Department of Biomedical Informatics, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China.
Bioinformatics. 2010 Jul 1;26(13):1644-50. doi: 10.1093/bioinformatics/btq241. Epub 2010 May 3.
It is popular to explore meaningful molecular targets and infer new functions of genes through gene functional similarity measuring and gene functional network construction. However, little work is available in this field for microRNA (miRNA) genes due to limited miRNA functional annotations. With the rapid accumulation of miRNAs, it is increasingly needed to uncover their functional relationships in a systems level.
It is known that genes with similar functions are often associated with similar diseases, and the relationship of different diseases can be represented by a structure of directed acyclic graph (DAG). This is also true for miRNA genes. Therefore, it is feasible to infer miRNA functional similarity by measuring the similarity of their associated disease DAG. Based on the above observations and the rapidly accumulated human miRNA-disease association data, we presented a method to infer the pairwise functional similarity and functional network for human miRNAs based on the structures of their disease relationships. Comparisons showed that the calculated miRNA functional similarity is well associated with prior knowledge of miRNA functional relationship. More importantly, this method can also be used to predict novel miRNA biomarkers and to infer novel potential functions or associated diseases for miRNAs. In addition, this method can be easily extended to other species when sufficient miRNA-associated disease data are available for specific species.
The online tool is available at http://cmbi.bjmu.edu.cn/misim
Supplementary data are available at Bioinformatics online.
通过基因功能相似性度量和基因功能网络构建来探索有意义的分子靶标并推断基因的新功能，这已经很流行。然而，由于 miRNA 功能注释有限，在这个领域几乎没有针对 microRNA (miRNA) 基因的工作。随着 miRNA 的快速积累，越来越需要在系统水平上揭示它们的功能关系。
已知具有相似功能的基因通常与相似的疾病相关联，并且不同疾病之间的关系可以用有向无环图 (DAG) 的结构来表示。miRNA 基因也是如此。因此，通过测量它们相关疾病 DAG 的相似性，推断 miRNA 功能相似性是可行的。基于上述观察以及快速积累的人类 miRNA-疾病关联数据，我们提出了一种基于疾病关系结构推断人类 miRNA 对功能相似性和功能网络的方法。比较表明，计算出的 miRNA 功能相似性与 miRNA 功能关系的先验知识密切相关。更重要的是，该方法还可用于预测新的 miRNA 生物标志物，并推断 miRNA 的新潜在功能或相关疾病。此外，当有足够的 miRNA 相关疾病数据可用于特定物种时，该方法可以很容易地扩展到其他物种。
在线工具可在 http://cmbi.bjmu.edu.cn/misim 上获得。
补充数据可在 Bioinformatics 在线获得。
