Fly-DPI: Database of protein interactomes for D. melanogaster in the approach of systems biology

BMC Bioinformatics

Volumn 7, Issue SUPPL.5, 2006, Pages

  Lin, Chung Yen ^a,b,c   Chen, Shu Hwa ^d   Cho, Chi Shiang ^a   Chen, Chia Ling ^a   Lin, Fan Kai ^a   Lin, Chieh Hua ^a   Chen, Pao Yang ^a   Lo, Chen Zen ^a   Hsiung, Chao A ^a  

^a NATIONAL HEALTH RESEARCH INSTITUTES   (Taiwan)

^b INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

^c NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^d GENOMICS RESEARCH CENTER   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL INFORMATION; DOMAIN-DOMAIN INTERACTIONS; DROSOPHILA MELANOGASTER; FILTERING STRATEGIES; LIKELIHOOD FUNCTIONS; PROTEIN INTERACTION NETWORKS; PROTEIN-PROTEIN INTERACTIONS; STATISTICAL MODELING; BIRD'S EYE VIEW; DATA SETS; EXPRESSION PATTERNS; FRUIT FLIES; HIGH SPECIFICITY; HIGH-THROUGHPUT; HYBRID MODEL; LOW PROBABILITY; ONLINE DATABASE; OPEN READING FRAME; PROTEIN ANNOTATION; PROTEIN INTERACTION; PROTEINS CONTROL; PROTEOMICS; REFERENCE SYSTEMS; SEARCH STRATEGIES; SHORTEST PATH; STATISTICAL MODELS; SYSTEMS BIOLOGY; YEAST TWO HYBRID;

DATABASE SYSTEMS; INFORMATION FILTERING; MOLECULAR BIOLOGY; RELIABILITY; BIOINFORMATICS;

PROTEINS;

ARTICLE; DROSOPHILA MELANOGASTER; FLY DPI DATABASE; HIGH THROUGHPUT SCREENING; MOLECULAR BIOLOGY; NONHUMAN; OPEN READING FRAME; PREDICTION; PROBABILITY; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEOMICS; RELIABILITY; SENSITIVITY AND SPECIFICITY; STATISTICAL MODEL; TWO HYBRID SYSTEM; ANIMAL; BIOLOGICAL MODEL; METHODOLOGY; SYSTEMS BIOLOGY;

AVES; DROSOPHILA MELANOGASTER;

ANIMALS; DATABASES, PROTEIN; DROSOPHILA MELANOGASTER; LIKELIHOOD FUNCTIONS; MODELS, BIOLOGICAL; PROTEIN INTERACTION MAPPING; SYSTEMS BIOLOGY;

EID: 33947407270     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-S5-S18     Document Type: Article

References (42)

