Abstract
The identification of protein complexes is becoming increasingly important to our understanding of cellular functionality. However, if a biologist wishes to investigate a certain protein, currently no method exists to assist him/her to accurately retrieve the possible protein partners that are expected to be in the same functional complex. Here, we introduce ProtRet, a web server that functions as an interface for an improved Pigeonhole approach to identify protein complexes in protein-protein interaction networks. The approach provides high-quality protein comparison that is particularly valuable because of its accurate statistical estimates based on fuzzy criterion and Hamming distance. The proposed method was tested on two high-throughput experimental protein-protein interaction data sets and two gold standard data sets and was able to retrieve more correct protein members than all existing methods. The web server is accessible from the link http://www.protret.com/.
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Zaki, N., Deris, S., Alashwal, A.: Protein-protein interaction detection based on substring sensitivity measure. Int. J. Biomed. Sci. 1(2) (2006). ISSN 1306–1216
Farutin, V., Robinson, K., Lightcap, E., Dancik, V., Ruttenberg, A., Letovsky, S., Pradines, J.: Edge-count probabilities for the identification of local protein communities and their organization. Proteins: Struct. Funct. Bioinform. 62, 800–818 (2006)
Hanna, E.M., Zaki, N.: Detecting protein complexes in protein interaction networks using a ranking algorithm with a refined merging procedure. BMC Bioinform. 15, 204 (2014)
Liu, H., Liu, J.: Clustering protein interaction data through chaotic genetic algorithm. In: Simulated Evolution and Learning. Lecture Notes in Computer Science, vol. 4247, pp. 858–864 (2006)
Bader, G., Hogue, H.: An automated method for finding molecular com-plexes in large protein-protein interaction networks. BMC Bioinform. 4, 2 (2003)
Adamcsek, B., Palla, G., Farkas, I.J., Derényi, I., Vicsek, T.: CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics 22, 1021–1023 (2006)
Zaki, N., Berengueres, J., Efimov, D.: Detection of protein complexes using a protein ranking algorithm. Proteins: Struct. Funct. Bioinform. 80(10), 2459–2468 (2012)
Guimei, L., Wong, L., Chua, H.N.: Complex discovery from weighted PPI networks. Bioinformatics 25, 1891–1897 (2009)
Nepusz, T., Yu, H., Paccanaro, A.: Detecting overlapping protein complexes in protein-protein interaction networks. Nat. Methods 9, 471–472 (2012)
Zaki, N., Dmitry, D., Berengueres, J.: Protein complex detection using interaction reliability assessment and weighted clustering coefficient. BMC Bioinform. 14, 1163 (2013)
King, A.D., Przulj, N., Jurisica, I.: Protein complex prediction via cost-based clustering. Bioinformatics 17, 3013–3020 (2004)
Enright, A.J., Dongen, S.V., Ouzounis, C.A.: An efficient algorithm for largescale detection of protein families. Nucl. Acids Res. 30, 1575–1584 (2002)
Macropol, K., Can, T., Singh, A.: RRW: repeated random walks on genome-scale protein networks for local cluster discovery. BMC Bioinform. 10, 283 (2009)
Herstein, I.N.: Topics In Algebra. Blaisdell Publishing Company, Waltham (1964)
Gavin, A.C., et al.: Functional organization of the yeast proteome by system-atic analysis of protein complexes. Nature 415, 141–147 (2002)
Gavin, A.C., et al.: Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631–636 (2006)
Leung, H., Xiang, Q., Yiu, S.M., Chin, F.: Predicting protein complexes from PPI data: a core-attachment approach. J. Comput. Biol. 16, 133–139 (2009)
Mewes, H.W., et al.: MIPS: analysis and annotation of proteins from whole genomes. Nucl. Acids Res. 32, D41–D44 (2004)
Pearson, W.R.: Flexible sequence similarity searching with the FASTA3 program package. Methods Mol. Biol. 132, 185–219 (2000)
Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25, 3389–3402 (1997)
Aaron J. Mackey, AJ., Haystead, TJ., Pearson, WR.: Algorithms for rapid protein identification with multiple short peptide sequences. Mol. Cell. Proteomics 1, 139-147 (2002)
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The authors acknowledge financial support from the ICT Fund (Grant # G00001472) and the UAEU (Grant # G00002659).
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Zaki, N., Al Yammahi, M., Habuza, T. (2020). ProtRet: A Web Server for Retrieving Proteins in a Functional Complex. In: Fdez-Riverola, F., Rocha, M., Mohamad, M., Zaki, N., Castellanos-Garzón, J. (eds) Practical Applications of Computational Biology and Bioinformatics, 13th International Conference. PACBB 2019. Advances in Intelligent Systems and Computing, vol 1005 . Springer, Cham. https://doi.org/10.1007/978-3-030-23873-5_1
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DOI: https://doi.org/10.1007/978-3-030-23873-5_1
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