Rapid Annotation of Anonymous Sequences from Genome Projects Using Semantic Similarities and a Weighting Scheme in Gene Ontology

PLoS ONE

Volumn 4, Issue 2, 2009, Pages

  Fontana, Paolo ^a   Cestaro, Alessandro ^a   Velasco, Riccardo ^a   Formentin, Elide ^b   Toppo, Stefano ^b  

^a RESEARCH AND INNOVATION CENTRE   (Italy)

^b UNIVERSITY OF PADOVA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84874396916     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0004619     Document Type: Article

References (48)

1. Tosatto SC, Toppo S, (2006) Large-scale prediction of protein structure and function from sequence. Curr Pharm Des 12: 2067-2086.
2. Jones CE, Baumann U, Brown AL, (2005) Automated methods of predicting the function of biological sequences using GO and BLAST. BMC Bioinformatics 6: 272.
3. Friedberg I, (2006) Automated protein function prediction-the genomic challenge. Brief Bioinform 7: 225-242.
4. Lee D, Redfern O, Orengo C, (2007) Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol 8: 995-1005.
5. The Gene Ontology project in 2008. Nucleic Acids Res 36: D440-444. (2008)
6. Hill DP, Smith B, McAndrews-Hill MS, Blake JA, (2008) Gene Ontology annotations: what they mean and where they come from. BMC Bioinformatics 9 (Suppl 5): S2.
7. Lee V, Camon E, Dimmer E, Barrell D, Apweiler R, (2005) 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.
8. Todd AE, Orengo CA, Thornton JM, (2001) Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 307: 1113-1143.
9. Tian W, Skolnick J, (2003) How well is enzyme function conserved as a function of pairwise sequence identity? J Mol Biol 333: 863-882.
10. Rost B, (2002) Enzyme function less conserved than anticipated. J Mol Biol 318: 595-608.
11. Sangar V, Blankenberg DJ, Altman N, Lesk AM, (2007) Quantitative sequence-function relationships in proteins based on gene ontology. BMC Bioinformatics 8: 294.
12. Myers CL, Barrett DR, Hibbs MA, Huttenhower C, Troyanskaya OG, (2006) Finding function: evaluation methods for functional genomic data. BMC Genomics 7: 187.
13. Godzik A, Jambon M, Friedberg I, (2007) Computational protein function prediction: are we making progress? Cell Mol Life Sci 64: 2505-2511.
14. King OD, Foulger RE, Dwight SS, White JV, Roth FP, (2003) Predicting gene function from patterns of annotation. Genome Res 13: 896-904.
15. 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.
16. Lord PW, Stevens RD, Brass A, Goble CA, (2003) Semantic similarity measures as tools for exploring the gene ontology. Pac Symp Biocomput pp. 601-612.
17. Tao Y, Sam L, Li J, Friedman C, Lussier YA, (2007) Information theory applied to the sparse gene ontology annotation network to predict novel gene function. Bioinformatics 23: i529-538.
18. Hirschman L, Yeh A, Blaschke C, Valencia A, (2005) Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinformatics 6 (Suppl 1): S1.
19. Altschul SF, Madden TL, Schaffer 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.
20. Martin DM, Berriman M, Barton GJ, (2004) GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics 5: 178.
21. Pesquita C, Faria D, Bastos H, Ferreira AE, Falcao AO, et al.(2008) Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinformatics 9 (Suppl 5): S4.
22. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, et al.(2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
23. Friedberg I, Harder T, Godzik A, (2006) JAFA: a protein function annotation meta-server. Nucleic Acids Res 34: W379-381.
24. Enault F, Suhre K, Claverie JM, (2005) Phydbac "Gene Function Predictor": a gene annotation tool based on genomic context analysis. BMC Bioinformatics 6: 247.
25. Groth D, Lehrach H, Hennig S, (2004) GOblet: a platform for Gene Ontology annotation of anonymous sequence data. Nucleic Acids Res 32: W313-317.
