Discover protein sequence signatures from protein-protein interaction data

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Fang, Jianwen ^a   Haasl, Ryan J ^a   Dong, Yinghua ^a   Lushington, Gerald H ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HIGH-THROUGHPUT TECHNOLOGIES; INTERACTING SITES; PROTEIN SEQUENCES; PROTEIN-PROTEIN INTERACTIONS; SACCHAROMYCES CEREVISIAE GENOME; SHARING INFORMATION; SUBCELLULAR LOCALIZATIONS; YEAST TWO-HYBRID SYSTEM;

GENES; HYBRID SYSTEMS; MASS SPECTROMETRY; YEAST;

PROTEINS;

SACCHAROMYCES CEREVISIAE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CELLULAR DISTRIBUTION; COMPUTER PROGRAM; CONSERVATION GENETICS; CONTROLLED STUDY; MASS SPECTROMETRY; NONHUMAN; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; VALIDATION PROCESS; CHEMICAL STRUCTURE; GENETICS; INFORMATION RETRIEVAL; NUCLEOTIDE SEQUENCE; PROCEDURES; SEQUENCE HOMOLOGY;

SACCHAROMYCES CEREVISIAE;

BINDING SITES; CONSERVED SEQUENCE; INFORMATION STORAGE AND RETRIEVAL; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY;

EID: 28544436381     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-277     Document Type: Article

References (30)

1. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P et al: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403(6770):623-627.
2. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y: A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proceedings of the National Academy of Sciences of the United States of America 2001, 98(8):4569-4574.
3. Tong AHY, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S et al: A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 2002, 295(5553):321-324.
4. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM et al: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415(6868):141-147.
5. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K et al: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002, 415(6868):180-183.
6. Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ et al: A genome-wide transcriptional analysis of the mitotic cell cycle. Molecular Cell 1998, 2(1):65-73.
7. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai HY, He YDD et al: Functional discovery via a compendium of expression profiles. Cell 2000, 102(1):109-126.
8. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The Database of Interacting Proteins: 2004 update. Nucleic Acids Research 2004, 32:D449-D451.
9. Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stumpflen V, Mewes HW et al: The MIPS mammalian protein-protein interaction database. Bioinformatics 2005, 21(6):832-834.
10. Sprinzak E, Margalit H: Correlated sequence-signatures as markers of protein-protein interaction. Journal of Molecular Biology 2001, 311(4):681-692.
11. Deng MH, Mehta S, Sun FZ, Chen T: Inferring domain-domain interactions from protein-protein interactions. Genome Research 2002, 12(10):1540-1548.
12. Wojcik J, Schachter V: Protein-Protein interaction map inference using interacting domain profile pairs. Bioinformatics 2001, 17:S296-S305.
13. Han DS, Kim HS, Jang WH, Lee SD, Suh JK: PreSPI: a domain combination based prediction system for protein-protein interaction. Nucleic Acids Research 2004, 32(21):6312-6320.
14. Li HQ, Li JY: Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasets. Bioinformatics 2005, 21(3):314-324.
15. Bailey TL, Elkan C: Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization. Machine Learning 1995, 21(1-2):51-80.
16. Bailey TL, Gribskov M: Methods and statistics for combining motif match scores. Journal of Computational Biology 1998, 5(2):211-221.
17. Kabsch W, Sander C: Dictionary of Protein Secondary Structure - Pattern-Recognition of Hydrogen-Bonded and Geometrical Features. Biopolymers 1983, 22(12):2577-2637.
18. Bornberg-Bauer E, Beaussart F, Kummerfeld S, Teichmann S, Weiner J: The evolution of domain arrangements in proteins and interaction networks. Cellular and Molecular Life Sciences 2005, 62(4):435-445.
19. Cai YD, Chou KC: Predicting 22 protein localizations in budding yeast. Biochemical and Biophysical Research Communications 2004, 323(2):425-428.
20. Chou KC, Cai YD: Predicting protein localization in budding yeast. Bioinformatics 2005, 21(7):944-950.
21. Bhasin M, Raghava GPS: ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST. Nucleic Acids Research 2004, 32:W414-W419.
22. Mrowka R, Patzak A, Herzel H: Is there a bias in proteome research? Genome Research 2001, 11(12):1971-1973.
23. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P: Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417(6887):399-403.
24. Bader GD, Hogue CWV: Analyzing yeast protein-protein interaction data obtained from different sources. Nature Biotechnology 2002, 20(10):991-997.
25. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L et al: InterPro, progress and status in 2005. Nucleic Acids Research 2005, 33:D201-D205.
26. Zdobnov EM, Apweiler R: InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17(9):847-848.
27. Frenkel-Morgenstern M, Voet H, Pietrokovski S: Enhanced statistics for local alignment of multiple alignments improves prediction of protein function and structure. Bioinformatics 2005, 21(13):2950-2956.
28. Pearson WR: Flexible sequence similarity searching with the FASTA3 program package. In: Methods in Molecular Biology. vol. 132; 2000: 185-219.
29. Kahsay RY, Wang GL, Gao G, Liao L, Dunbrack R: Quasi-consensus-based comparison of profile hidden Markov models for protein sequences. Bioinformatics 2005, 21(10):2287-2293.
30. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK: Global analysis of protein localization in budding yeast. Nature 2003, 425(6959):686-691.