Computational prediction of Host-Parasite protein interactions between P. falciparum and H. sapiens

PLoS ONE

Volumn 6, Issue 11, 2011, Pages

  Wuchty, Stefan ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHAPERONE; PROTOZOAL PROTEIN; PROTEIN;

ARTICLE; CONTROLLED STUDY; HOST CELL; HOST PARASITE INTERACTION; HUMAN; MACHINE LEARNING; MOLECULAR GENETICS; NONHUMAN; PLASMODIUM FALCIPARUM; PREDICTION; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; STATISTICAL ANALYSIS; ANIMAL; BIOLOGY; COMPARATIVE STUDY; MALARIA FALCIPARUM; METABOLISM; PARASITOLOGY; PHYSIOLOGY;

HOMO SAPIENS; PLASMODIUM FALCIPARUM;

ANIMALS; COMPUTATIONAL BIOLOGY; HOST-PARASITE INTERACTIONS; HUMANS; MALARIA, FALCIPARUM; MOLECULAR CHAPERONES; PLASMODIUM FALCIPARUM; PROTEIN INTERACTION MAPPING; PROTEINS; SIGNAL TRANSDUCTION;

EID: 81255128913     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0026960     Document Type: Article

References (48)

1. Uetz P, Dong YA, Zeretzke C, Atzler C, Baiker A, et al. (2006) Herpesviral protein networks and their interaction with the human proteome. Science 311: 239-242.
2. Calderwood MA, Venkatesan K, Xing L, Chase MR, Vazquez A, et al. (2007) Epstein-Barr virus and virus human protein interaction maps. Proc Natl Acad Sci U S A 104: 7606-7611.
3. de Chassey B, Navratil V, Tafforeau L, Hiet MS, Aublin-Gex A, et al. (2008) Hepatitis C virus infection protein network. Mol Syst Biol 4: 230.
4. Bandyopadhyay S, Kelley R, Ideker T, (2006) Discovering regulated networks during HIV-1 latency and reactivation. Pac Symp Biocomput pp. 354-366.
5. Konig R, Zhou Y, Elleder D, Diamond TL, Bonamy GM, et al. (2008) Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 135: 49-60.
6. Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, et al. (2009) Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog 5: e1000437.
7. Konig R, Stertz S, Zhou Y, Inoue A, Hoffmann HH, et al. (2010) Human host factors required for influenza virus replication. Nature 463: 813-817.
8. Brass AL, Dykxhoorn DM, Benita Y, Yan N, Engelman A, et al. (2008) Identification of host proteins required for HIV infection through a functional genomic screen. Science 319: 921-926.
9. Dyer MD, Murali TM, Sobral BW, (2008) The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathog 4: e32.
10. Vignali M, McKinlay A, LaCount DJ, Chettier R, Bell R, et al. (2008) Interaction of an atypical Plasmodium falciparum ETRAMP with human apolipoproteins. Malar J 7: 211.
11. Dyer MD, Murali TM, Sobral BW, (2007) Computational prediction of host-pathogen protein-protein interactions. Bioinformatics 23: i159-166.
12. Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A, (2007) Host pathogen protein interactions predicted by comparative modeling. Protein Sci 16: 2585-2596.
13. Ewing RM, Chu P, Elisma F, Li H, Taylor P, et al. (2007) Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol 3: 89.
14. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178.
15. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, et al. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122: 957-968.
16. Chatraryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, et al. (2007) MINT: the Molecular INTeraction database. Nucleic Acids Res 35: D572-574.
17. Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, et al. (2007) IntAct-open source resource for molecular interaction data. Nucleic Acids Res 35: D561-565.
18. Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, et al. (2008) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res.
19. Peri S, Navarro JD, Kristiansen TZ, Amanchy R, Surendranath V, et al. (2004) Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res 32: D497-501.
20. LaCount DJ, Vignali M, Chettier R, Phansalkar A, Bell R, et al. (2005) A protein interaction network of the malaria parasite Plasmodium falciparum. Nature 438: 103-107.
