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CmirC：一个整合数据库，包含与癌症中拷贝数变异共定位的聚类 miRNA。

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

机构信息

Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.

Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.

出版信息

Funct Integr Genomics. 2022 Dec;22(6):1229-1241. doi: 10.1007/s10142-022-00909-w. Epub 2022 Oct 26.

DOI:10.1007/s10142-022-00909-w
PMID:36287286
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9701657/
Abstract

Genomic rearrangements and copy number variations (CNVs) are the major regulators of clustered microRNAs (miRNAs) expression. Several clustered miRNAs are harbored in and around chromosome fragile sites (CFSs) and cancer-associated genomic hotspots. Aberrant expression of such clusters can lead to oncogenic or tumor suppressor activities. Here, we developed CmirC (Clustered miRNAs co-localized with CNVs), a comprehensive database of clustered miRNAs co-localized with CNV regions. The database consists of 481 clustered miRNAs co-localized with CNVs and their expression patterns in 35 cancer types of the TCGA. The portal also provides information on CFSs, miRNA cluster candidates, genomic coordinates, target gene networks, and gene functionality. The web portal is integrated with advanced tools such as JBrowse, NCBI-BLAST, GeneSCF, visNetwork, and NetworkD3 to help the researchers in data analysis, visualization, and browsing. This portal provides a promising avenue for integrated data analytics and offers additional evidence for the complex regulation of clustered miRNAs in cancer. The web portal is freely accessible at http://slsdb.manipal.edu/cmirclust to explore clinically significant miRNAs.

摘要

基因组重排和拷贝数变异 (CNVs) 是簇状 microRNA (miRNA) 表达的主要调控因子。一些簇状 miRNAs 位于染色体脆性位点 (CFSs) 和癌症相关基因组热点周围。这些簇的异常表达可能导致致癌或肿瘤抑制活性。在这里，我们开发了 CmirC（与 CNV 共定位的簇状 miRNAs），这是一个与 CNV 区域共定位的簇状 miRNAs 的综合数据库。该数据库包含 481 个与 CNV 共定位的簇状 miRNAs 及其在 TCGA 中 35 种癌症类型中的表达模式。该门户还提供关于 CFSs、miRNA 簇候选物、基因组坐标、靶基因网络和基因功能的信息。该门户网站集成了先进的工具，如 JBrowse、NCBI-BLAST、GeneSCF、visNetwork 和 NetworkD3，以帮助研究人员进行数据分析、可视化和浏览。该门户为集成数据分析提供了一个有前途的途径，并为癌症中簇状 miRNAs 的复杂调控提供了额外的证据。该门户网站可免费访问 http://slsdb.manipal.edu/cmirclust，以探索具有临床意义的 miRNAs。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4cf6/9701657/681109575a14/10142_2022_909_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4cf6/9701657/69ca8894b5ba/10142_2022_909_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4cf6/9701657/9529bd4cd718/10142_2022_909_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4cf6/9701657/fe824b38d085/10142_2022_909_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4cf6/9701657/d55abbc15e55/10142_2022_909_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4cf6/9701657/9a8ecf99764e/10142_2022_909_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4cf6/9701657/681109575a14/10142_2022_909_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4cf6/9701657/69ca8894b5ba/10142_2022_909_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4cf6/9701657/9529bd4cd718/10142_2022_909_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4cf6/9701657/fe824b38d085/10142_2022_909_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4cf6/9701657/d55abbc15e55/10142_2022_909_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4cf6/9701657/9a8ecf99764e/10142_2022_909_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4cf6/9701657/681109575a14/10142_2022_909_Fig6_HTML.jpg

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