miRNA sets are defined as groups of miRNAs that have meaningful relationships. If any two miRNAs have meaningful relationships, for example they are associated with the same diseases, they are then integrated into one miRNA set. Here, miRNA sets were collected according to miRNA family, genome locations, function, associated diseases, and tissue specificity. Studies have indicated that miRNAs in one family are most likely derived from duplications of common ancestor miRNAs [18 (link),19 (link)], and tend to act together in various functional processes [20 (link),21 (link)]. Therefore, miRNAs in one family can be considered as one miRNA set. The miRNA family data from the miRBase database was downloaded [7 (link)] and utilized in this study.
miRNAs are not located randomly in the genome but tend to exist in clusters [22 (link)]. MiRNAs in a cluster are likely to be co-transcribed and have similar expression patterns [23 (link)]. Therefore, these clustered miRNAs may be involved in similar biological processes. In this study, miRNA clusters were identified by grouping miRNAs that were within a distance of 50 kb in the chromosomes, according to the observation of Baskerville and Bartel [23 (link)]. The integrated miRNAs were also manually integrated into different sets according to their functions, as reported in publications. For example, miRNAs that were associated with the immune system were collected from a recent review paper published in Cell [24 (link)]. The miRNA sets were generated by miRNA-associated diseases based on the Human MicroRNA Disease Database (HMDD,http://cmbi.bjmu.edu.cn/hmdd ), a database for miRNA disease associations [3 (link)]. The tissue-specific index values of miRNA were obtained from the study of Lu et al.[3 (link)], and tissue-specific miRNA sets were generated by collecting miRNAs with tissue specificity index values of greater than or equal to 0.7. Finally, according to the methods described above, 257 miRNA sets were generated. These miRNA sets are available for download at the TAM website.
miRNAs are not located randomly in the genome but tend to exist in clusters [22 (link)]. MiRNAs in a cluster are likely to be co-transcribed and have similar expression patterns [23 (link)]. Therefore, these clustered miRNAs may be involved in similar biological processes. In this study, miRNA clusters were identified by grouping miRNAs that were within a distance of 50 kb in the chromosomes, according to the observation of Baskerville and Bartel [23 (link)]. The integrated miRNAs were also manually integrated into different sets according to their functions, as reported in publications. For example, miRNAs that were associated with the immune system were collected from a recent review paper published in Cell [24 (link)]. The miRNA sets were generated by miRNA-associated diseases based on the Human MicroRNA Disease Database (HMDD,
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