A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions

PLoS ONE

Volumn 4, Issue 10, 2009, Pages

  Louie, Brenton ^a,b   Higdon, Roger ^a,b   Kolker, Eugene ^a,b  

^a SEATTLE CHILDREN S RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; MATHEMATICAL ANALYSIS; PREDICTION; PROTEIN DATABASE; PROTEIN FUNCTION; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STATISTICAL MODEL; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; METHODOLOGY; MOLECULAR GENETICS; PROTEIN ANALYSIS; SEQUENCE ANALYSIS;

PROTEIN;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; PROTEIN INTERACTION MAPPING; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 70449552832     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0007546     Document Type: Article

References (52)

1. Galperin MY, Koonin EV (1998) Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption. In Silico Biol. (Gedrukt) 1: 55-67.
2. Karp PD (1998) What we do not know about sequence analysis and sequence databases. Bioinformatics 14: 753-754.
3. Brenner SE (1999) Errors in genome annotation. Trends in Genetics 15: 132-133. doi:10.1016/S0168-9525(99)01706-0.
4. Thomas GH (1999) Completing the E. coli proteome: a database of gene products characterised since the completion of the genome sequence. Bioinformatics 15: 860-861.
5. Bork P (2000) Powers and pitfalls in sequence analysis: the 70% hurdle. Genome Res 10: 398-400.
6. Devos D, Valencia A (2000) Practical limits of function prediction. Proteins: Structure, Function, and Genetics 41: 98-107. doi:10.1002/ 1097-0134(20001001)41:1,98::AID-PROT120.3.0.CO;2-S.
7. Wilson CA, Kreychman J, Gerstein M (2000) Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores1. Journal of Molecular Biology 297: 233-249. doi:10.1006/jmbi.2000.3550.
8. Hegyi H, Gerstein M (2001) Annotation Transfer for Genomics: Measuring Functional Divergence in Multi-Domain Proteins. Genome Res 11: 1632-1640. doi:10.1101/gr.183801.
9. Gilks WR, Audit B, De Angelis D, Tsoka S, Ouzounis CA (2002) Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics 18: 1641-1649. doi:10.1093/bioinformatics/18.12.1641.
10. Ouzounis C, Karp P (2002) The past, present and future of genome-wide reannotation. Genome Biology 3: comment2001.1-comment2001.6. doi:10.1186/ gb-2002-3-2-comment2001.
11. Koonin EV, Galperin MY (2003) Sequence - evolution - function. Springer.
12. Iliopoulos I, Tsoka S, Andrade MA, Enright AJ, Carroll M, et al. (2003) Evaluation of annotation strategies using an entire genome sequence. Bioinformatics 19: 717-726. doi:10.1093/bioinformatics/btg077.
13. Kolker E, Purvine S, Galperin MY, Stolyar S, Goodlett DR, et al. (2003) Initial Proteome Analysis of Model Microorganism Haemophilus influenzae Strain Rd KW20. J Bacteriol 185: 4593-4602. doi:10.1128/ JB.185.15.4593-4602.2003.
14. Kolker E, Makarova KS, Shabalina S, Picone AF, Purvine S, et al. (2004) Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. Nucl Acids Res 32: 2353-2361. doi:10.1093/nar/ gkh555.
15. Raghunathan A, Price ND, Galperin MY, Makarova KS, Purvine S, et al. (2004) In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium. OMICS 8: 25-41. doi:10.1089/ 153623104773547471.
16. Roberts RJ (2004) Identifying Protein Function - A Call for Community Action. PLoS Biol 2: e42. doi:10.1371/journal.pbio.0020042.
17. Kolker E, Picone AF, Galperin MY, Romine MF, Higdon R, et al. (2005) Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations. Proceedings of the National Academy of Sciences of the United States of America 102: 2099-2104. doi:10.1073/pnas.0409111102.
18. Valencia A (2005) Automatic annotation of protein function. Current Opinion in Structural Biology 15: 267-274. doi:10.1016/j.sbi.2005.05.010.
19. Galperin MY, Kolker E (2006) New metrics for comparative genomics. Current Opinion in Biotechnology 17: 440-447. doi:10.1016/ j.copbio.2006.08.007.
20. Frishman D (2007) Protein Annotation at Genomic Scale: The Current Status. Chemical Reviews 107: 3448-3466. doi:10.1021/cr068303k.
21. Lee TJ, Paulsen I, Karp P (2008) Annotation-based inference of transporter function. Bioinformatics 24: i259-267. doi:10.1093/ bioinformatics/btn180.
22. Louie B, Tarczy-Hornoch P, Higdon R, Kolker E (2008) Validating annotations for uncharacterized proteins in Shewanella oneidensis. OMICS 12: 211-215. doi:10.1089/omi.2008.0051.
