Overlapping Community Detection on a Graph of Chemicals, Diseases and Genes for Drug Repositioning and Adverse Reactions Prediction
Developing a drug from scratch is a very long and expensive process that has a small probability of success. For this reason, pharmaceutical companies are devoting their efforts to find drugs that could be repositioned. When using a drug to treat a disease is necessary to consider what adverse reactions it may cause, this is why the prediction of adverse reactions is highly related to drug repositioning. We propose the detection of overlapping communities over a biological network of chemicals, diseases and genes in order to find drug-disease pairs that could be used as basis for later drug repositioning and adverse reactions prediction analysis. Of the evaluated overlapping community detection algorithms, OSLOM got the best results, producing 724 communities from which was possible to extract 215944 drug-disease pairs not present in the analyzed graph. We illustrate the usefulness of this set through examples of associations between pairs found in the scientific literature.
Amberger, J. S., C. A. Bocchini, F. Schiettecatte, A. F. Scott and A. Hamosh (2015). "OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders." Nucleic acids research 43(Database issue): D789-D798.
Andrea, L., F. Santo and K. János (2009). "Detecting the overlapping and hierarchical community structure in complex networks." New Journal of Physics 11(3): 033015.
Assenov, Y., F. Ramírez, S.-E. Schelhorn, T. Lengauer and M. Albrecht (2008). "Computing topological parameters of biological networks." Bioinformatics 24 2: 282-284.
Baumes, J., M. K. Goldberg, M. S. Krishnamoorthy, M. Magdon-Ismail and N. Preston (2005). Finding communities by clustering a graph into overlapping subgraphs. IADIS AC. N. Guimarães and P. T. Isaías, IADIS: 97-104.
Becker, K. G., K. C. Barnes, T. J. Bright and S. A. Wang (2004). "The Genetic Association Database." Nature Genetics 36: 431.
Chen, H., H. Zhang, Z. Zhang, Y. Cao and W. Tang (2015). "Network-Based Inference Methods for Drug Repositioning." Computational and Mathematical Methods in Medicine 2015: 7.
Davis, A. P., C. J. Grondin, K. Lennon-Hopkins, C. Saraceni-Richards, D. Sciaky, B. L. King, T. C. Wiegers and C. J. Mattingly (2015). "The Comparative Toxicogenomics Database's 10th year anniversary: update 2015." Nucleic acids research 43(Database issue): D914-D920.
Derenyi, I., G. Palla and T. Vicsek (2005). "Clique percolation in random networks." Phys Rev Lett 94(16): 160202.
Echeverri, A. F., A. Vidal, C. A. Canas, A. Agualimpia, G. J. Tobon and F. Bonilla-Abadia (2015). "Etanercept-induced pityriasis lichenoides chronica in a patient with rheumatoid arthritis." Case Rep Dermatol Med 2015: 168063.
Eckert, H. and J. Bajorath (2007). "Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches." Drug discovery today 12 5-6: 225-233.
Fortunato, S. (2010). "Community detection in graphs." Physics Reports 486(3): 75-174.
Frank, H., H. Michael, S. Alexander and G. Jochen (2011). "Identification of overlapping communities and their hierarchy by locally calculating community-changing resolution levels." Journal of Statistical Mechanics: Theory and Experiment 2011(01): P01023.
Girvan, M. and M. E. Newman (2002). "Community structure in social and biological networks." Proc Natl Acad Sci U S A 99(12): 7821-7826.
Gregory, S. (2010). "Finding overlapping communities in networks by label propagation." New Journal of Physics 12(10): 103018.
Holcmann, M. and M. Sibilia (2015). "Mechanisms underlying skin disorders induced by EGFR inhibitors." Molecular & cellular oncology 2(4): e1004969-e1004969.
Illés, F., Á. Dániel, P. Gergely and V. Tamás (2007). "Weighted network modules." New Journal of Physics 9(6): 180.
Kanehisa, M. and S. Goto (2000). "KEGG: kyoto encyclopedia of genes and genomes." Nucleic Acids Res 28(1): 27-30.
Kibbe, W. A., C. Arze, V. Felix, E. Mitraka, E. Bolton, G. Fu, C. J. Mungall, J. X. Binder, J. Malone, D. Vasant, H. E. Parkinson and L. M. Schriml (2015). Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nucleic Acids Research.
