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Volumn 7, Issue 4, 2006, Pages

Benchmarking ortholog identification methods using functional genomics data

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; CONTROLLED STUDY; FUNCTIONAL GENOMICS; HUMAN; MOUSE; NONHUMAN; ORTHOLOGY; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN INTERACTION; QUALITY CONTROL; SENSITIVITY ANALYSIS; ALGORITHM; ANIMAL; EVALUATION; GENE EXPRESSION; GENE ORDER; GENETIC DATABASE; GENETICS; GENOMICS; METABOLISM; METHODOLOGY; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PHYSIOLOGY; PROTEIN ANALYSIS; SEQUENCE HOMOLOGY;

EID: 33745022802     PISSN: 1474760X     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2006-7-4-r31     Document Type: Article
Times cited : (129)

References (45)
  • 1
    • 0014800108 scopus 로고
    • Distinguishing homologous from analogous proteins
    • Fitch WM: Distinguishing homologous from analogous proteins. Syst Zool 1970, 19:99-113.
    • (1970) Syst Zool , vol.19 , pp. 99-113
    • Fitch, W.M.1
  • 2
    • 26444488575 scopus 로고    scopus 로고
    • Expression divergence between duplicate genes
    • Li WH, Yang J, Gu X: Expression divergence between duplicate genes. Trends Genet 2005, 21:602-607.
    • (2005) Trends Genet , vol.21 , pp. 602-607
    • Li, W.H.1    Yang, J.2    Gu, X.3
  • 3
    • 18144444203 scopus 로고    scopus 로고
    • Using orthologous and paralogous proteins to identify specificity determining residues
    • PREPRINT0002
    • Mirny LA, Gelfand MS: Using orthologous and paralogous proteins to identify specificity determining residues. Genome Biol 2002, 3:PREPRINT0002.
    • (2002) Genome Biol , vol.3
    • Mirny, L.A.1    Gelfand, M.S.2
  • 4
    • 33745044275 scopus 로고    scopus 로고
    • Chimpanzee sequencing whitepaper
    • Chimpanzee sequencing whitepaper [http://genome.wustl.edu/ ancillary/data/whitepapers/ Pan_troglodytes_WP2.pdf]
  • 5
    • 0033956060 scopus 로고    scopus 로고
    • The COG database: A tool for genome-scale analysis of protein functions and evolution
    • Tatusov RL, Galperin MY, Natale DA, Koonin EV: The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000, 28:33-36.
    • (2000) Nucleic Acids Res , vol.28 , pp. 33-36
    • Tatusov, R.L.1    Galperin, M.Y.2    Natale, D.A.3    Koonin, E.V.4
  • 6
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • Remm M, Storm CE. Sonnhammer EL: Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 2001, 314:1041-1052.
    • (2001) J Mol Biol , vol.314 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.2    Sonnhammer, E.L.3
  • 7
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • Li L, Stoeckert CJ Jr, Roos DS: OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003, 13:2178-2189.
    • (2003) Genome Res , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert Jr., C.J.2    Roos, D.S.3
  • 10
    • 0037407924 scopus 로고    scopus 로고
    • Predicting gene function by conserved co-expression
    • van Noort V, Snel B, Huynen MA: Predicting gene function by conserved co-expression. Trends Genet 2003, 19:238-242.
    • (2003) Trends Genet , vol.19 , pp. 238-242
    • van Noort, V.1    Snel, B.2    Huynen, M.A.3
  • 12
    • 0013017592 scopus 로고    scopus 로고
    • RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
    • Zmasek CM, Eddy SR: RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics 2002, 3:14.
    • (2002) BMC Bioinformatics , vol.3 , pp. 14
    • Zmasek, C.M.1    Eddy, S.R.2
  • 13
    • 3242677236 scopus 로고    scopus 로고
    • Comparative genomics for reliable protein-function prediction from genomic data
    • Huynen MA, Snel B, van Noort V: Comparative genomics for reliable protein-function prediction from genomic data. Trends Genet 2004, 20:340-344.
    • (2004) Trends Genet , vol.20 , pp. 340-344
    • Huynen, M.A.1    Snel, B.2    van Noort, V.3
  • 14
    • 1042280957 scopus 로고    scopus 로고
    • Phylogenomic inference of protein molecular function: Advances and challenges
    • Sjolander K: Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics 2004, 20:170-179.
    • (2004) Bioinformatics , vol.20 , pp. 170-179
    • Sjolander, K.1
  • 15
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • Stuart JM, Segal E, Koller D, Kim SK: A gene-coexpression network for global discovery of conserved genetic modules. Science 2003, 302:249-255.
    • (2003) Science , vol.302 , pp. 249-255
    • Stuart, J.M.1    Segal, E.2    Koller, D.3    Kim, S.K.4
  • 18
    • 33745016534 scopus 로고    scopus 로고
    • Protein World Webserver
    • Protein World Webserver [http://www.cmbi.ru.nl/pw]
  • 20
    • 13444306641 scopus 로고    scopus 로고
    • NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • (Database)
    • Pruitt KD, Tatusova T, Maglott DR: NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2005, 33(Database):D501-504.
    • (2005) Nucleic Acids Res , vol.33
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 22
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith TF, Waterman MS: Identification of common molecular subsequences. J Mol Biol 1981, 147:195-197.
