Abstract
Many fundamental processes involve protein-protein interactions. Recent advances in technology make it possible to perform large-scale, genome-wide interaction mapping experiments that result in an always increasing amount of data. Protein-protein interaction databases are thus becoming a major resource for investigating biological networks and pathways. In this chapter we describe the Molecular INTeraction database (MINT). The MINT database aims at storing, in a structured format, information about protein-protein interactions (PPIs) by extracting experimental details from work published in peer-reviewed journals.
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References
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.
Hermjakob, H., Montecchi-Palazzi, L., Lewington, C., Mudali, S., Kerrien, S., Orchard, S., Vingron, M., Roechert, B., Roepstorff, P., Valencia, A., et al. (2004) IntAct: an open source molecular interaction database. Nucleic Acids Res. 32, D452–D455.
Chatr-aryamontri, A., Ceol, A., Palazzi, L. M., Lardelli, G., Schneider, M. V., Castagnoli, L., and Cesareni G. (2007) MINT: the Molecular INTeraction database. Nucleic Acids Res. 35, D572–D574.
Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., et al. (2004) The HUPO PSI’s molecular interaction format—a community standard for the representation of protein interaction data. Nat. Biotechnol. 22, 177–183.
Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.
Bairoch, A., Apweiler, R., Wu, C. H., Barker, W. C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., et al. (2005) The Universal Protein Resource (UniProt). Nucleic Acids Res. 33, D154–D159.
Birney, E., Andrews, D., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cox, T., Cunningham, F., Curwen, V., Cutts, T., et al. (2006) Ensembl 2006. Nucleic Acids Res. 34, D556–D561.
Grumbling, G., and Strelets, V. (2006) FlyBase: anatomical data, images and queries. Nucleic Acids Res. 34, D484–D488.
Hirschman, J. E., Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hong, E. L., Livstone, M. S., Nash, R., et al. (2006) Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res. 34, D442–D445.
Schwarz, E. M., Antoshechkin, I., Bastiani, C., Bieri, T., Blasiar, D., Canaran, P., Chan, J., Chen, N., Chen, W. J., Davis, P., et al. (2006) WormBase: better software, richer content. Nucleic Acids Res. 34, D475–D478.
Kikuno, R., Nagase, T., Nakayama, M., Koga, H., Okazaki, N., Nakajima, D., and Ohara, O. (2004) HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE. Nucleic Acids Res. 32, D502–D504.
Joshi-Tope, G., Gillespie, M., Vastrik, I., D’Eustachio, P., Schmidt, E., de Bono, B., Jassal, B., Gopinath, G. R., Wu, G. R., Matthews, L., et al. (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 33, D428–D432.
McKusick, V. A. (1998) Mendelian Inheritance in Man. A Catalog of Human Genes and Genetic Disorders. Johns Hopkins University Press, Baltimore, MD.
Chatr-Aryamontri, A., Ceol, A., Licata, L., and Cesareni, G. (2008) Protein interactions: integration leads to belief. Trends Biochem Sci. May 8, 2008.
Breitkreutz, B. J., Stark, C., and Tyers, M. (2003) Osprey: a network visualization system. Genome Biol. 4, R22.
Bader, G. D. and Hogue, C. W. (2002) Analyzing yeast protein-protein interaction data obtained from different sources. Nat. Biotechnol. 20, 991–997.
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© 2008 Humana Press, Totowa, NJ
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Chatr-aryamontri, A., Zanzoni, A., Ceol, A., Cesareni, G. (2008). Searching the Protein Interaction Space Through the MINT Database. In: Thompson, J.D., Ueffing, M., Schaeffer-Reiss, C. (eds) Functional Proteomics. Methods in Molecular Biology, vol 484. Humana Press. https://doi.org/10.1007/978-1-59745-398-1_20
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DOI: https://doi.org/10.1007/978-1-59745-398-1_20
Publisher Name: Humana Press
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Online ISBN: 978-1-59745-398-1
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