Lancichinetti, A. and S. Fortunato (2009). "Community detection algorithms: a comparative analysis." Phys Rev E Stat Nonlin Soft Matter Phys 80(5 Pt 2): 056117.
Lancichinetti, A., F. Radicchi, J. J. Ramasco and S. Fortunato (2011). "Finding statistically significant communities in networks." PloS one 6(4): e18961-e18961.
Leskovec, J., K. J. Lang and M. Mahoney (2010). Empirical comparison of algorithms for network community detection. Proceedings of the 19th international conference on World wide web. Raleigh, North Carolina, USA, ACM: 631-640.
Martin, A., M. E. Ochagavia, L. C. Rabasa, J. Miranda, J. Fernandez-de-Cossio and R. Bringas (2010). "BisoGenet: a new tool for gene network building, visualization and analysis." BMC bioinformatics 11: 91-91.
Molloy, M. and B. Reed (1995). "A critical point for random graphs with a given degree sequence." Random Struct. Algorithms 6(2-3): 161-180.
Nepusz, T., A. Petroczi, L. Negyessy and F. Bazso (2008). "Fuzzy communities and the concept of bridgeness in complex networks." Phys Rev E Stat Nonlin Soft Matter Phys 77(1 Pt 2): 016107.
Ochagavia, M. E., A. Martin, F. Torres, J. Miranda, J. Fernández-de-Cossio, C. Suárez, J. M. Fernández and R. Bringas; (2003). BisoPharma: An integrated system for gene-disease-drug network building.
Palla, G., I. Derenyi, I. Farkas and T. Vicsek (2005). "Uncovering the overlapping community structure of complex networks in nature and society." Nature 435(7043): 814-818.
Raghavan, U. N., R. Albert and S. Kumara (2007). "Near linear time algorithm to detect community structures in large-scale networks." Physical review. E, Statistical, nonlinear, and soft matter physics 76 3 Pt 2: 036106.
Shannon, P., A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski and T. Ideker (2003). "Cytoscape: a software environment for integrated models of biomolecular interaction networks." Genome Res 13(11): 2498-2504.
Sikk, K., S. Haldre, S. M. Aquilonius and P. Taba (2011). "Manganese-Induced Parkinsonism due to Ephedrone Abuse." Parkinsons Dis 2011: 865319.
Turpin, P. J., G. P. Taylor, M. N. Logan and M. J. Wood (1988). "Teicoplanin in the treatment of skin and soft tissue infections." Journal of Antimicrobial Chemotherapy 21(suppl_A): 117-122.
Welter, D., J. MacArthur, J. Morales, T. Burdett, P. Hall, H. Junkins, A. Klemm, P. Flicek, T. Manolio, L. Hindorff and H. Parkinson (2014). "The NHGRI GWAS Catalog, a curated resource of SNP-trait associations." Nucleic Acids Res 42(Database issue): D1001-1006.
Wishart, D. S., C. Knox, A. C. Guo, S. Shrivastava, M. Hassanali, P. Stothard, Z. Chang and J. Woolsey (2006). "DrugBank: a comprehensive resource for in silico drug discovery and exploration." Nucleic Acids Res 34(Database issue): D668-672.
Wu, C., R. C. Gudivada, B. J. Aronow and A. G. Jegga (2013). "Computational drug repositioning through heterogeneous network clustering." BMC Systems Biology 7(5): S6.
Xie, J., S. Kelley and B. K. Szymanski (2013). "Overlapping community detection in networks: The state-of-the-art and comparative study." ACM Comput. Surv. 45(4): 1-35.
Xie, J., B. K. Szymanski and X. Liu (2011). "SLPA: Uncovering Overlapping Communities in Social Networks via a Speaker-Listener Interaction Dynamic Process." 2011 IEEE 11th International Conference on Data Mining Workshops: 344-349.
Yang, H., C. Qin, Y. H. Li, L. Tao, J. Zhou, C. Y. Yu, F. Xu, Z. Chen, F. Zhu and Y. Z. Chen (2016). "Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information." Nucleic Acids Res 44(D1): D1069-1074.
Zhanga, S., R.-S. Wangb and X.-S. Zhanga (2006). Identification of overlapping community structure in complex networks using fuzzy c-means clustering.