CmirC: an integrated database of clustered miRNAs co-localized with copy number variations in cancer

Area of Science:

• Genomics
• Cancer Biology
• Bioinformatics

Background:

• Genomic rearrangements and copy number variations (CNVs) significantly regulate clustered microRNAs (miRNAs) expression.
• Many clustered miRNAs are located near chromosome fragile sites (CFSs) and cancer-associated genomic hotspots.
• Dysregulated expression of these miRNA clusters can contribute to oncogenesis or tumor suppression.

Purpose of the Study:

• To develop CmirC, a comprehensive database for clustered miRNAs co-localized with CNVs.
• To provide a resource for analyzing miRNA expression patterns in various cancer types.
• To facilitate research into the role of clustered miRNAs in cancer development and progression.

Main Methods:

• Compiled a database of 481 clustered miRNAs co-localized with CNVs.
• Integrated expression data from 35 cancer types from The Cancer Genome Atlas (TCGA).
• Incorporated information on CFSs, miRNA cluster candidates, genomic coordinates, and target gene networks.
• Integrated advanced bioinformatics tools including JBrowse, NCBI-BLAST, GeneSCF, visNetwork, and NetworkD3.

Main Results:

• The CmirC database contains 481 clustered miRNAs co-localized with CNVs.
• Expression patterns of these miRNAs across 35 TCGA cancer types are available.
• The portal offers data on CFSs, target gene networks, and gene functionality.
• Integrated tools facilitate data analysis, visualization, and browsing.

Conclusions:

• CmirC serves as a valuable resource for exploring the complex regulation of clustered miRNAs in cancer.
• The database provides integrated analytics for understanding clinically significant miRNAs.
• It offers further evidence for the role of CNVs in regulating clustered miRNA expression in oncogenesis.