A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Pacifico, Svetlana ^a,b   Liu, Guozhen ^a   Guest, Stephen ^a   Parrish, Jodi R ^a   Fotouhi, Farshad ^b   Finley Jr , Russell L ^a  

^a WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Wayne State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL ANALYSIS; COMPUTATIONAL PREDICTIONS; COMPUTATIONAL TECHNIQUE; GENETIC INTERACTION; GRAPHICAL REPRESENTATIONS; HIGH-THROUGHPUT SCREENS; MULTIPLE INTERACTIONS; WEB-BASED APPLICATIONS;

DATA INTEGRATION; GENES; PROTEINS; RELATIONAL DATABASE SYSTEMS; TOOLS;

SEARCH ENGINES;

ACCESS TO INFORMATION; ARTICLE; COMPUTER INTERFACE; COMPUTER PREDICTION; COMPUTER PROGRAM; CONTROLLED STUDY; DROSOPHILA; GENE INTERACTION; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC IDENTIFICATION; HIGH THROUGHPUT SCREENING; INFORMATION PROCESSING; INFORMATION STORAGE; INTERNET; MATHEMATICAL COMPUTING; NONHUMAN; PROCESS DESIGN; PROTEIN INTERACTION; PUBLISHING; WEB BROWSER; DATA BASE; GENE EXPRESSION PROFILING; GENETICS; INFORMATION RETRIEVAL; METABOLISM; PROCEDURES; PROTEIN ANALYSIS; SYSTEM ANALYSIS;

DROSOPHILA PROTEIN;

DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; DROSOPHILA PROTEINS; GENE EXPRESSION PROFILING; INFORMATION STORAGE AND RETRIEVAL; INTERNET; PROTEIN INTERACTION MAPPING; SOFTWARE; SYSTEMS INTEGRATION; USER-COMPUTER INTERFACE;

EID: 33646380337     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-195     Document Type: Article

References (56)

