A combined approach for genome wide protein function annotation/prediction

Proteome Science

Volumn 11, Issue , 2013, Pages

  Benso, Alfredo ^a,b   Di Carlo, Stefano ^a   ur Rehman, Hafeez ^a   Politano, Gianfranco ^a   Savino, Alessandro ^a,b   Suravajhala, Prashanth ^c  

^a POLITECNICO DI TORINO   (Italy)

^b Edificio Centri Comuni   (Italy)

^c Bioclues Organization   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; FUNCTIONAL GENOMICS; GENE ONTOLOGY; GENOME; HUMAN; MODEL; NONHUMAN; PREDICTION; PROTEIN FUNCTION; PROTEIN MOTIF; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY; STRUCTURE ACTIVITY RELATION;

EID: 84997161467     PISSN: None     EISSN: 14775956     Source Type: Journal    
DOI: 10.1186/1477-5956-11-S1-S1     Document Type: Article

References (32)

1. Roberts RJ: Identifying protein function-a call for community action. PLoS Biol 2004, 2(3):E42.
2. Galperin Y, Koonin V: A Survey-Conserved Hypothetical Proteins: Prioritization of Targets For Experimental Study. Nucleic Acids Research 2004, 32(18):5452-5463.
3. Letovsky S, Kasif S: Predicting Protein Function from Protein-Protein Interaction Data: A Probabilistic Approach. Bioinformatics 2003, 19(1): i197-i204.
4. Karaoz U, Murali TM, et al: Whole-Genome Annotation by Using Evidence Integration in Functional-Linkage Networks. Proc Nat’l Academy of Sciences USA 2004, 101:2888-2893.
5. Schwikowski B, Uetz P, Fields S: A Network of Protein-Protein Interactions in Yeast. Nature Biotech- nology 2000, 18:1257-1261.
6. Yosef N, Sharan R, Stafford N: Improved Network-Based Identification of Protein Orthologs. Bioinfor- matics 2008, 24(16):i200-i206.
7. Fields S, Song O: A Novel Genetic System to Detect Protein-Protein Interactions. Nature 1989, 340:245-246.
8. Andreas Bauer BK: Affinity Purification-Mass Spectrometry. European Journal of Biochemistry 2003, 270:570-578.
9. Sharan R, Ulitsky I, Shamir R: Network-Based Prediction of Protein Function. Molecular Systems Biology 2007, 3:1-13.
10. Chua H, Sung W, Wong L: Exploiting Indirect Neighbors and Topological Weight to Predict Protein Function from Protein-Protein Interactions. Bioinformatics 2006, 19:i197-i204.
11. Bogdanov P, Singh AK: Molecular Function Prediction Using Neighborhood Features. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2010, 7(2):208-217.
12. Deng M, Tu Z, Sun F, Chen T: Mapping Gene Ontology to Proteins Based on Protein-Protein Inter- action Data. Bioinformatics 2004, 20:895-902.
13. Deng M, Zhang K, Mehta S, Chen T, Sun F: Prediction of Protein Function Using Protein-Protein Interaction Data. J Computational Biology 2003, 10:947-960.
14. Letovsky S, Kasif S: Predicting Protein Function from Protein/Protein Interaction Data: A Proba- bilistic Approach. Bioinformatics 2003, 19: i197-i204.
15. Nariai N, Kolaczyk E, Kasif S: Probabilistic Protein Function Prediction from Heterogeneous Genome- Wide Data. PLoS ONE 2007, 2(3):e337.
16. Carroll S, Pavlovic V: Protein Classification Using Probabilistic Chain Graphs and the Gene Ontology Structure. Bioinformatics 2006, 22(15):1871-1878.
17. Mitrofanova A, Pavlovic V, Mishra B: Prediction of Protein Functions with Gene Ontology and Interspecies Protein Homology Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2011, 8(3):775-784.
18. ur Rehman H, Benso A, Di Carlo S, Politano G, Savino A, Suravajhala P: Combining Homolog and Motif Similarity Data with Gene Ontology Relationships for Protein Function Prediction. Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference 2012, 1-4.
19. Mitrofanova A, et al: Integrative Protein Function Transfer Using Factor Graphs and Heterogeneous Data Sources. IEEE International Conference on Bioinformatics and Biomedicine IEEE Computer Society 2008, 314-318.
20. The Gene Ontology Database. [Online] 2012 [http://www.geneontology. org].
21. del Pozo A, Pazos F, Valencia A: Defining functional distances over Gene Ontology. BMC Bioinformatics 2008, 9:50-65.
22. Mistry M, Pavlidis P: Gene Ontology Term Overlap as a Measure of Gene Functional Similarity. BMC Bioinformatics 2008, 9:327-338[http://www. biomedcentral.com/1471-2105/9/327].
23. Pandey G, Myers CL, Kumar V: Incorporating Functional Inter-relationships into Protein Function Prediction Algorithms. BMC Bioinformatics 2009, 10:142-164, Doi:10.1186/1471-2105-10-142.
24. The UniProt Consortium: Reorganizing the Protein Space at the Universal Protein Resource (UniProt). Nucleic Acids Res 2012, 40:D71-D75.
25. Kerrien S, et al: The IntAct Molecular Interaction Database in 2012. [PMID: 22121220]. 2012 [http://www.ebi.ac.uk/intact].
26. Salwinski L, et al: The Database of Interacting Proteins. Nucl Acids Res 2004, 32:449-51[http://dip.doe-mbi.ucla.edu].
27. BiodigitalValley: ProteinQuest, a web based platform for the mining of Medline papers. [Online] 2013 [http://www.proteinquest.com].
28. Hulo N, Bairoch A, Bulliard V, Cerutti L, et al: The PROSITE Database. Nucl Acids Res 2006, 34:D227-230[http://prosite.expasy.org].
29. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic Local Alignment Search Tool. J Mol Biol 215 1990, 215(3):403-410[http://blast.ncbi.nlm.nih. gov/Blast.cgi].
30. NCBI: Basic Local Alignment Search Tool My NCBI [Sign In] [Register] Jump to Page Content blast: Basic Alignment Search Toole. [Online] [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins].
31. Benso A, Di Carlo S, ur Rehman H, Politano G, Savino A: Using Gnome Wide Data for Protein Function Prediction by Exploiting Gene Ontology Relationships. Automation Quality and Testing Robotics (AQTR), IEEE 2012, 497-502.
32. Jaeger S, Sers C, Leser U: Combining Modularity, Conservation, and Interactions of Proteins Significantly increases Precision and Coverage of Protein Function Prediction. BMC Genomics 2010, 11:717-735.