A top-down approach to infer and compare domain-domain interactions across eight model organisms

PLoS ONE

Volumn 4, Issue 3, 2009, Pages

  Guda, Chittibabu ^a   King, Brian R ^a,b   Pal, Lipika R ^a,c   Guda, Purnima ^a  

^a STATE UNIVERSITY OF NEW YORK   (United States)

^b MANSFIELD UNIVERSITY   (United States)

^c UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; ADENYLOSUCCINATE SYNTHASE; AMINO ACID TRANSFER RNA LIGASE; CORE PROTEIN; CYTOCHROME C; FERRITIN; GLOBIN; HISTONE TRANSFER RNA LIGASE; HOMEODOMAIN PROTEIN; INTEGRASE; LSM SMALL NUCLEAR RIBONUCLEOPROTEIN; MADS DOMAIN PROTEIN; MEMBRANE PROTEIN; MITOGEN ACTIVATED PROTEIN KINASE; PHOSPHOGLYCERATE KINASE; PROTEASOME; PROTEIN MUTS; PROTEIN MUTS II; PROTEIN MUTS IV; PROTEIN RNAP; RNA POLYMERASE; RNA POLYMERASE SIGMA70; ROSETTA STONE PROTEIN; SMALL NUCLEAR RIBONUCLEOPROTEIN; STAT PROTEIN; THIOREDOXIN; TRANSCRIPTION FACTOR GATA; TRANSCRIPTION FACTOR HES 1; TRANSCRIPTION FACTOR REL; UNCLASSIFIED DRUG;

ACCURACY; ALGORITHM; ARABIDOPSIS; ARTICLE; CAENORHABDITIS ELEGANS; CELLULAR DISTRIBUTION; CONSERVATION BIOLOGY; CONTROLLED STUDY; DROSOPHILA; ESCHERICHIA COLI; HUMAN; INTERMETHOD COMPARISON; MOUSE; NONHUMAN; PLASMODIUM; PREDICTION; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; SCORING SYSTEM; SPECIES COMPARISON; YEAST; ANIMAL; BIOLOGY; METHODOLOGY; PROTEIN ANALYSIS; PROTEOMICS;

ARABIDOPSIS; CAENORHABDITIS ELEGANS;

ANIMALS; COMPUTATIONAL BIOLOGY; HUMANS; PROTEIN INTERACTION MAPPING; PROTEOMICS;

EID: 63749117839     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0005096     Document Type: Article

References (39)

1. Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, et al. (2006) IntAct - Open Source Resource for Molecular Interaction Data. Nucleic Acids Res 35: D561-565.
2. Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, et al. (2002) A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 295: 321-324.
3. Wang Z, Moult J (2001) SNPs, protein structure, and disease. Hum Mutat 17: 263-270.
4. Resch A, Xing Y, Modrek B, Gorlick M, Riley R, et al. (2004) Assessing the impact of alternative splicing on domain interactions in the human proteome. J Proteome Res 3: 76-83.
5. Loregian A, Marsden HS, Palu G (2002) Protein-protein interactions as targets for antiviral chemotherapy. Rev Med Virol 12: 239-262.
6. Zutshi R, Brickner M, Chmielewski J (1998) Inhibiting the assembly of protein-protein interfaces. Curr Opin Chem Biol 2: 62-66.
7. Dueber JE, Yeh BJ, Bhattacharyya RP, Lim WA (2004) Rewiring cell signaling: the logic and plasticity of eukaryotic protein circuitry. Curr Opin Struct Biol 14: 690-699.
8. Ekman D, Bjorklund AK, Frey-Skott J, Elofsson A (2005) Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. J Mol Biol 348: 231-243.
9. Wright CF, Teichmann SA, Clarke J, Dobson CM (2005) The importance of sequence diversity in the aggregation and evolution of proteins. Nature 438: 878-881.
10. Deng M, Mehta S, Sun F, Chen T (2002) Inferring domain-domain interactions from protein-protein interactions. Genome Res 12: 1540-1548.
11. Ng SK, Zhang Z, Tan SH (2003) Integrative approach for computationally inferring protein domain interactions. Bioinformatics 19: 923-929.
12. Riley R, Lee C, Sabatti C, Eisenberg D (2005) Inferring protein domain interactions from databases of interacting proteins. Genome Biol 6: R89.
13. Guimaraes KS, Jothi R, Zotenko E, Przytycka TM (2006) Predicting domain-domain interactions using a parsimony approach. Genome Biol 7: R104.
14. Guimaraes KS, Przytycka TM (2008) Interrogating domain-domain interactions with parsimony based approaches. BMC Bioinformatics 9: 171.
15. Nye TM, Berzuini C, Gilks WR, Babu MM, Teichmann SA (2005) Statistical analysis of domains in interacting protein pairs. Bioinformatics 21: 993-1001.
16. Lee H, Deng M, Sun F, Chen T (2006) An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics 7: 269.
17. Kim WK, Ison JC (2005) Survey of the geometric association of domain-domain interfaces. Proteins 61: 1075-1088.
18. Shoemaker BA, Panchenko AR, Bryant SH (2006) Finding biologically relevant protein domain interactions: conserved binding mode analysis. Protein Sci 15: 352-361.
19. Jothi R, Cherukuri PF, Tasneem A, Przytycka TM (2006) Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. J Mol Biol 362: 861-875.
20. Prieto C, De Las Rivas J (2006) APID: Agile Protein Interaction Data Analyzer. Nucleic Acids Res 34: W298-302.
21. Itzhaki Z, Akiva E, Altuvia Y, Margalit H (2006) Evolutionary conservation of domain-domain interactions. Genome Biol 7: R125.
22. Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, et al. (2005) Detecting protein function and protein-protein interactions from genome sequences. Science 285: 751-753.
23. Finn RD, Marshall M, Bateman A (2005) iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics 21: 410-412.
24. Sprinzak E, Margalit H (2001) Correlated sequence-signatures as markers of protein-protein interaction. J Mol Biol 311: 681-692.
25. Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature 402: 86-90.
26. Vucetic S, Obradovic Z (2001) Classification on data with biased class distribution. Lecture Notes Comp Sci 2167: 527-538.
27. Guda C, Subramaniam S (2005) pTARGET: A new method for predicting protein sub-cellular localization in eukaryotes. Bioinformatics 21: 3963-3969.
28. King BR, Guda C (2007) ngLOC: an n-gram-based Bayesian method for estimating the subcellular proteomes of eukaryotes. Genome Biol 8: R68.
29. Brown KR, Jurisica I (2005) Online predicted human interaction database. Bioinformatics 21: 2076-2082.
30. Smadja F, McKeown KR, Hatzivassiloglou V (1996) Translating collocations for bilingual lexicons: a statistical approach. Computational Linguistics 22: 1-38.
31. Apic G, Gough J, Teichmann SA (2001) Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol 310: 311-325.
32. Vogel C, Teichmann SA, Pereira-Leal J (2005) The relationship between domain duplication and recombination. J Mol Biol 346: 355-365.
33. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
34. Han D, Kim HS, Seo J, Jang W (2003) A domain combination based probabilistic framework for protein-protein interaction prediction. Genome Inform 14: 250-259.
35. Liu Y, Liu N, Zhao H (2005) Inferring protein-protein interactions through high-throughput interaction data from diverse organisms. Bioinformatics 21: 3279-3285.
36. Stein A, Russell RB, Aloy P (2005) 3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res 33: D413-417.
37. Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, et al. (2006) Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 38: 285-293.
38. Ofran Y, Rost B (2007) Protein-protein interaction hotspots carved into sequences. PLoS Comput Biol 3(7): e119.
39. Schuster-Bockler B, Bateman A (2007) Reuse of structural domain-domain interactions in protein networks. BMC Bioinformatics 8: 259.