    • (1981) J Mol Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 24
    • 0032568596 scopus 로고    scopus 로고
    • Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
    • Brenner SE, Chothia C, Hubbard TJ: Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci USA 1998, 95:6073-6078.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 6073-6078
    • Brenner, S.E.1    Chothia, C.2    Hubbard, T.J.3
  • 26
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson WR, Lipman DJ: Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988, 85:2444-2448.
    • (1988) Proc Natl Acad Sci USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 27
    • 33745036815 scopus 로고    scopus 로고
    • Center for Molecular and Biomolecular informatics
    • Center for Molecular and Biomolecular informatics [http://www.cmbi.ru.nl]
  • 28
    • 33745013959 scopus 로고    scopus 로고
    • InParanoid Program
    • InParanoid Program [http://inparanoid.cgb.ki.se/prog/inparanoid.tar.gz]
  • 29
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright AJ, Van Dongen S, Ouzounis CA: An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002, 30:1575-1584.
    • (2002) Nucleic Acids Res , vol.30 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 31
    • 33745014429 scopus 로고    scopus 로고
    • EnsMart v. 19.3 [ftp://ftp.ensembl.org/pub/current_mart]
    • EnsMart v. 19.3 [ftp://ftp.ensembl.org/pub/current_mart]
  • 32
    • 33644787447 scopus 로고    scopus 로고
    • OrthoMCL-DB: Querying a comprehensive multi-species collection of ortholog groups
    • (Database)
    • Chen F, Mackey AJ, Stoeckert CJ Jr, Roos DS: OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res 2006, 34(Database):D363-368.
    • (2006) Nucleic Acids Res , vol.34
    • Chen, F.1    Mackey, A.J.2    Stoeckert Jr., C.J.3    Roos, D.S.4
  • 33
    • 0027968068 scopus 로고
    • Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3    Clustal, W.4
  • 34
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4:406-425.
    • (1987) Mol Biol Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 35
    • 33745053212 scopus 로고    scopus 로고
    • Supplementary Data: Orthology Comparison
    • Supplementary Data: Orthology Comparison [http://www.cmbi.ru.nl/~timhulse/orthocomp]
  • 36
    • 33745049781 scopus 로고    scopus 로고
    • Gene Logic BioExpress Database Product
    • Gene Logic BioExpress Database Product [http://www.genelogic.com/genomics/bioexpress/]
  • 37
    • 0018874206 scopus 로고
    • Progress in medical information management. Systematized nomenclature of medicine (SNOMED)
    • Cote RA, Robboy S: Progress in medical information management. Systematized nomenclature of medicine (SNOMED). JAMA 1980, 243:756-762.
    • (1980) JAMA , vol.243 , pp. 756-762
    • Cote, R.A.1    Robboy, S.2
  • 38
    • 33745021956 scopus 로고    scopus 로고
    • Supplementary Data for Stuart et al. [15]
    • Supplementary Data for Stuart et al. [15] [http://cmgm.stanford.edu/~kimlab/multiplespecies/Data]
  • 40
    • 0036088133 scopus 로고    scopus 로고
    • DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions
    • Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, Eisenberg D: DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 2002, 30:303-305.
    • (2002) Nucleic Acids Res , vol.30 , pp. 303-305
    • Xenarios, I.1    Salwinski, L.2    Duan, X.J.3    Higney, P.4    Kim, S.M.5    Eisenberg, D.6
  • 41
    • 0034618661 scopus 로고    scopus 로고
    • Evidence for 14 homeobox gene clusters in human genome ancestry
    • Pollard SL, Holland PW: Evidence for 14 homeobox gene clusters in human genome ancestry. Curr Biol 2000, 10:1059-1062.
    • (2000) Curr Biol , vol.10 , pp. 1059-1062
    • Pollard, S.L.1    Holland, P.W.2
  • 42
    • 20444476656 scopus 로고    scopus 로고
    • Structural divergence and distant relationships in proteins: Evolution of the globins
    • Lecomte JT, Vuletich DA, Lesk AM: Structural divergence and distant relationships in proteins: evolution of the globins. Curr Opin Struct Biol 2005, 15:290-301.
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 290-301
    • Lecomte, J.T.1    Vuletich, D.A.2    Lesk, A.M.3
  • 43
    • 0347761358 scopus 로고    scopus 로고
    • Expression and function of conserved nuclear receptor genes in Caenorhabditis elegans
    • Gissendanner CR, Crossgrove K, Kraus KA, Maina CV, Sluder AE: Expression and function of conserved nuclear receptor genes in Caenorhabditis elegans. Dev Biol 2004, 266:399-416.
    • (2004) Dev Biol , vol.266 , pp. 399-416
    • Gissendanner, C.R.1    Crossgrove, K.2    Kraus, K.A.3    Maina, C.V.4    Sluder, A.E.5
  • 45
    • 0033564627 scopus 로고    scopus 로고
    • Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin
    • Salgado-Garrido J, Bragado-Nilsson E, Kandels-Lewis S, Seraphin B: Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin. EMBO J 1999, 18:3451-3462.
    • (1999) EMBO J , vol.18 , pp. 3451-3462
    • Salgado-Garrido, J.1    Bragado-Nilsson, E.2    Kandels-Lewis, S.3    Seraphin, B.4


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