23. Frishman D, Valencia A (2008) Modern Genome Annotation: The Biosapiens Network. 1st ed. Springer.
24. Karp PD, Paley S, Zhu J (2001) Database verification studies of SWISS-PROT and GenBank. Bioinformatics 17: 526-532. doi:10.1093/ bioinformatics/17.6.526.
25. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
26. Ye J, McGinnis S, Madden TL (2006) BLAST: improvements for better sequence analysis. Nucl Acids Res 34: W6-9. doi:10.1093/nar/gkl164.
27. Smith T, Waterman M (1981) Identification of common molecular subsequences. J Mol Biol 147: 197, 195.
28. Henikoff S, Henikoff JG (1994) Protein Family Classification Based on Searching a Database of Blocks. Genomics 19: 97-107. doi:10.1006/ geno.1994.1018.
29. Gough J, Karplus K, Hughey R, Chothia C (2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structurel. Journal of Molecular Biology 313: 903-919. doi:10.1006/jmbi.2001.5080.
30. Martin D, Berriman M, Barton G (2004) GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics 5: 178. doi:10.1186/1471-2105-5-178.
31. Deonier RC, Tavaré S, Waterman MS (2005) Computational Genome Analysis: An Introduction. Springer.
32. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, et al. (2009) InterPro: the integrative protein signature database. Nucl Acids Res 37: D211-215. doi:10.1093/nar/gkn785.
33. Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, et al. (2009) CDD: specific functional annotation with the Conserved Domain Database. Nucl Acids Res 37: D205-210. doi:10.1093/nar/gkn845.
34. Devos D, Valencia A (2001) Intrinsic errors in genome annotation. Trends in Genetics 17: 429-431. doi:10.1016/S0168-9525(01)02348-4.
35. Frishman D, Albermann K, Hani J, Heumann K, Metanomski A, et al. (2001) Functional and structural genomics using PEDANT. Bioinformatics 17: 44-57.
36. Jones C, Brown A, Baumann U (2007) Estimating the annotation error rate of curated GO database sequence annotations. BMC Bioinformatics 8: 170. doi:10.1186/1471-2105-8-170.
37. Joshi T, Xu D (2007) Quantitative assessment of relationship between sequence similarity and function similarity. BMC Genomics 8: 222. doi:10.1186/1471-2164-8-222.
38. Sangar V, Blankenberg DJ, Altman N, Lesk AM (2007) Quantitative sequence-function relationships in proteins based on gene ontology. BMC Bioinformatics 8: 294. doi:10.1186/1471-2105-8-294.
39. Addou S, Rentzsch R, Lee D, Orengo CA (2009) Domain-Based and Family-Specific Sequence Identity Thresholds Increase the Levels of Reliable Protein Function Transfer. Journal of Molecular Biology 387: 416-430. doi:10.1016/j.jmb.2008.12.045.
40. Rost B (1999) Twilight zone of protein sequence alignments. Protein Eng 12: 85-94. doi:10.1093/protein/12.2.85.
41. Galperin MY, Koonin EV (2004) 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucl Acids Res 32: 5452-5463. doi:10.1093/nar/gkh885.
42. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene Ontology: tool for the unification of biology. Nat Genet 25: 25-29. doi:10.1038/75556.
43. Lord PW, Stevens RD, Brass A, Goble CA (2003) Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 19: 1275-1283. doi:10.1093/ bioinformatics/btg153.
44. McGinnis S, Madden TL (2004) BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucl Acids Res 32: W20-25. doi:10.1093/nar/gkh435.
45. Maglott D, Ostell J, Pruitt KD, Tatusova T (2005) Entrez Gene: gene-centered information at NCBI. Nucl Acids Res 33: D54-58. doi:10.1093/nar/gki031.
46. Camon E, Magrane M, Barrell D, Lee V, Dimmer E, et al. (2004) The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucl Acids Res 32: D262-266. doi:10.1093/nar/gkh021.
47. Pruitt KD, Tatusova T, Maglott DR (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35: D61-D65. doi:10.1093/nar/ gkl842.
48. Hastie T, Friedman J, Tibshirani R (2007) The Elements of Statistical Learning. Springer.
49. Pesquita C, Faria D, Bastos H, Ferreira A, Falcao A, et al. (2008) Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinformatics 9: S4. doi:10.1186/1471-2105-9-S5-S4.
50. Lin D (1998) An Information-Theoretic Definition of Similarity. IN PROCEEDINGS OF THE 15TH INTERNATIONAL CONFERENCE ON MACHINE LEARNING: 296-304.
51. McCullagh P, Nelder JA (1989) Generalized Linear Models, Second Edition. 2nd ed. Chapman & Hall/CRC.
52. Akaike H (1974) A new look at the statistical model identification. Automatic Control, IEEE Transactions on 19: 723, 716.