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| In this paper, we construct a disease network of mental retardation that integrates human PPI network and known disease-causing genes. The human PPI network is regarded as the background of the disease network, and the known disease-causing genes of mental retardation are embedded in the background based on the correspondences between the genes and their protein products. We determine the modular organization of this disease network by the way that the known disease-causing genes are considered as the "seeds", which can be extended by the procedures of Markov cluster algorithm (MCL) and Clique percolation method (CPM) respectively to identify disease genes associated modular structures. The results show that 28 modular structures are detected, and 32.14% of them correspond to well-known human protein complexes. We find that the genes within these modular structures have higher homogeneity in biological process, molecular function and cellular component of Gene Ontology (GO). In addition, the known disease genes as the hubs of the modular structures always correspond to housekeeping genes (maintenance genes) that are ubiquitously expressed widely in most human tissues, and the hub genes are often the essential genes that play special role in the cellular life. We also find that 78.57% of the modular structures participate in multiple Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and the hub genes perform a very important part in the pathways. |
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| Keywords:Modular structure, PPI network, Mental retardation, Disease-causing genes |
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