Bioinformatic analysis of cancer-related microRNAs and their target genes

MicroRNAs (miRNAs) are a class of ～22 nucleotide endogenous noncoding RNAs which regulate gene expression by targeting complementary transcripts. Recent studies have found that miRNAs are closely related to tumorigenesis and can act as oncogenes or tumor suppressor genes to influence the occurrence and development of tumor. To further reveal characteristics of cancer-related miRNAs and the functions of miRNA targets, we obtained 475 miRNAs involved in cancer through database searching and information retrieval. We systematically analyzed and compared the features including conservation, SNP distribution, cancer spectrum width, and transcriptional regulation between cancer and non-cancer related miRNAs as well as between intergenic and intragenic miRNAs. Our results showed that cancer-related miRNAs have higher conservation and lower SNP frequency compared to non-cancer-related miRNAs, and the cancer spectrum of one miRNA is positively correlated with its conservation. Genome analysis showed that cancer-related miRNAs tend to present as clusters compared with non-cancer-related miRNAs. Further association analysis between cancer progression and host genes, cancer-related miRNAs or target genes found that the host genes of some non-cancer related miRNAs tend to be targeted by cancer-related miRNAs. This study provides theoretical basis for further understanding the relationship between miRNA and cancer progression as well as the miRNA-based cancer diagnosis.