The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 Viewer

Genome Research

Volumn 13, Issue 6 B, 2003, Pages 1534-1541

  Suzuki, Harukazu ^a,c   Saito, Rintaro ^a,d   Kanamori, Mutsumi ^a   Kai, Chikatoshi ^a   Schönbach, Christian ^a   Nagashima, Takeshi ^a   Hosaka, Junko ^a   Hayashizaki, Yoshihide ^a,b,c  

^a RIKEN YOKOHAMA INSTITUTE   (Japan)

^b RIKEN   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^d KEIO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

LUCIFERASE;

ARTICLE; CELL COMMUNICATION; INFORMATION PROCESSING; MEDLINE; MOLECULAR CLONING; ONLINE SYSTEM; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN PROTEIN INTERACTION; RELIABILITY; REPORTER GENE; SIGNAL TRANSDUCTION;

ANIMALS; DATA DISPLAY; DATABASES, GENETIC; DATABASES, PROTEIN; INTERNET; MAMMALS; MICE; PROTEIN INTERACTION MAPPING; REFERENCE STANDARDS; SOFTWARE;

MAMMALIA;

EID: 0038349339     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.956303     Document Type: Article

References (33)

1. Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, J.D., Amanatides, P.G., Scherer, S.E., Li, P.W., Hoskins, R.A., Galle, R.F., et al. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
2. Antonny, B. and Schekman, R. 2001. ER export: Public transportation by the COPII coach. Curr. Opin. Cell. Biol. 13: 438-443.
3. 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.
4. Castro, P., Liang, H., Liang, J.C., and Nagarajan, L. 2002. A novel, evolutionarily conserved gene family with putative sequence-specific single-stranded DNA-binding activity. Genomics 80: 78-85.
5. The C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282: 2012-2018.
6. Goffeau, A., Barrell, B.G., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J.D., Jacq, C., Johnston, M., et al. 1996. Life with 6000 genes. Science 274: 546, 563-567.
7. Grigoriev, A. 2001. A relationship between gene expression and protein interactions on the proteome scale: Analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Res. 29: 3513-3519.
8. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. 98: 4569-4574.
9. Kanamori, M., Suzuki, H., Saito, R., Muramatsu, M., and Hayashizaki, Y. 2002. T2BP, a novel TRAF2 binding protein, can activate NF-κB and AP-1 without TNF stimulation. Biochem. Biophys. Res. Commun. 290: 1108-1113.
10. Kawai, J., Shinagawa, A., Shibata, K., Yoshino, M., Itoh, M., Ishii, Y., Arakawa, T., Hara, A., Fukunishi, Y., Konno, H., et al. 2001. Functional annotation of a full-length mouse cDNA collection. Nature 409: 685-690.
11. Kawamata, N., Sakajiri, S., Sugimoto, K.J., Isobe, Y., Kobayashi, H., and Oshimi, K. 2002. A novel chromosomal translocation t(1;14)(q25;q32) in pre-B acute lymphoblastic leukemia involves the LIM homeodomain protein gene, Lhx4. Oncogene 21: 4983-4991.
12. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
13. Legrain, P., Wojcik, J., and Gauthier, J.M. 2001. Protein-protein interaction maps: A lead towards cellular functions. Trends Genet. 17: 346-352.
14. Matthews, L.R., Vaglio, P., Reboul, J., Ge, H., Davis, B.P., Garrels, J., Vincent, S., and Vidal, M. 2001. Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Res. 11: 2120-2126.
15. Nagashima, T., Silva, D.G., Petrovsky, N., Socha, L.A., Suzuki, H., Saito, R., Kasukawa, T., Kurochkin, I.V., Konagaya, A., and Schönbach, C. 2003. Inferring higher functional information for RIKEN mouse full-length cDNA clones with FACTS. Genome Res. 13: (this issue).
16. Okazaki, Y., Furuno, M., Kasukawa, T., Adachi, J., Bono, H., Kondo, S., Nikaido, I., Osato, N., Saito, R., Suzuki, H., et al. 2002. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420: 563-573.
17. Oliver, S. 2000. Guilt-by-association goes global. Nature 403: 601-603.
18. Pawson, T. and Nash, P. 2000. Protein-protein interactions define specificity in signal transduction. Genes & Dev. 14: 1027-1047.
19. Rabbitts, T.H. 1998. LMO T-cell translocation oncogenes typify genes activated by chromosomal translocations that alter transcription and developmental processes. Genes & Dev. 12: 2651-2657.
20. Saito, R., Suzuki, H., and Hayashizaki, Y. 2002. Interaction generality, a measurement to assess the reliability of a protein-protein interaction. Nucleic Acids Res. 30: 1163-1168.
21. Suzuki, H., Fukunishi, Y., Kagawa, I., Saito, R., Oda, H., Endo, T., Kondo, S., Bono, H., Okazaki, Y., and Hayashizaki, Y. 2001. Protein-Protein interaction panel using mouse full-length cDNAs. Genome Res. 11: 1758-1765.
22. Tani, K., Mizoguchi, T., Iwamatsu, A., Hatsuzawa, K., and Tagaya, M. 1999. p125 is a novel mammalian Sec23p-interacting protein with structural similarity to phospholipid-modifying proteins. J. Biol. Chem. 274: 20505-20512.
23. Uetz, P., Giot, L., Cagney, G., Mansfield, T.A., Judson, R.S., Knight, J.R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627.
24. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A., et al. 2001. The sequence of the human genome. Science 291: 1304-1351.
25. Visvader, J.E., Venter, D., Hahm, K., Santamaria, M., Sum, E.Y., O'Reilly, L., White, D., Williams, R., Armes, J., and Lindeman, G.J. 2001. The LIM domain gene LMO4 inhibits differentiation of mammary epithelial cells in vitro and is overexpressed in breast cancer. Proc. Natl. Acad. Sci. 98: 14452-14457.
26. 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.
27. Wajant, H. and Scheurich, P. 2001. Tumor necrosis factor receptor-associated factor (TRAF) 2 and its role in TNF signaling. Int. J. Biochem. Cell Biol. 33: 19-32.
28. Walhout, A.J., Boulton, S.J., and Vidal, M. 2000a. Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm. Yeast 17: 88-94.
29. Walhout, A.J., Sordella, R., Lu, X., Hartley, J.L., Temple, G.F., Brasch, M.A., Thierry-Mieg, N., and Vidal, M. 2000b. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287: 116-122.
30. Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
31. Wieland, F. and Harter, C. 1999. Mechanisms of vesicle formation: Insights from the COP system. Curr. Opin. Cell. Biol. 11: 440-446.
32. Wu, H.K., Heng, H.H., Siderovski, D.P., Dong, W.F., Okuno, Y., Shi, X.M., Tsui, L.C., and Minden, M.D. 1996. Identification of a human LIM-Hox gene, hLH-2, aberrantly expressed in chronic myelogenous leukaemia and located on 9q33-34.1. Oncogene 12: 1205-1212.
33. 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.