye/ear evolutionary relationship
    • Piatigorsky J. Gene sharing, lens crystallins and speculations on an eye/ear evolutionary relationship. Integr Comp Biol 2003, 43:492-499.
    • (2003) Integr Comp Biol , vol.43 , pp. 492-499
    • Piatigorsky, J.1
  • 17
    • 84863639111 scopus 로고    scopus 로고
    • Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs
    • Altenhoff A.M., Studer R.A., Robinson-Rechavi M., Dessimoz C. Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs. PLoS Comput Biol 2012, 8:e1002514.
    • (2012) PLoS Comput Biol , vol.8
    • Altenhoff, A.M.1    Studer, R.A.2    Robinson-Rechavi, M.3    Dessimoz, C.4
  • 18
    • 22544441094 scopus 로고    scopus 로고
    • ProFunc: a server for predicting protein function from 3D structure
    • Laskowski R.A., Watson J.D., Thornton J.M. ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 2005, 33:W89-W93.
    • (2005) Nucleic Acids Res , vol.33
    • Laskowski, R.A.1    Watson, J.D.2    Thornton, J.M.3
  • 20
    • 0014800108 scopus 로고
    • Distinguishing homologous from analogous proteins
    • Fitch W.M. Distinguishing homologous from analogous proteins. Syst Zool 1970, 19:99-113.
    • (1970) Syst Zool , vol.19 , pp. 99-113
    • Fitch, W.M.1
  • 21
    • 79959828326 scopus 로고    scopus 로고
    • Testing the ortholog conjecture with comparative functional genomic data from mammals
    • Nehrt N.L., Clark W.T., Radivojac P., Hahn M.W. Testing the ortholog conjecture with comparative functional genomic data from mammals. PLoS Comput Biol 2011, 7:e1002073.
    • (2011) PLoS Comput Biol , vol.7
    • Nehrt, N.L.1    Clark, W.T.2    Radivojac, P.3    Hahn, M.W.4
  • 22
    • 34248155322 scopus 로고    scopus 로고
    • Function prediction of uncharacterized proteins
    • Hawkins T., Kihara D. Function prediction of uncharacterized proteins. J Bioinform Comput Biol 2007, 5:1-30.
    • (2007) J Bioinform Comput Biol , vol.5 , pp. 1-30
    • Hawkins, T.1    Kihara, D.2
  • 23
    • 20444456581 scopus 로고    scopus 로고
    • Automatic annotation of protein function
    • Valencia A. Automatic annotation of protein function. Curr Opin Struct Biol 2005, 15:267-274.
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 267-274
    • Valencia, A.1
  • 24
    • 13444266370 scopus 로고    scopus 로고
    • Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
    • Hamosh A., Scott A.F., Amberger J.S., Bocchini C.A., McKusick V.A. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2005, 33:D514-D517.
    • (2005) Nucleic Acids Res , vol.33
    • Hamosh, A.1    Scott, A.F.2    Amberger, J.S.3    Bocchini, C.A.4    McKusick, V.A.5
  • 25
    • 84858983547 scopus 로고    scopus 로고
    • KEGG for integration and interpretation of large-scale molecular data sets
    • Kanehisa M., Goto S., Sato Y., Furumichi M., Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2011, 40:D109-D114.
    • (2011) Nucleic Acids Res , vol.40
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3    Furumichi, M.4    Tanabe, M.5
  • 26
    • 33750267965 scopus 로고    scopus 로고
    • ORENZA: a web resource for studying ORphan ENZyme activities
    • Lespinet O., Labedan B. ORENZA: a web resource for studying ORphan ENZyme activities. BMC Bioinformatics 2006, 7:436.
    • (2006) BMC Bioinformatics , vol.7 , pp. 436
    • Lespinet, O.1    Labedan, B.2
  • 30
    • 35348817330 scopus 로고    scopus 로고
    • Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering
    • Browning S.R., Browning B.L. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 2007, 81:1084-1097.
    • (2007) Am J Hum Genet , vol.81 , pp. 1084-1097
    • Browning, S.R.1    Browning, B.L.2
  • 31
    • 67651222400 scopus 로고    scopus 로고
    • A flexible and accurate genotype imputation method for the next generation of genome-wide association studies
    • Howie B.N., Donnelly P., Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 2009, 5:e1000529.
    • (2009) PLoS Genet , vol.5
    • Howie, B.N.1    Donnelly, P.2    Marchini, J.3
  • 34
    • 33750353461 scopus 로고    scopus 로고
    • Predicting the effects of amino acid substitutions on protein function
    • Ng P.C., Henikoff S. Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet 2006, 7:61-80.
