An iterative approach of protein function prediction

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Chi, Xiaoxiao ^a   Hou, Jingyu ^a  

^a DEAKIN UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

EVALUATION METRICS; EVALUATION RESULTS; FUNCTION PREDICTION; PREDICTION PRECISION; PREDICTION QUALITY; PROTEIN FUNCTION PREDICTION; PROTEIN INTERACTION; PROTEIN-PROTEIN INTERACTIONS;

ALGORITHMS; DATA PROCESSING; FORECASTING; FUNCTION EVALUATION; ITERATIVE METHODS; QUALITY CONTROL; SEMANTICS;

PROTEINS;

PROTEIN;

ALGORITHM; ARTICLE; GENETICS; GENOMICS; HUMAN; METABOLISM; MOLECULAR GENETICS; PROTEIN PROTEIN INTERACTION;

ALGORITHMS; GENOMICS; HUMANS; MOLECULAR SEQUENCE ANNOTATION; PROTEIN INTERACTION MAPS; PROTEINS;

EID: 80755159399     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-437     Document Type: Article

References (20)

1. Ching W, Li L, Chan Y, Mamitsuka H. A Study of Network-based Kernel Methods on Protein-Protein Interaction for Protein Functions Prediction. Proceedings of The Third International Symposium on Optimization and System Biology 2009, 25-32.
2. Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Güldener U, Mannhaupt G, Münsterkötter M. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Research 2004, 32:5539-5545. 10.1093/nar/gkh894, 524302, 15486203.
3. Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J, Davis A, Dolinski K, Dwight S, Eppig J. Gene ontology: tool for the unification of biology. Nature Genetics 2000, 25:25-29. 10.1038/75556, 3037419, 10802651.
4. Chua H, Wong L. Predicting Protein Functions from Protein Interaction Networks. Biological Data Mining in Protein Interaction Networks 2009, 204-223.
5. Deng M, Zhang K, Mehta S, Chen T, Sun F. Prediction of protein function using protein-protein interaction data. IEEE Computer Society Bioinformatics Conference (CSB'02) 2002, 197-206.
6. Wang M, Shang X, Zhang S, Li Z. Using Direct and Indirect Neighbours to Predict Protein Function in GO-Evaluated PPI Data Set. Intelligent System and Applications(ISA) 2010, 1-4.
7. Schwikowski B, Uetz P, Fields S. A network of protein-protein interactions in yeast. Nature Biotechnology 2000, 18:1257-1261. 10.1038/82360, 11101803.
8. Hishigaki H, Nakai K, Ono T, Tanigami A, Takagi T. Assessment of prediction accuracy of protein function from protein-protein interaction data. Yeast 2001, 18:523-531. 10.1002/yea.706, 11284008.
9. Brun C, Chevenet F, Martin D, Wojcik J, Guénoche A, Jacq B. Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network. Genome Biology 2004, 5:6-18.
10. Samanta M, Liang S. Predicting protein functions from redundancies in large-scale protein interaction networks. Proceedings of the National Academy of Sciences of the United States of America (PNAS) 2003, 100:12579-12583.
11. Chua H, Sung W, Wong L. Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics 2006, 22:1623-1630. 10.1093/bioinformatics/btl145, 16632496.
12. Chen G, Wang J, Li M. GO semantic similarity based analysis for huaman protein interactions. Proceedings of 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing 2009, 207-210.
13. Resnik P. Using information content to evaluate semantic similarity in a taxonomy. Proceedings of International Joint Conference for Artificial Intelligence 1995, 448-453.
14. Jiang J, Conrath D. Semantic similarity based on corpus statistics and lexical taxonomy. Proceedings of International Conference Research on Computational Linguistics 1997, 19-33.
15. Lin D. An information-theoretic definition of similarity. Proceedings of the Fifteenth International Conference on Machine Learning 1998, 296-304.
16. Pandey G, Myers C, Kumar V. Incorporating functional inter-relationships into protein function prediction algorithms. BMC Bioinformatics 2009, 10:142. 10.1186/1471-2105-10-142, 2693438, 19435516.
17. Misteli T. Protein dynamics: implications for nuclear architecture and gene expression. Science 2001, 291:843-847. 10.1126/science.291.5505.843, 11225636.
18. Dwight S, Harris M, Dolinski K, Ball C, Binkley G, Christie K, Fisk D, Issel-Tarver L, Schroeder M, Sherlock G. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Research 2002, 30:69-72. 10.1093/nar/30.1.69, 99086, 11752257.
19. Zeng E, Ding C, Narasimhan G, Holbrook S. Estimating support for protein-protein interaction data with applications to function prediction. Proceedings of 2008 Computer Systems Bioinformatics (CSB) Conference 2008, 73-84.
20. Chi X, Hou J. Iteratively Predict Protein Functions From Protein-Protein Interactions. Proceedings of the International Conference on Cellular, Molecular Biology, Biophysics and Bioengineering (CMBB) 2010, 219-222.