1. Golemis E: Protein-Protein Interactions: A Molecular Cloning Manual. New York: Cold Spring Harbor Laboratory Press; 2001.
2. Fromont-Racine M, Rain JC, Legrain P: Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nat Genet 1997, 16(3):277-282.
3. Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, et al.: A Protein Interaction Map of Drosophila melanogaster. Science 2003, 302(5651):1727-1736.
4. Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, Yamamoto K, Kuhara S, Sakaki Y: 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 2000, 97(3):1143-1147.
5. Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, et al.: A Map of the Interactome Network of the Metazoan C. elegans. Science 2004, 303(5657):540-543.
6. Rain JC, Selig L, De Reuse H, Battaglia V, Reverdy C, Simon S, Lenzen G, Petel F, Wojcik J, Schachter V, et al.: The protein-protein interaction map of Helicobacter pylori. Nature 2001, 409(6817):211-215.
7. Reboul J, Vaglio P, Rual JF, Lamesch P, Martinez M, Armstrong CM, Li S, Jacotot L, Bertin N, Janky R, et al.: C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat Genet 2003, 34(1):35-41.
8. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S: A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome. Cell 2005, 122(6):957-968.
9. Suzuki H, Fukunishi Y, Kagawa I, Saito R, Oda H, Endo T, Kondo S, Bono H, Okazaki Y, Hayashizaki Y: Protein-Protein Interaction Panel Using Mouse Full-Length cDNAs. 2001, 11:1758-1765.
10. 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.
11. Deng M, Mehta S, Sun F, Chen T: Inferring domain-domain interactions from protein-protein interactions. Genome Res 2002, 12(10):1540-1548.
12. Sprinzak E, Margalit H: Correlated sequence-signatures as markers of protein-protein interaction. Journal of Molecular Biology 2001, 311(4):681-692.
13. Wojcik J, Schachter V: Protein-protein interaction map inference using interacting domain profile pairs. Bioinformatics 2001, 17(Suppl 1):S296-305.
14. Tader GD, Betel D, Hogue CW: BIND: the biomolecular interaction network database. Nucleic Acids Res 2003, 31(1):248-250.
15. Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, Eisenberg D: DIP, the database of interacting proteins: A research tool for studying cellular networks of protein interactions. Nucleic Acids Res 2002, 30(1):303-305.
16. HuAZ, Mellor J, Wu J, DeLisi C: VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics 2004, 5(1):17.
17. BrAitkreutz BJ, Stark C, Tyers M: Osprey: a network visualization system. Genome Biology 2003, 4(3):R22.
18. Ju BH, Han K: Complexity management in visualizing protein interaction networks. Bioinformatics 2003, 19(Suppl 1):i177-i179.
19. Batagelj V, Mrvar A: Pajek - analysis and visualization of large networks. 2002.
20. David A: Tulip. Lecture Notes Comput Sci 2002:435-437.
21. Bock JR, Gough DA: Predicting protein-protein interactions from primary structure. Bioinformatics 2001, 17(5):455-460.
22. Han D, Kim HS, Seo J, Jang W: A domain combination based probabilistic framework for protein-protein interaction prediction. Genome InformSerWorkshop Genome Inform 2003, 14:250-259.
23. HaA DS, Kim HS, Jang WH, Lee SD, Suh JK: PreSPI: a domain combination based prediction system for protein-protein interaction. Nucleic Acids Res 2004, 32(21):6312-6320.
24. Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D: Detecting protein function and protein-protein interactions from genome sequences. Science 1999, 285(5428):751-753.
25. Valencia A, Pazos F: Computational methods for the prediction of protein interactions. Curr Opin Struct Biol 2002, 12(3):368-373.
26. Walhout AJ, Sordella R, Lu X, Hartley JL, Temple GF, Brasch MA, Thierry-Mieg N, Vidal M: Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 2000, 287(5450):116-122.
27. Camon E, Magrane M, Barrell D, Binns D, Fleischmann W, Kersey P, Mulder N, Oinn T, Maslen J, Cox A, et al.: The Gene Ontology Annotation (GOA) Project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res 2003, 13(4):662-672.
28. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M: The KEGG resource for deciphering the genome. Nucleic Acids Res 2004, 32(1):D277-D280.
29. The FlyBase C: The FlyBase database of the Drosophila genome projects and community literature. Nucl Acids Res 2003, 31(1):172-175.
30. Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Tatusova TA, et al.: Database resources of the National Center for Biotechnology. Nucleic Acids Res 2003, 31(1):28-33.
31. Lin CY, Chen CL, Cho CS, Wang LM, Chang CM, Chen PY, Lo CZ, Hsiung CA: hp-DPI: Helicobacter pylori database of protein interactomes - embracing experimental and inferred interactions. Bioinformatics 2005, 21(7):1288-1290.
32. Levanon D, Goldstein RE, Bernstein Y, Tang H, Goldenberg D, Stifani S, Paroush Z, Groner Y: Transcriptional repression by AML1 and LEF-1 is mediated by the TLE/Groucho corepressors. Proc Natl Acad Sci USA 1998, 95(20):11590-11595.
33. Zhu CC, Dyer MA, Uchikawa M, Kondoh H, Lagutin OV, Oliver G: Six3-mediated auto repression and eye development requires its interaction with members of the Grouchorelated family of co-repressors. Development 2002, 129(12):2835-2849.
34. Barolo S, Stone T, Bang AG, Posakony JW: Default repression and notch signaling: Hairless acts as an adaptor to recruit the corepressors Groucho and dCtBP to suppressor of hairless. Genes Dev 2002, 16(15):1964-1976.
35. Neves A, Priess JR: The REF-1 family of bHLH transcription factors pattern C. elegans embryos through Notch-dependent and Notch-independent pathways. Dev Cell 2005, 8(6):867-879.
36. Formstecher E, Aresta S, Collura V, Hamburger A, Meil A, Trehin A, Reverdy C, Betin V, Maire S, Brun C, et al.: Protein interaction mapping: A Drosophila case study. Genome Res 2005, 15(3):376-384.
37. Stanyon CA, Liu G, Mangiola BA, Patel N, Giot L, Kuang B, Zhang H, Zhong J, Finley RL Jr: A Drosophila protein-interaction map centered on cell-cycle regulators. Genome Biol 2004, 5(12):R96.
38. DryGdale RA, Crosby MA: FlyBase: genes and gene models. Nucleic Acids Res 2005:D390-D395.
39. Pawson T, Nash P: Assembly of cell regulatory systems through protein interaction domains. Science 2003, 300(5618):445-452.
40. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, et al.: The Universal Protein Resource (UniProt). Nucleic Acids Res 2005:D154-D159.
41. 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 Res 2005:D201-D205.
42. Lin N, Wu B, Jansen R, Gerstein M, Zhao H: Information assessment on predicting protein-protein interactions. BMC Bioinformatics 2004, 5:154-164.