Computational protocol: SRMDAP: SimRank and Density-Based Clustering Recommender Model for miRNA-Disease Association Prediction

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Protocol publication

[…] Three datasets were used in our approach. Experimentally verified miRNA-mRNA interactions were downloaded from the miRTarBase database to construct the miRNA similarity network [] (http://mirtarbase.mbc.nctu.edu.tw/, Release 6.0: Sept-15-2015). Meanwhile, experimentally verified disease-related mRNAs were downloaded from the DisGeNET database [] (http://www.disgenet.org/web/DisGeNET/menu/home, DisGeNET 4.0: October 2016) to construct a disease similarity network. Experimentally verified miRNA-disease network was downloaded from the HMDD v2.0 database [] (http://www.cuilab.cn/hmdd, Jun-14-2014 Version). [...] SimRank [] was employed to calculate the disease and miRNA similarities based on miRNA-mRNA interaction network and disease-related mRNA associations. SimRank is a model to measure the degree of similarity between any two objects on the basis of the information of the topology graph, which has been successfully applied to web page ranking [], recommender systems [], outlier detection [], network graph clustering [], and approximate query processing [], among others. The SimRank model defines the similarity of two nodes based on a recursive thinking. When other nodes pointing to the two nodes are similar, then the two nodes are similar. SimRank defines the similarity of two nodes as follows:(1)sa,b=1a=bCIa·Ib∑j∈Ib ∑i∈Iasi,ja≠b0Ia=∅  or  Ib=∅,where s(a, b) is the similarity between nodes a and b and C ∈ [0, 1] is a decay factor. I(a) denotes all node sets that point to node a, and |I(a)| is the number of elements of I(a).The adjacency matrix of the miRNA-mRNA interaction bipartite network is represented as A, where A(i, j) in row i and column j is 1 if miRNA i is associated with mRNA j, and 0 otherwise. The matrix A is normalized by column to determine the matrix W1, and the similarity matrix can be calculated as follows:(2)SM=C1·W1T·SM·W1+1−C1·I,where SM is the miRNA similarity matrix and SM(i, j) is the similarity between miRNAs i and j. W1T is the transpose matrix of W1, C1 is a decay factor, and I is the unit matrix. […]

Pipeline specifications

Software tools MISIM, Simrank
Databases HMDD miRTarBase DisGeNET
Application Transcriptome data enrichment
Organisms Homo sapiens