The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
An experimentally derived confidence score for binary protein-protein interactions
Open accessAbstract
Information on protein-protein interactions is of central importance for many areas of biomedical research. At present no method exists to systematically and experimentally assess the quality of individual interactions reported in interaction mapping experiments. To provide a standardized confidence-scoring method that can be applied to tens of thousands of protein interactions, we have developed an interaction tool kit consisting of four complementary, high-throughput protein interaction assays. We benchmarked these assays against positive and random reference sets consisting of well documented pairs of interacting human proteins and randomly chosen protein pairs, respectively. A logistic regression model was trained using the data from these reference sets to combine the assay outputs and calculate the probability that any newly identified interaction pair is a true biophysical interaction once it has been tested in the tool kit. This general approach will allow a systematic and empirical assignment of confidence scores to all individual protein-protein interactions in interactome networks.
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Cites
High-Quality Binary Protein Interaction Map of the Yeast Interactome Network
Yu, H., Braun, P., Yıldırım, M. A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N., et al. (2008) · Science · doi:10.1126/science.1158684 · Cited by 1,392
Self-citationNext-generation high-density self-assembling functional protein arrays
Ramachandran, N., Raphael, J. V., Hainsworth, E., Demirkan, G., Fuentes, M. G., Rolfs, A., Hu, Y., & LaBaer, J. (2008) · Nature Methods · doi:10.1038/nmeth.1210 · Cited by 303
Cited by
A reference map of the human binary protein interactome
Luck, K., Kim, D.-K., Lambourne, L., Spirohn, K., Begg, B. E., Bian, W., Brignall, R., Cafarelli, T., Campos-Laborie, F. J., Charloteaux, B., et al. (2020) · Nature · doi:10.1038/s41586-020-2188-x · Cited by 1,197
Self-citationStructure-based prediction of protein–protein interactions on a genome-wide scale
Zhang, Q. C., Petrey, D., Deng, L., Qiang, L., Shi, Y., Thu, C. A., Bisikirska, B., Lefebvre, C., Accili, D., Hunter, T., et al. (2012) · Nature · doi:10.1038/nature11503 · Cited by 723
Widespread macromolecular interaction perturbations in human genetic disorders
Sahni, N., Yi, S., Taipale, M., Fuxman Bass, J. I., Coulombe-Huntington, J., Yang, F., Peng, J., Weile, J., Karras, G. I., Wang, Y., et al. (2015) · Cell · doi:10.1016/j.cell.2015.04.013 · Cited by 594
Self-citationTissue-specific alternative splicing remodels protein-protein interaction networks
Ellis, J. D., Barrios-Rodiles, M., Çolak, R., Irimia, M., Kim, T., Calarco, J. A., Wang, X., Pan, Q., O'Hanlon, D., Kim, P. M., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.05.037 · Cited by 431
Self-citationWu, P., Lin, S., Cao, G., Wu, J., Jin, H., Wang, C., Wong, M. H., Yang, Z., & Cai, Z. (2022) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2022.129361 · Cited by 428
Metadata
- Authors
- Braun, P., Tasan, M., Dreze, M., Barrios-Rodiles, M., Lemmens, I., Yu, H., Sahalie, J. M., Murray, R. R., Roncari, L., de Smet, A.-S., Venkatesan, K., Rual, J.-F., Vandenhaute, J., Cusick, M. E., Pawson, T., Hill, D. E., Tavernier, J., Wrana, J. L., Roth, F. P., & Vidal, M.
- Venue
- Nature Methods
- Published
- 2008-12-07
- Volume
- 6
- Issue
- 1
- Pages
- 91-97
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2149148688
- Cited by
- 443
- References
- 2
- FWCI
- 12.66
- Type
- journal article
- Language
- en
- Open access
- green
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