    • (2006) Annu Rev Genomics Hum Genet , vol.7 , pp. 61-80
    • Ng, P.C.1    Henikoff, S.2
  • 35
    • 22244437614 scopus 로고    scopus 로고
    • Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity
    • Stone E.A., Sidow A. Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. Genome Res 2005, 15:978-986.
    • (2005) Genome Res , vol.15 , pp. 978-986
    • Stone, E.A.1    Sidow, A.2
  • 37
    • 65649108490 scopus 로고    scopus 로고
    • Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods
    • Thusberg J., Vihinen M. Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods. Hum Mutat 2009, 30:703-714.
    • (2009) Hum Mutat , vol.30 , pp. 703-714
    • Thusberg, J.1    Vihinen, M.2
  • 38
    • 77954992105 scopus 로고    scopus 로고
    • AUTO-MUTE: web-based tools for predicting stability changes in proteins due to single amino acid replacements
    • Masso M., Vaisman I.I. AUTO-MUTE: web-based tools for predicting stability changes in proteins due to single amino acid replacements. Protein Eng Des Sel 2010, 23:683-687.
    • (2010) Protein Eng Des Sel , vol.23 , pp. 683-687
    • Masso, M.1    Vaisman, I.I.2
  • 39
    • 79959942908 scopus 로고    scopus 로고
    • SDM-a server for predicting effects of mutations on protein stability and malfunction
    • Worth C.L., Preissner R., Blundell T.L. SDM-a server for predicting effects of mutations on protein stability and malfunction. Nucleic Acids Res 2011, 39:W215-W222.
    • (2011) Nucleic Acids Res , vol.39
    • Worth, C.L.1    Preissner, R.2    Blundell, T.L.3
  • 42
    • 68149165614 scopus 로고    scopus 로고
    • Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
    • Kumar P., Henikoff S., Ng P.C. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 2009, 4:1073-1081.
    • (2009) Nat Protoc , vol.4 , pp. 1073-1081
    • Kumar, P.1    Henikoff, S.2    Ng, P.C.3
  • 43
    • 34547100092 scopus 로고    scopus 로고
    • SNAP: predict effect of non-synonymous polymorphisms on function
    • Bromberg Y., Rost B. SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res 2007, 35:3823-3835.
    • (2007) Nucleic Acids Res , vol.35 , pp. 3823-3835
    • Bromberg, Y.1    Rost, B.2
  • 44
    • 55549145156 scopus 로고    scopus 로고
    • In silico analysis of missense substitutions using sequence-alignment based methods
    • Tavtigian S.V., Greenblatt M.S., Lesueur F., Byrnes G.B. In silico analysis of missense substitutions using sequence-alignment based methods. Hum Mutat 2008, 29:1327-1336.
    • (2008) Hum Mutat , vol.29 , pp. 1327-1336
    • Tavtigian, S.V.1    Greenblatt, M.S.2    Lesueur, F.3    Byrnes, G.B.4
  • 50
    • 70349314263 scopus 로고    scopus 로고
    • Structural and functional restraints in the evolution of protein families and superfamilies
    • Gong S., Worth C.L., Bickerton G.R., Lee S., Tanramluk D., Blundell T.L. Structural and functional restraints in the evolution of protein families and superfamilies. Biochem Soc Trans 2009, 37:727-733.
    • (2009) Biochem Soc Trans , vol.37 , pp. 727-733
    • Gong, S.1    Worth, C.L.2    Bickerton, G.R.3    Lee, S.4    Tanramluk, D.5    Blundell, T.L.6
  • 52
    • 70349470948 scopus 로고    scopus 로고
    • Structural and functional constraints in the evolution of protein families
    • Worth C.L., Gong S., Blundell T.L. Structural and functional constraints in the evolution of protein families. Nat Rev Mol Cell Biol 2009, 10:709-720.
    • (2009) Nat Rev Mol Cell Biol , vol.10 , pp. 709-720
    • Worth, C.L.1    Gong, S.2    Blundell, T.L.3
  • 53
    • 78650895972 scopus 로고    scopus 로고
    • Loss-of-function variants in the genomes of healthy humans
    • MacArthur D.G., Tyler-Smith C. Loss-of-function variants in the genomes of healthy humans. Hum Mol Genet 2010, 19:R125-R130.
    • (2010) Hum Mol Genet , vol.19
    • MacArthur, D.G.1    Tyler-Smith, C.2
  • 54
    • 33746559647 scopus 로고    scopus 로고
    • Mutation in TRMU related to transfer RNA modification modulates the phenotypic expression of the deafness-associated mitochondrial 12S ribosomal RNA mutations
    • Guan M.X., Yan Q., Li X., Bykhovskaya Y., Gallo-Teran J., Hajek P., Umeda N., Zhao H., Garrido G., Mengesha E., et al. Mutation in TRMU related to transfer RNA modification modulates the phenotypic expression of the deafness-associated mitochondrial 12S ribosomal RNA mutations. Am J Hum Genet 2006, 79:291-302.
