Computational prediction of protein function based on weighted mapping of domains and GO terms

BioMed Research International

Volumn 2014, Issue , 2014, Pages

  Teng, Zhixia ^a,b   Guo, Maozu ^a   Dai, Qiguo ^a   Wang, Chunyu ^a   Li, Jin ^a,c   Liu, Xiaoyan ^a  

^a HARBIN INSTITUTE OF TECHNOLOGY   (China)

^b NORTHEAST FORESTRY UNIVERSITY   (China)

^c HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; FACTUAL DATABASE; GENE ONTOLOGY; MATHEMATICAL PARAMETERS; NUCLEOTIDE SEQUENCE; PREDICTION; PROBABILITY; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FUNCTION; SEEKFUN METHOD; WEIGHTED MAPPING; ALGORITHM; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; PHYSIOLOGY; PROCEDURES; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE; PROTEOMICS; REPRODUCIBILITY; STATISTICAL MODEL;

PROTEIN;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MODELS, STATISTICAL; PROBABILITY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 84901278025     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2014/641469     Document Type: Article

References (42)

1. Barrell D., Dimmer E., Huntley R. P., Binns D., O'Donovan C., Apweiler R., The GOA database in 2009-an integrated Gene Ontology Annotation resource. Nucleic Acids Research 2009 37 1 D396 D403 2-s2.0-58149187893 10.1093/nar/gkn803
2. Hennig S., Groth D., Lehrach H., Automated gene ontology annotation for anonymous sequence data. Nucleic Acids Research 2003 31 13 3712 3715 2-s2.0-0041620215 10.1093/nar/gkg582 (Pubitemid 37442229)
3. Khan S., Situ G., Decker K., Schmidt C. J., GoFigure: automated gene ontology annotation. Bioinformatics 2003 19 18 2484 2485 2-s2.0-0348143187 10.1093/bioinformatics/btg338 (Pubitemid 38016653)
4. Zehetner G., OntoBlast function: from sequence similarities directly to potential functional annotations by ontology terms. Nucleic Acids Research 2003 31 13 3799 3803 2-s2.0-0043122923 10.1093/nar/gkg555 (Pubitemid 37442250)
5. Martin D. M. A., Berriman M., Barton G. J., GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics 2004 5, article 178 2-s2.0-13244268370 10.1186/1471-2105-5-178 (Pubitemid 40195331)
6. Hawkins T., Luban S., Kihara D., Enhanced automated function prediction using distantly related sequences and contextual association by PFP. Protein Science 2006 15 6 1550 1556 2-s2.0-33744471931 10.1110/ps.062153506 (Pubitemid 43800030)
7. Hawkins T., Chitale M., Luban S., Kihara D., PFP: automated prediction of gene ontology functional annotations with confidence scores using protein sequence data. Proteins: Structure, Function and Bioinformatics 2009 74 3 566 582 2-s2.0-59849089151 10.1002/prot.22172
8. Chitale M., Hawkins T., Park C., Kihara D., ESG: extended similarity group method for automated protein function prediction. Bioinformatics 2009 25 14 1739 1745 2-s2.0-67649868148 10.1093/bioinformatics/btp309
9. Wass M. N., Sternberg M. J. E., ConFunc-functional annotation in the twilight zone. Bioinformatics 2008 24 6 798 806 2-s2.0-40749111548 10.1093/bioinformatics/btn037 (Pubitemid 351386918)
10. Clark W. T., Radivojac P., Analysis of protein function and its prediction from amino acid sequence. Proteins: Structure, Function and Bioinformatics 2011 79 7 2086 2096 2-s2.0-79958759599 10.1002/prot.23029
11. Pellegrini M., Marcotte E. M., Thompson M. J., Eisenberg D., Yeates T. O., Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proceedings of the National Academy of Sciences of the United States of America 1999 96 8 4285 4288 2-s2.0-0033551248 10.1073/pnas.96.8.4285 (Pubitemid 29190328)
12. Huynen M., Snel B., Lathe W. III, Bork P., Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Research 2000 10 8 1204 1210 2-s2.0-0033832615 10.1101/gr.10.8.1204
13. Enault F., Suhre K., Claverie J.-M., Phydbac "Gene Function Predictor": a gene annotation tool based on genomic context analysis. BMC Bioinformatics 2005 6, article 247 2-s2.0-27644434408 10.1186/1471-2105-6-247 (Pubitemid 41548708)
14. Ersgelhardt B. E., Jordan M. I., Muratore K. E., Brersfser S. E., Protein molecular function prediction by Bayesian phylogenomics. PLoS Computational Biology 2005 1 5, article e45 2-s2.0-33645310990 10.1371/joumal.pcbi.0010045
15. Gaudet P., Livstone M. S., Lewis S. E., Thomas P. D., Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in Bioinformatics 2011 12 5 449 462 2-s2.0-80053180122 10.1093/bib/bbr042
16. Deng M., Zhang K., Mehta S., Chen T., Sun F., Prediction of protein function using protein-protein interaction data. Journal of Computational Biology 2003 10 6 947 960 2-s2.0-0742304254 10.1089/106652703322756168 (Pubitemid 38156407)
17. Vazquez A., Flammini A., Maritan A., Vespignani A., Global protein function prediction from protein-protein interaction networks. Nature Biotechnology 2003 21 6 697 700 2-s2.0-0038699587 10.1038/nbt825 (Pubitemid 36638099)