26. Hawkins T, Luban S, Kihara D, (2006) Enhanced automated function prediction using distantly related sequences and contextual association by PFP. Protein Sci 15: 1550-1556.
27. Mulder N, Apweiler R, (2007) InterPro and InterProScan: tools for protein sequence classification and comparison. Methods Mol Biol 396: 59-70.
28. Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, et al.(2007) A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2: e1326.
29. De Michele R, Formentin E, Todesco M, Toppo S, Carimi F, et al.(2009) Transcriptome analysis of Medicago truncatula leaf senescence: similarities and differences in metabolic and transcriptional regulations as compared with Arabidopsis, nodule senescence and nitric oxide signalling. New Phytol 181: 563-575.
30. Resnik P, (1999) Semantic similarity in a taxonomy: An information-based measure and its application to problems of ambiguity in natural language. Journal of Artificial Intelligence Research 11: 95-130.
31. Jiang JJ, Conrath DW, (1997) Semantic similarity based on corpus statistics and lexical taxonomy Taipei, Taiwan pp. 19-33.
32. Leacock C, Chodorow M, (1998) Combining Local Context and WordNet Similarity for Word Sense Identification. In: Fellbaum C, editors. WordNet: An Electronic Lexical Database Cambridge, MA MIT Press pp. 265-283.
33. Lin D, (1998) An Information-Theoretic Definition of Similarity. pp. 296-304 Proceedings of the Fifteenth International Conference on Machine Learning (ICML'98): Morgan Kaufmann Publishers Inc.
34. Guo X, Liu R, Shriver CD, Hu H, Liebman MN, (2006) Assessing semantic similarity measures for the characterization of human regulatory pathways. Bioinformatics 22: 967-973.
35. Wang JZ, Du Z, Payattakool R, Yu PS, Chen CF, (2007) A new method to measure the semantic similarity of GO terms. Bioinformatics 23: 1274-1281.
36. Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, et al.(2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res 36: D577-581.
37. Jones CE, Brown AL, Baumann U, (2007) Estimating the annotation error rate of curated GO database sequence annotations. BMC Bioinformatics 8: 170.
38. Li W, Godzik A, (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659.
39. Parrish JR, Gulyas KD, Finley RL Jr, (2006) Yeast two-hybrid contributions to interactome mapping. Curr Opin Biotechnol 17: 387-393.
40. Buza TJ, McCarthy FM, Wang N, Bridges SM, Burgess SC, (2008) Gene Ontology annotation quality analysis in model eukaryotes. Nucleic Acids Res 36: e12.
41. Eichinger L, Pachebat JA, Glockner G, Rajandream MA, Sucgang R, et al.(2005) The genome of the social amoeba Dictyostelium discoideum. Nature 435: 43-57.
42. Majer F, Schmid DG, Altena K, Bierbaum G, Kupke T, (2002) The flavoprotein MrsD catalyzes the oxidative decarboxylation reaction involved in formation of the peptidoglycan biosynthesis inhibitor mersacidin. J Bacteriol 184: 1234-1243.
43. Kimura M, Ishihama A, (2004) Tfg3, a subunit of the general transcription factor TFIIF in Schizosaccharomyces pombe, functions under stress conditions. Nucleic Acids Res 32: 6706-6715.
44. Joshi T, Xu D, (2007) Quantitative assessment of relationship between sequence similarity and function similarity. BMC Genomics 8: 222.
45. Sasson O, Kaplan N, Linial M, (2006) Functional annotation prediction: all for one and one for all. Protein Sci 15: 1557-1562.
46. Verspoor K, Cohn J, Mniszewski S, Joslyn C, (2006) A categorization approach to automated ontological function annotation. Protein Sci 15: 1544-1549.
47. Park JC, Kim TE, Park J, (2008) Monitoring the evolutionary aspect of the Gene Ontology to enhance predictability and usability. BMC Bioinformatics 9 (Suppl 3): S7.
48. Rodrigues AP, Grant BJ, Godzik A, Friedberg I, (2007) The 2006 automated function prediction meeting. BMC Bioinformatics 8 (Suppl 4): S1-4.