A preliminary study on the prediction of human protein functions

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 6686 LNCS, Issue PART 1, 2011, Pages 334-343

  Bologna, Guido ^a   Veuthey, Anne Lise ^a   Pagni, Marco ^b   Lane, Lydie ^a,c   Bairoch, Amos ^a,c  

^a Swiss Institute of Bioinformartics   (Switzerland)

^b Vital IT Group   (Switzerland)

^c UNIVERSITY OF GENEVA   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

DATA SETS; FUNCTIONAL INFORMATION; GENE ONTOLOGY; HUMAN PROTEINS; HUMAN PROTEOME; MULTI-LABEL; TARGET VALUES; FUNCTIONAL PREDICTIONS; MULTI-LABEL LEARNING;

GENES; ONTOLOGY; PROTEINS; SUPERVISED LEARNING; FORECASTING;

FORECASTING; LEARNING SYSTEMS;

EID: 79956342316     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-21344-1_35     Document Type: Conference Paper

References (17)

1. Aerts, S., Lambrechts, D., Maity, S., Van Loo, P., Coessens, B., De Smet, F., Tranchevent, L.C., De Moor, B., Marynen, P., Hassan, B., et al.: Gene prioritization through genomic data fusion. Nat. Biotechnol. 24(5), 537-544 (2006)
2. Barutcuoglu, Z., Schapire, R.E., Troyanskaya, O.G.: Hierarchical multi-label prediction of gene function. Bioinformatics 22(7), 830-836 (2006)
3. Breiman, L., Friedman, J., Olshen, R.A., Stone, C.J.: Classification and regression trees. Wadsworth, Belmont (1984)
4. Cai, C.Z., Han, L.Y., Ji, Z.L., Chen, X., Chen, Y.Z.: SVM-Prot: web based support vector machine software for functional classification of a protein from its primary sequence. Nucleic Acids Research 31(13), 3692-3697 (2003)
5. Eisenberg, D., Schwarz, E., Komaromy, M., Wall, R.: Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J. Mol. Biol. 179(1), 125-142 (1984)
6. Hu, L., Huang, T., Shi, X., Lu, W.C., Cai, Y.D., Chou, K.C.: Predicting functions of proteins in mouse based on weighted protein-protein interaction network and protein hybrid properties. PLoS One 6(1), e14556 (2011)
7. Jensen, L.J., Gupta, R., Staerfeldt, H.-H., Brunak, S.: Prediction of human protein function according to gene ontology categories. Bioinformatics 19(5), 635-642 (2003)
8. Kazawa, H., Izumitani, T., Taira, H., Maeda, E.: Maximal margin labelling for multi-topic text categorization. In: Saul, L.K., Weiss, Y., Bottou, L. (eds.) Advances in Neural Information Processing Systems 17, pp. 649-656. MIT Press, Cambridge (2005)
9. Mewes, H.W., Heumann, K., Kaps, A., Mayer, K., Pfeiffer, F., Stocker, S., Frishman, D.: MIPS: a database for protein sequences and complete genomes. Nucl. Acids Research 27, 44-48 (1999)
10. Pena-Castillo, L., Tasan, M., Myers, C.L., Lee, H., Joshi, T., Zhang, C., Guan, Y., Leone, M., Pagnani, A., Kim, W.K., et al.: A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol. 9(suppl. 1), S2 (2008)
11. Ranea, J.A., Yeats, C., Grant, A., Orengo, C.A.: Predicting protein function with hierarchical phylogenetic profiles: the Gene3D Phylo-Tuner method applied to eukaryotic genomes. PLoS Comput. Biol. 3(11), e237 (2007)
12. The Gene Ontology Consortium. The gene ontology project in 2008. Nucleic Acid Research 36(1), D440-D444 (November 2007)
13. Tsoumakas, G., Katakis, I.: Multi-label classification: an overview. International Journal of Data Warehouse and Mining 3(3), 1-13 (2007)
14. Vapnik, V.: The nature of statistical learning. Springer, Heidelberg (1995)
15. Vens, C., Struyf, J., Schietgat, L., Dzeroski, S.: Decision trees for hierarchical multi-label classification. Machine Learning 73(2), 185-214 (2008)
16. Zhang, M.L., Zhou, Z.H.: Multi-label neural networks with applications to functional genomics and text categorization. IEEE Transactions on Knowledge and Data Engineering 18(10), 1338-1351 (2006)
17. Zhu, M., Gao, L., Guo, Z., Li, Y., Wang, D., Wang, J., Wang, C.: Globally predicting protein functions based on co-expressed protein-protein interaction networks and ontology taxonomy similarities. Gene 391(1-2), 113-119 (2007)