miRNA and the edges between green nodes and blue nodes represent the associations between miRNAs and diseases. A miRNA-associated disease network (MDN) is constructed if any two diseases share one common associated miRNAs, as shown in (B). Found at: doi:10.1371/journal.pone.0003420.s001 (6.79 MB TIF) Figure S2 The human miRNA disease network (MDN). Red nodes, green nodes and pink nodes represent cardiovascular diseases, cancers, and other diseases, respectively. Found at: doi:10.1371/journal.pone.0003420.s002 (2.89 MB TIF) miRNAs with high tissue specificity index values at: doi:10.1371/journal.pone.0003420.s003 (0.00 miRNA families at: doi:10.1371/journal.pone.0003420.s004 (0.00 miRNA clusters at: doi:10.1371/journal.pone.0003420.s005 (0.00 MicroRNAs and Human Disease MB MB MB miRNA SNPs The human miRNAs are classified into conserved miRNAs and human-specific miRNAs by miRNA family annotations[19]. If a miRNA has other family members in other species, it will be treated as conserved miRNAs; otherwise, it will be treated as human-specific miRNAs. We downloaded human SNP data from dbSNP by using the University of California, Santa Cruz (UCSC) genome browser[27]. miRNA sets In this study, we used two types of miRNA sets: families of miRNAs and neighboring miRNAs. We first downloaded all the human miRNAs from miRBase[19]. We next extracted 75 human miRNA families from miRBase (Supplementary Text S2). As Bartel et al. reported, 50 kb is an abrupt transition of coexpression between pairs of miRNAs. MiRNAs separated by ,50 kb showed high coexpression and miRNAs occurring at a distance of more than 50 kb showed low coexpression[22]. Using this cutoff, we identified 65 miRNA clusters (Supplementary Text S3). Statistical computing All statistical computations were performed in the statistical platform ‘‘R’’. 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