1. Phizicky E, Bastiaens PI, Zhu H, Snyder M, Fields S: Protein analysis on a proteomic scale. Nature 2003, 422(6928):208-215.
2. Uetz P, Finley RLJ: From protein networks to biological systems. FEBS Lett 2005, 579(8):1821-1827.
3. Cusick M, Klitgord N, Vidal M, Hill DE: Interactome: Gateway into systems biology. Hum Mol Genet 2005.
4. Fields S, Song O: A novel genetic system to detect protein-protein interactions. Nature 1989, 340(6230):245-246.
5. Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley RLJ, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM: A protein interaction map of Drosophila melanogaster. Science 2003, 302(5651):1727-1736.
6. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y: A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 2001, 98(8):4569-4574.
7. Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual JF, Lamesch P, Xu L, Tewari M, Wong SL, Zhang LV, Berriz GF, Jacotot L, Vaglio P, Reboul J, Hirozane-Kishikawa T, Li Q, Gabel HW, Elewa A, Baumgartner B, Rose DJ, Yu H, Bosak S, Sequerra R, Fraser A, Mango SE, Saxton WM, Strome S, Van Den Heuvel S, Piano F, Vandenhaute J, Sardet C, Gerstein M, Doucette-Stamm L, Gunsalus KC, Harper JW, Cusick ME, Roth FP, Hill DE, Vidal M: A map of the interactome network of the metazoan C. elegans. Science 2004, 303(5657):540-543.
8. Stanyon CA, Liu G, Mangiola BA, Patel N, Giot L, Kuang B, Zhang H, Zhong J, Finley RLJ: A Drosophila protein-interaction map centered on cell-cycle regulators. Genome Biol 2004, 5(12):R96.
9. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403(6770):623-627.
10. Formstecher E, Aresta S, Collura V, Hamburger A, Meil A, Trehin A, Reverdy C, Betin V, Maire S, Brun C, Jacq B, Arpin M, Bellaiche Y, Bellusci S, Benaroch P, Bornens M, Chanet R, Chavrier P, Delattre O, Doye V, Fehon R, Faye G, Galli T, Girault JA, Goud B, de Gunzburg J, Johannes L, Junier MP, Mirouse V, Mukherjee A, Papadopoulo D, Perez F, Plessis A, Rosse C, Saule S, Stoppa-Lyonnet D, Vincent A, White M, Legrain P, Wojcik J, Camonis J, Daviet L: Protein interaction mapping: a Drosophila case study. Genome Res 2005, 15(3):376-384.
11. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Hofert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415(6868):141-147.
12. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002, 415(6868):180-183.
13. Bouwmeester T, Bauch A, Ruffner H, Angrand PO, Bergamini G, Croughton K, Cruciat C, Eberhard D, Gagneur J, Ghidelli S, Hopf C, Huhse B, Mangano R, Michon AM, Schirle M, Schlegl J, Schwab M, Stein MA, Bauer A, Casari G, Drewes G, Gavin AC, Jackson DB, Joberty G, Neubauer G, Rick J, Kuster B, Superti-Furga G: A physical and functional map of the human TNF-alpha/ NF-kappa B signal transduction pathway. Nat Cell Biol 2004, 6(2):97-105.
14. Bader GD, Hogue CW: Analyzing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol 2002, 20(10):991-997.
15. Deane CM, Salwinski L, Xenarios I, Eisenberg D: Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics 2002, 1(5):349-356.
16. 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.
17. Boutros M, Kiger AA, Armknecht S, Kerr K, Hild M, Koch B, Haas SA, Consortium HF, Paro R, Perrimon N: Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 2004, 303(5659):832-835.
18. Tewari M, Hu PJ, Ahn JS, Ayivi-Guedehoussou N, Vidalain PO, Li S, Milstein S, Armstrong CM, Boxem M, Butler MD, Busiguina S, Rual JF, Ibarrola N, Chaklos ST, Bertin N, Vaglio P, Edgley ML, King KV, Albert PS, Vandenhaute J, Pandey A, Riddle DL, Ruvkun G, Vidal M: Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network. Mol Cell 2004, 13(4):469-482.
19. Kim JK, Gabel HW, Kamath RS, Tewari M, Pasquinelli A, Rual JF, Kennedy S, Dybbs M, Bertin N, Kaplan JM, Vidal M, Ruvkun G: Functional genomic analysis of RNA interference in C. elegans. Science 2005, 308(5725):1164-1167.
20. Kelley BP, Sharan R, Karp RM, Sittler T, Root DE, Stockwell BR, Ideker T: Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci U S A 2003, 100(20):11394-11399.
21. Aloy P, Bottcher B, Ceulemans H, Leutwein C, Mellwig C, Fischer S, Gavin AC, Bork P, Superti-Furga G, Serrano L, Russell RB: Structure-based assembly of protein complexes in yeast. Science 2004, 303(5666):2026-2029.
22. Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA: Protein interaction maps for complete genomes based on gene fusion events. Nature 1999, 402(6757):86-90.
23. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M: A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 2003, 302(5644):449-453.
24. Lu L, Arakaki AK, Lu H, Skolnick J: Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome. Genome Res 2003, 13(6A):1146-1154.
25. Lu LJ, Xia Y, Paccanaro A, Yu H, Gerstein M: Assessing the limits of genomic data integration for predicting protein networks. Genome Res 2005, 15(7):945-953.
26. Reiss DJ, Schwikowski B: Predicting protein-peptide interactions via a network-based motif sampler. Bioinformatics 2004, 20 Suppl 1:1274-1282.
27. Zhang LV, Wong SL, King OD, Roth FP: Predicting co-complexed protein pairs using genomic and proteomic data integration. BMC Bioinformatics 2004, 5(1):38.
28. Bader GD, Betel D, Hogue CW: BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res 2003, 31(1):248-250.
29. Brown KR, Jurisica I: Online predicted human interaction database. Bioinformatics 2005, 21(9):2076-2082.
30. Mellor JC, Yanai I, Clodfelter KH, Mintseris J, DeLisi C: Predictome: a database of putative functional links between proteins. Nucleic Acids Res 2002, 30(1):306-309.
31. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 2004, 32 Database issue:D449-51.
32. Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G: MINT: a Molecular INTeraction database. FEBS Lett 2002, 513(1):135-140.
33. von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B: STRING: a database of predicted functional associations between proteins. Nucleic Acids Res 2003, 31(1):258-261.
34. Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A, Margalit H, Armstrong J, Bairoch A, Cesareni G, Sherman D, Apweiler R: IntAct: an open source molecular interaction database. Nucleic Acids Res 2004, 32 Database issue:D452-5.
35. Breitkreutz BJ, Stark C, Tyers M: The GRID: the General Repository for Interaction Datasets. Genome Biol 2003, 4(3):R23.
36. Consortium TF: The FlyBase database of the Drosophila genome projects and community literature. Nucliec Acids Res 2003, 31(1):172-175.
37. Flybase [http://flybase.org]
38. Matthews LR, Vaglio P, Reboul J, Ge H, Davis BP, Garrels J, Vincent S, Vidal M: Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Res 2001, 11(12):2120-2126.
39. Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M: Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res 2004, 14(6):1107-1118.
40. Mewes HW, Amid C, Arnold R, Frishman D, Guldener U, Mannhaupt G, Munsterkotter M, Pagel P, Strack N, Stumpflen V, Warfsmann J, Ruepp A: MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res 2004, 32 Database issue:D41-4.
41. Kelley R, Ideker T: Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol 2005, 23(5):561-566.
42. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25-29.
43. proteome.wayne.edu World Wide Web Site [http://proteome.wayne.edu].
44. Barabasi AL, Oltvai ZN: Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5(2):101-113.
45. Bader GD, Hogue CW: An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4(1):2.
46. Schwikowski B, Uetz P, Fields S: A network of protein-protein interactions in yeast. Nat Biotechnol 2000, 18(12):1257-1261.
47. Rives AW, Galitski T: Modular organization of cellular networks. Proc Natl Acad Sci U S A 2003, 100(3):1128-1133.
48. Vazquez A, Flammini A, Maritan A, Vespignani A: Global protein function prediction from protein-protein interaction networks. Nat Biotechnol 2003, 21(6):697-700.
49. Goldberg DS, Roth FP: Assessing experimentally derived interactions in a small world. Proc Natl Acad Sci U S A 2003, 100(8):4372-4376.
50. Bader JS, Chaudhuri A, Rothberg JM, Chant J: Gaining confidence in high-throughput protein interaction networks. Nat Biotechnol 2004, 22(1):78-85.
51. Jackson PK, Eldridge AG: The SCF ubiquitin ligase: an extended look. Mol Cell 2002, 9(5):923-925.
52. Bai C, Sen P, Hofmann K, Ma L, Goebl M, Harper JW, Elledge SJ: SKP I connects cell cycle regulators to the ubiquitin proteolysis machinery through a novel motif, the F-box. Cell 1996, 86(2):263-274.
53. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504.
54. Breitkreutz BJ, Stark C, Tyers M: Osprey: a network visualization system. Genome Biol 2003, 4(3):R22.
55. Hu Z, Mellor J, Wu J, DeLisi C: VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics 2004, 5(1):17.
56. Fraser AG, Marcotte EM: A probabilistic view of gene function. Nat Genet 2004, 36(6):559-564.