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. Author manuscript; available in PMC: 2015 Sep 4.
Published in final edited form as: Circ Cardiovasc Genet. 2014 Aug;7(4):548–557. doi: 10.1161/CIRCGENETICS.113.000125

Table 1.

Summary of TraceRNA Algorithms

Algorithm or Database Output Function of Algorithm
miRTarBase Experimentally verified miRNA:target interactions Identify validated miRNAs
SVMicrO Scores of miRNA-gene binding prediction by using a large number of binding site and 3’UTR features Predict miRNAs binding
BCMicrO Scores of miRNAs-genes binding predictions by fusion of 6 algorithms
SiteTest Scores of miRNAs-genes binding predictions using 3’UTR features
ceRNA-SVMicrO
ceRNA-BCMicrO
ceRNA-SiteTest		 Scores for predicted ceRNAs by sequence-pairing Predict ceRNAs by sequence-pairing
Expression Correlation Pearson correlation of GOI and predicted ceRNAs by sequence-pairing Calculate correlation between predicted ceRNAs by sequence-pairing
SeqExp Fusion (Borda merging method) Scores from fusing sequence-level predictions and expression correlation Fuse sequence-level predictions and co-expression
ceRNA-Net List of gene pairs (nodes) and scores of their directed interactions Discover regulatory networks