18. Pazos F., Sternberg M. J. E., Automated prediction of protein function and detection of functional sites from structure. Proceedings of the National Academy of Sciences of the United States of America 2004 101 41 14754 14759 2-s2.0-6944227836 10.1073/pnas.0404569101 (Pubitemid 39410747)
19. Pal D., Eisenberg D., Inference of protein function from protein structure. Structure 2005 13 1 121 130 2-s2.0-11844292002 10.1016/j.str.2004.10. 015 (Pubitemid 40092480)
20. Bandyopadhyay D., Huan J., Liu J., Prins J., Snoeyink J., Wang W., Tropsha A., Structure-based function inference using protein family-specific fingerprints. Protein Science 2006 15 6 1537 1543 2-s2.0-33744491290 10.1110/ps.062189906 (Pubitemid 43800028)
21. Liu Z.-P., Wu L.-Y., Wang Y., Chen L., Zhang X.-S., Predicting gene ontology functions from protein's regional surface structures. BMC Bioinformatics 2007 8, article 475 2-s2.0-41149141455 10.1186/1471-2105-8-475 (Pubitemid 351659638)
22. Skolnick J., Brylinski M., FINDSITE: a combined evolution/structure-based approach to protein function prediction. Briefings in Bioinformatics 2009 10 4 378 391 2-s2.0-67449108422 10.1093/bib/bbp017
23. Sael L., Chitale M., Kihara D., Structure- and sequence-based function prediction for non-homologous proteins. Journal of Structural and Functional Genomics 2012 13 2 111 123 10.1007/s10969-012-9126-6
24. Huttenhower C., Hibbs M., Myers C., Troyanskaya O. G., A scalable method for integration and functional analysis of multiple microarray datasets. Bioinformatics 2006 22 23 2890 2897 2-s2.0-33751359281 10.1093/bioinformatics/ btl492 (Pubitemid 44811560)
25. Brady S., Shatkay H., EpiLoc: a (working) text-based system for predicting protein subcellular location. Pacific Symposium on Biocomputing 2008 604 615 2-s2.0-40549096793
26. Wong A., Shatkay H., Protein function prediction using text-based features extracted from the biomedical literature: the CAFA challenge. BMC Bioinformatics 2013 14 supplement 3, article S14 10.1186/1471-2105-14-S3-S14
27. Devos D., Valencia A., Practical limits of function prediction. Proteins 2000 41 1 98 107 (Pubitemid 30666916)
28. Bashton M., Chothia C., The generation of new protein functions by the combination of domains. Structure 2007 15 1 85 99 2-s2.0-33846059668 10.1016/j.str.2006.11.009 (Pubitemid 46091745)
29. Punta M., Coggill P. C., Eberhardt R. Y., The Pfam protein families database. Nucleic Acids Research 2012 40 1 D290 D301 10.1093/nar/gkr1065
30. Murzin A. G., Brenner S. E., Hubbard T., Chothia C., SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology 1995 247 4 536 540 2-s2.0-0028961335 10.1006/jmbi.1995.0159
31. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J., Basic local alignment search tool. Journal of Molecular Biology 1990 215 3 403 410 2-s2.0-0025183708 10.1006/jmbi.1990.9999 (Pubitemid 20364473)
32. Finn R. D., Clements J., Eddy S. R., HMMER web server: interactive sequence similarity searching. Nucleic Acids Research 2011 39, supplement 2 W29 W37 2-s2.0-79959931985 10.1093/nar/gkr367
33. Schug J., Diskin S., Mazzarelli J., Brunk B. P., Stoeckert C. J. Jr., Predicting gene ontology functions from ProDom and CDD protein domains. Genome Research 2002 12 4 648 655 2-s2.0-0036228634 10.1101/gr.222902 (Pubitemid 34308644)
34. Hayete B., Bienkowska J. R., Gotrees: predicting go associations from protein domain composition using decision trees. Pacific Symposium on Biocomputing 2005 127 138 2-s2.0-15944404663
35. Mulder N. J., Apweiler R., Attwood T. K., New developments in the InterPro database. Nucleic Acids Research 2007 35, supplement 1 D224 D288 10.1093/nar/gkl841 (Pubitemid 46056203)
36. Song N., Sedgewick R. D., Durand D., Domain architecture comparison for multidomain homology identification. Journal of Computational Biology 2007 14 4 496 516 2-s2.0-34250333457 10.1089/cmb.2007.A009 (Pubitemid 46911221)
37. Forslund K., Sonnhammer E. L. L., Predicting protein function from domain content. Bioinformatics 2008 24 15 1681 1687 2-s2.0-48249113702 10.1093/bioinformatics/btn312
38. Rentzsch R., Orengo C. A., Protein function prediction using domain families. BMC Bioinformatics 2013 14 supplement 3, article S5 10.1186/1471-2105-14-S3-S5
39. Zhao X.-M., Wang Y., Chen L., Aihara K., Protein domain annotation with integration of heterogeneous information sources. Proteins: Structure, Function and Genetics 2008 72 1 461 473 2-s2.0-44949143041 10.1002/prot.21943 (Pubitemid 351809180)
40. Messih M. A., Chitale M., Bajic V. B., Kihara D., Gao X., Protein domain recurrence and order can enhance prediction of protein functions. Bioinformatics 2012 28 18 i444 i450 10.1093/bioinformatics/bts398
41. Fang H., Gough J., A domain-centric solution to functional genomics via dcGO Predictor. BMC Bioinformatics 2013 14 supplement 3, article S9 10.1186/1471-2105-14-S3-S9
42. Teng Z., Guo M., Liu X., Dai Q., Wang C.-Y., Xuan P., Measuring gene functional similarity based on group-wise comparison of GO terms. Bioinformatics 2013 29 11 1424 1432 10.1093/bioinformatics/btt160