Computational prediction of host-pathogen protein-protein interactions

Bioinformatics

Volumn 23, Issue 13, 2007, Pages

  Dyer, Matthew D ^a,b   Murali, T M ^a   Sobral, Bruno W ^b  

^a VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

^b VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ANALYTIC METHOD; BAYES THEOREM; COMPUTER ANALYSIS; CONFERENCE PAPER; DNA MICROARRAY; GENE EXPRESSION PROFILING; HOST PATHOGEN INTERACTION; HUMAN; LIFE CYCLE; NONHUMAN; PATHOGENICITY; PLASMODIUM FALCIPARUM; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING;

HOMO SAPIENS; PLASMODIUM FALCIPARUM;

EID: 34547852250     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm208     Document Type: Conference Paper

References (46)

1. Altschul, S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
2. Ashburner, M. et al. (2000) Gene Ontology: Tool for the unification of biology. The Gene Ontology consortium. Nat. Genet., 25, 25-29.
3. Bairoch, A. et al. (2005) The Universal Protein Resource (UniProt). Nucleic Acids Res., 33, D154-D159.
4. Baruch, D.I. et al. (1996) Plasmodium falciparum erythrocyte membrane 1 is a parasitized erythrocyte receptor for adherence to CD36, thrombospondin, and intracellular adhesion molecule 1. Proc. Natl Acad. Sci. USA, 93, 3497-3502.
5. Baum, J. et al. (2005) Invasion by P. falciparum merozoites suggests a hierarchy of molecular interactions. PLoS Pathog., 1 e37.
6. Biargo, C. et al. (2003) A gene-family encoding small exported proteins is conserved across Plasraodium genus. Mol. Biochem. Parasitol., 126, 209-218.
7. Bozdech, Z. et al. (2003) The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol., 1, e5.
8. Carrolo, M. et al. (2003) Hepatocyte growth factor and its receptor are required for malaria infection. Nat. Med., 9, 1363-1369.
9. Cowman, A.F. and Crabb, B.S. (2006) Invasion of red blood cells by malaria parasites. Cell, 124, 755-766.
10. Edgar, R. et al. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res., 30, 207-210.
11. Gavin, A.-C. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415, 141-147.
12. Gilbert, D. (2005) Biomolecular Interaction Network Database. Brief. Bioinformatics, 6, 194-198.
13. Giot, L. et al. (2003) A protein interaction map of Drosophila melanogaster. Science, 302, 1727-1736.
14. Grigoriev, A. (2001) A relationship between gene expression and protein interaction on the proteome scale: Analysis of the bacteriophage t7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Res., 29, 3513-3519.
15. Guldener, U. et al. (2006) Mpact: The MIPS protein interaction resource on yeast. Nucleic Acids Res., 34, D436-D441.
16. Hermjakob, H. et al. (2004) IntAct: An open source molecular interaction database. Nucleic Acids Res., 32, D452-D455.
17. Hiller, N. et al. (2004) A host-targeting signal in virulence proteins reveals a secretome in malarial infection. Science, 306, 1934-1937.
18. Ho, Y. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183.
19. Ito, T. et al. (2000) Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl Acad. Sci. USA, 97, 1143-1147.
20. Ito, T. et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA, 98, 4569-4574.
21. Jansen R. et al. (2002) Relating whole-genome expression data with protein-protein interactions. Genome Res., 12, 37-46.
22. Jansen, R. et al. (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302, 449-453.
23. Joshi-Tope, G. et al. (2005) REACTOME: A knowledgebase of biological pathways. Nucleic Acids Res., 33, D428-D432.
24. Kauth, C.W. et al. (2006) Interactions between merozoite surface proteins 1, 6, and 7 of the malaria parasite Plasmodium falciparum. J. Biol. Chem., 281, 31517-31527.
25. Kim, W.K. et al. (2002) Large scale statistical prediction of protein-protein interaction by potentially interacting domain (PID) pair. Genome Inform. Ser. Workshop Genome. Inform., 13, 42-50.
26. Kooij, T.W.A. et al. (2006) Plasmodium post-genomics: Better the bug you know? Nat. Rev., 4, 344-357.
27. Le Roch, K.G. et al. (2003) Discovery of gene function by expression profiling of the malaria parasite life cycle. Science, 301, 1503-1508.
28. Li, S. et al. (2004) A map of the interactome network of the metazoan C. elegans. Science, 303, 540-543.
29. Ng, S.K. et al. (2003) Integrative approach for computationally inferring protein domain interactions. Bioinformatics, 19, 923-929.
30. Ockenhouse, C.F. et al. (2006) Common and divergent immune response signaling pathways discovered in peripheral blood mononuclear cell gene expression patterns in presymptomatic and clinically apparent malaria. Infect. Immun., 74, 5561-5573.
31. O'Donnell, R. and Blackman, M.J. (2005) The role of malaria meroite proteases in red blood cell invasion. Curr. Opin. Microbiol., 8 422-427.
32. Qi, Y. et al. (2006) Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins, 63, 490-500.
33. Quevillon, E. et al. (2005) InterProScan: Protein domains identifier. Nucleic Acids Res., 33, W116-W120.
34. Roggwiller, E. et al. (1997) Host urokinase-type plasminogen activator participates in the release of malaria merozoites from infected erythrocytes. Mol. Biochem. Parasitol., 86, 49-59.
35. Rual, J.-F. et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature, 437, 1173-1178.
36. Salwinski, L. et al. (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res., 32, D449-D451.
37. Sharan, R. et al. (2005) Conserved patterns of protein interaction in multiple species. PNAS, 102, 1974-1979.
38. Sprinzak, E. and Margalit, H. (2001) Correlated sequence-signatures as markers of protein-protein interaction. J. Mol. Biol., 311, 681-692.
39. Stelzl, U. et al. (2005) A human protein-protein interaction network: A resource for annotating the proteome. Cell, 122, 957-968.
40. Stoeckert, C.J.Jr, et al. (2006) PlasmoDB v5: New looks, new genomes. Trends Parasitol., 22, 543-546.
41. Stubbs, J. et al. (2005) Molecular mechanism for switching of P. falciparum invasion pathways into human erythrocytes. Science 309, 1384-1387.
42. Suthram, S. et al. (2006) A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics, 7, 360.
43. Uetz, P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
44. Withers-Martinez, C. et al. (2004) Subtilisin-like proteases of the malaria parasite. Mol. Microbiol., 53, 55-63.
45. Yu, H. et al. (2004) Annotation transfer between genomes: protein-protein interologs and protein-dna regulogs. Genome Res., 14, 1107-1118.
46. Zhang, L. et al. (2004) Predicting co-complexed protein pairs using genomic and proteomic data integration. BMC Bioinformatics, 5, 38.