21. Remm M, Storm CE, Sonnhammer EL, (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314: 1041-1052.
22. Breiman L, (2001) Random Forests. Machine Learning 45: 5-32.
23. Shen J, Zhang J, Luo X, Zhu W, Yu K, et al. (2007) Predicting protein-protein interactions based only on sequence information. Proc Natl Acad Sci USA 104: 4337-4341.
24. Schadt EE, Molony C, Chudin E, Hao K, Yang X, et al. (2008) Mapping the genetic architecture of gene expression in human liver. PLoS Biol 6: e107.
25. Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, et al. (2009) PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res 37: D539-543.
26. Beissbarth T, Speed TP, (2004) GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 20: 1464-1465.
27. Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, et al. (2009) PID: The Pathway Interaction Database. Nucl Acids Res 37: D674-679.
28. Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B 57: 289-300.
29. Pavithra SR, Kumar R, Tatu U, (2007) Systems analysis of chaperone networks in the malarial parasite Plasmodium falciparum. PLoS Comput Biol 3: 1701-1715.
30. Chen G, Goeddel DV, (2002) TNF-R1 signaling: a beautiful pathway. Science 296: 1634-1635.
31. Woronicz JD, Gao X, Cao Z, Rothe M, Goeddel DV, (1997) IkappaB kinase-beta: NF-kappaB activation and complex formation with IkappaB kinase-alpha and NIK. Science 278: 866-869.
32. Bouwmeester T, Bauch A, Ruffner H, Angrand PO, Bergamini G, et al. (2004) A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat Cell Biol 6: 97-105.
33. Wuchty S, Siwo G, Ferdig MT, (2010) Viral organization of human proteins. PLoS One 5: e11796.
34. Barabasi AL, (2009) Scale-free networks: a decade and beyond. Science 325: 412-413.
35. Pesce ER, Cockburn IL, Goble JL, Stephens LL, Blatch GL, (2010) Malaria heat shock proteins: drug targets that chaperone other drug targets. Infect Disord Drug Targets 10: 147-157.
36. Acharya P, Kumar R, Tatu U, (2007) Chaperoning a cellular upheaval in malaria: heat shock proteins in Plasmodium falciparum. Mol Biochem Parasitol 153: 85-94.
37. Haldar K, Kamoun S, Hiller NL, Bhattacharje S, van Ooij C, (2006) Common infection strategies of pathogenic eukaryotes. Nat Rev Microbiol 4: 922-931.
38. Hiller NL, Bhattacharjee S, van Ooij C, Liolios K, Harrison T, et al. (2004) A host-targeting signal in virulence proteins reveals a secretome in malarial infection. Science 306: 1934-1937.
39. Marti M, Good RT, Rug M, Knuepfer E, Cowman AF, (2004) Targeting malaria virulence and remodeling proteins to the host erythrocyte. Science 306: 1930-1933.
40. Sargeant TJ, Marti M, Caler E, Carlton JM, Simpson K, et al. (2006) Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites. Genome Biol 7: R12.
41. de Koning-Ward TF, Gilson PR, Boddey JA, Rug M, Smith BJ, et al. (2009) A newly discovered protein export machine in malaria parasites. Nature 459: 945-949.
42. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32: D258-261.
43. Brehelin L, Dufayard JF, Gascuel O, (2008) PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data. BMC Bioinformatics 9: 440.
44. Flicek P, Amode MR, Barrell D, Beal K, Brent S, et al. (2011) Ensembl 2011. Nucleic Acids Res 39: D800-806.
45. Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, et al. (2009) PID: the Pathway Interaction Database. Nucleic Acids Res 37: D674-679.
46. Roux-Dalvai F, Gonzalez de Peredo A, Simo C, Guerrier L, Bouyssie D, et al. (2008) Extensive analysis of the cytoplasmic proteome of human erythrocytes using the peptide ligand library technology and advanced mass spectrometry. Mol Cell Proteomics 7: 2254-2269.
47. Wuchty S, (2004) Evolution and topology in the yeast protein interaction network. Genome Res 14: 1310-1314.
48. Simpson EH, (1949) Measurement of diversity. Nature 163: 688.