    • (2006) Am J Hum Genet , vol.79 , pp. 291-302
    • Guan, M.X.1    Yan, Q.2    Li, X.3    Bykhovskaya, Y.4    Gallo-Teran, J.5    Hajek, P.6    Umeda, N.7    Zhao, H.8    Garrido, G.9    Mengesha, E.10
  • 56
    • 70349901079 scopus 로고    scopus 로고
    • Stability effects of mutations and protein evolvability
    • Tokuriki N., Tawfik D.S. Stability effects of mutations and protein evolvability. Curr Opin Struct Biol 2009, 19:596-604.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 596-604
    • Tokuriki, N.1    Tawfik, D.S.2
  • 57
    • 66149102833 scopus 로고    scopus 로고
    • Modeling effects of human single nucleotide polymorphisms on protein-protein interactions
    • Teng S., Madej T., Panchenko A., Alexov E. Modeling effects of human single nucleotide polymorphisms on protein-protein interactions. Biophys J 2009, 96:2178-2188.
    • (2009) Biophys J , vol.96 , pp. 2178-2188
    • Teng, S.1    Madej, T.2    Panchenko, A.3    Alexov, E.4
  • 58
    • 69549111112 scopus 로고    scopus 로고
    • Correlating protein function and stability through the analysis of single amino acid substitutions
    • Bromberg Y., Rost B. Correlating protein function and stability through the analysis of single amino acid substitutions. BMC Bioinformatics 2009, 10(Suppl 8):S8.
    • (2009) BMC Bioinformatics , vol.10 , Issue.SUPPL. 8
    • Bromberg, Y.1    Rost, B.2
  • 59
    • 0036300807 scopus 로고    scopus 로고
    • Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties
    • Ferrer-Costa C., Orozco M., de la Cruz X. Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties. J Mol Biol 2002, 315:771-786.
    • (2002) J Mol Biol , vol.315 , pp. 771-786
    • Ferrer-Costa, C.1    Orozco, M.2    de la Cruz, X.3
  • 60
    • 33751541671 scopus 로고    scopus 로고
    • Characterization of compensated mutations in terms of structural and physico-chemical properties
    • Ferrer-Costa C., Orozco M., de la Cruz X. Characterization of compensated mutations in terms of structural and physico-chemical properties. J Mol Biol 2007, 365:249-256.
    • (2007) J Mol Biol , vol.365 , pp. 249-256
    • Ferrer-Costa, C.1    Orozco, M.2    de la Cruz, X.3
  • 63
    • 68049090922 scopus 로고    scopus 로고
    • Missing in action: enzyme functional annotations in biological databases
    • Furnham N., Garavelli J.S., Apweiler R., Thornton J.M. Missing in action: enzyme functional annotations in biological databases. Nat Chem Biol 2009, 5:521-525.
    • (2009) Nat Chem Biol , vol.5 , pp. 521-525
    • Furnham, N.1    Garavelli, J.S.2    Apweiler, R.3    Thornton, J.M.4
  • 64
    • 74549221383 scopus 로고    scopus 로고
    • Annotation error in public databases: misannotation of molecular function in enzyme superfamilies
    • Schnoes A.M., Brown S.D., Dodevski I., Babbitt P.C. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol 2009, 5:e1000605.
    • (2009) PLoS Comput Biol , vol.5
    • Schnoes, A.M.1    Brown, S.D.2    Dodevski, I.3    Babbitt, P.C.4
  • 66
    • 15944418238 scopus 로고    scopus 로고
    • Representing structure-function relationships in mechanistically diverse enzyme superfamilies
    • Pegg S.C., Brown S., Ojha S., Huang C.C., Ferrin T.E., Babbitt P.C. Representing structure-function relationships in mechanistically diverse enzyme superfamilies. Pac Symp Biocomput 2005, 35:8-369.
    • (2005) Pac Symp Biocomput , vol.35 , pp. 8-369
    • Pegg, S.C.1    Brown, S.2    Ojha, S.3    Huang, C.C.4    Ferrin, T.E.5    Babbitt, P.C.6
  • 67
    • 79958017886 scopus 로고    scopus 로고
    • Toward mechanistic classification of enzyme functions
    • Almonacid D.E., Babbitt P.C. Toward mechanistic classification of enzyme functions. Curr Opin Chem Biol 2011, 15:435-442.
    • (2011) Curr Opin Chem Biol , vol.15 , pp. 435-442
    • Almonacid, D.E.1    Babbitt, P.C.2


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