Create and assess protein networks through molecular characteristics of individual proteins

Bioinformatics

Volumn 22, Issue 14, 2006, Pages

  Ofran, Yanay ^a   Yachdav, Guy ^a   Mozes, Eyal ^a   Soong, Ta Tsen ^a   Nair, Rajesh ^a   Rost, Burkhard ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID BETA PROTEIN;

ALZHEIMER DISEASE; AUTOMATION; BIOINFORMATICS; CELL COMPARTMENTALIZATION; CELLULAR DISTRIBUTION; CONFERENCE PAPER; CONTROLLED STUDY; INFORMATION PROCESSING; MOLECULAR BIOLOGY; MOLECULAR MECHANICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION;

EID: 33747894631     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl258     Document Type: Conference Paper

References (26)

1. Bader,G.D., Donaldson,I., Wolting,C., Ouellette,B.F., Pawson,T. and Hogue,C.W. (2001) BIND - The Biomolecular Interaction Network Database. Nucleic Acids Res, 29, 242-245.
2. Barabasi,A.L. and Oltvai,Z.N. (2004) Network biology: Understanding the cell's functional organization. Nat Rev Genet, 5, 101-113.
3. Bork,P., Jensen,L.J., von Mering,C., Ramani,A.K., Lee,I. and Marcotte,E.M. (2004) Protein interaction networks from yeast to human. Curr Opin Struct Biol, 14, 292-299.
4. Chapman,P.F., Falinska,A.M., Knevett,S.G. and Ramsay,M.F. (2001) Genes, models and Alzheimer's disease. Trends Genet, 17, 254-261.
5. Cusick,M.E., Klitgord,N., Vidal,M. and Hill,D.E. (2005) Interactome: gateway into systems biology. Hum Mol Genet, 14 Spec No. 2, R171-181.
6. Deane,C.M., Salwinski,L., Xenarios,I. and Eisenberg,D. (2002) Protein interactions: Two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics, 1, 349-356.
7. Ge,H., Walhout,A.J. and Vidal,M. (2003) Integrating 'omic' information: a bridge between genomics and systems biology. Trends Genet, 19, 551-560.
8. Goto,S., Bono,H., Ogata,H., Fujibuchi,W., Nishioka,T., Sato,K. and Kanehisa,M. (1997) Organizing and computing metabolic pathway data in terms of binary relations. Pac Symp Biocomput, 175-186.
9. Grigoriev,A. (2003) On the number of protein-protein interactions in the yeast proteome. Nucleic Acids Res, 31, 4157-4161.
10. Hartwell,L.H., Hopfield,J.J., Leibler,S. and Murray,A.W. (1999) From molecular to modular cell biology. Nature, 402, C47-52.
11. 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. and Apweiler,R. (2004) IntAct: An open source molecular interaction database. Nucleic Acids Res, 32, D452-455.
12. Lord,P.W., Stevens,R.D., Brass,A. and Goble,C.A. (2003) Investigating semantic similarity measures across the Gene Ontology: The relationship between sequence and annotation. Bioinformatics, 19, 1275-1283.
13. Nair,R. and Rost,B. (2005) Mimicking cellular sorting improves prediction of subcellular localization. J Mol Biol, 348, 85-100.
14. Peri,S., Navarro,J.D., Amanchy,R., Kristiansen,T.Z., Jonnalagadda,C.K., Surendranath,V., Niranjan,V., Muthusamy,B., Gandhi,T.K., Gronborg,M., Ibarrola,N., Deshpande,N., Shanker,K., Shivashankar,H.N., Rashmi,B.P., Ramya,M.A., Zhao,Z., Chandrika,K.N., Padma,N., Harsha,H.C., Yatish,A.J., Kavitha,M.P., Menezes,M., Choudhury,D.R., Suresh,S., Ghosh,N., Saravana,R., Chandran,S., Krishna,S., Joy,M., Anand,S.K., Madavan,V., Joseph,A., Wong,G.W., Schiemann,W.P., Constantinescu,S.N., Huang,L., Khosravi-Far,R., Steen,H., Tewari,M., Ghaffari,S., Blobe,G.C., Dang,C.V., Garcia,J.G., Pevsner,J., Jensen,O.N., Roepstorff,P., Deshpande,K.S., Chinnaiyan,A.M., Hamosh,A., Chakravarti,A. and Pandey,A. (2003) Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res, 13, 2363-2371.
15. Ramani,A.K., Bunescu,R.C., Mooney,R.J. and Marcotte,E.M. (2005) Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol, 6, R40.
16. Rhodes,D.R., Tomlins,S.A., Varambally,S., Mahavisno,V., Barrette,T., Kalyana-Sundaram,S., Ghosh,D., Pandey,A. and Chinnaiyan,A.M. (2005) Probabilistic model of the human protein-protein interaction network. Nat Biotechnol, 23, 951-959.
17. Rost,B., Fariselli,P. and Casadio,R. (1996) Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci, 5, 1704-1718.
18. Selkoe,D.J. (2001) Alzheimer's disease: Genes, proteins, and therapy. Physiol Rev, 81, 741-766.
19. Shannon,P., Markiel,A., Ozier,O., Baliga,N.S., Wang,J.T., Ramage,D., Amin,N., Schwikowski,B. and Ideker,T. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res, 13, 2498-2504.
20. Sprinzak,E., Sattath,S. and Margalit,H. (2003) How reliable are experimental protein-protein interaction data? J Mol Biol, 327, 919-923.
21. Vazquez,A., Flammini,A., Maritan,A. and Vespignani,A. (2003) Global protein function prediction from protein-protein interaction networks. Nat Biotechnol, 21, 697-700.
22. von Mering,C., Jensen,L.J., Snel,B., Hooper,S.D., Krupp,M., Foglierini,M., Jouffre,N., Huynen,M.A. and Bork,P. (2005) STRING: Known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res, 33, D433-437.
23. von Mering,C., Krause,R., Snel,B., Cornell,M., Oliver,S.G., Fields,S. and Bork,P. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 417, 399-403.
24. Wuchty,S., Oltvai,Z.N. and Barabasi,A.L. (2003) Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat Genet, 35, 176-179.
25. Xenarios,I., Salwinski,L., Duan,X.J., Higney,P., Kim,S.M. and Eisenberg,D. (2002) DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions. Nucleic Acids Res, 30, 303-305.
26. Zanzoni,A., Montecchi-Palazzi,L., Quondam,M., Ausiello,G., Helmer-Citterich,M. and Cesareni,G. (2002) MINT: A Molecular INTeraction database. FEBS Lett, 513, 135-140.