Computing microRNA-gene interaction networks in pan-cancer using miRDriver.
Computing microRNA-gene interaction networks in pan-cancer using miRDriver.
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DOI：
10.1038/s41598-022-07628-z
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发表时间：
2022-03-08
影响因子：
4.6
通讯作者：
Bozdag S
中科院分区：
文献类型：
--
作者：
Bose B;Moravec M;Bozdag S
已知癌症中的 DNA 拷贝数异常区域含有癌症驱动基因和短非编码 RNA 分子，即 microRNA。在这项研究中，我们整合了拷贝数畸变、DNA 甲基化、基因和 microRNA 表达等多组学数据集，利用基于 LASSO 的回归方法从泛癌中频繁畸变的 DNA 区域中识别出特征性 microRNA-基因关联。我们研究了癌症基因组图谱 (TCGA) 数据库中与 18 种不同癌症类型相关的 7294 名患者样本，并确定了几种癌症特异性和常见的 microRNA-基因相互作用，这些相互作用富含经过实验验证的 microRNA-靶标相互作用。我们重点介绍了几种致癌和肿瘤抑制 microRNA，它们具有癌症特异性，并且在多种癌症类型中常见。在选择多种癌症类型中显着已知的 microRNA-基因相互作用方面，我们的方法大大优于五种最先进的方法。一些 microRNA 和基因被发现与肿瘤存活和进展相关。发现选定的目标基因在癌症相关通路、癌症标志和基因本体 (GO) 术语中显着丰富。此外，在多种癌症类型中发现了亚型特异性的潜在基因特征。
DNA copy number aberrated regions in cancer are known to harbor cancer driver genes and the short non-coding RNA molecules, i.e., microRNAs. In this study, we integrated the multi-omics datasets such as copy number aberration, DNA methylation, gene and microRNA expression to identify the signature microRNA-gene associations from frequently aberrated DNA regions across pan-cancer utilizing a LASSO-based regression approach. We studied 7294 patient samples associated with eighteen different cancer types from The Cancer Genome Atlas (TCGA) database and identified several cancer-specific and common microRNA-gene interactions enriched in experimentally validated microRNA-target interactions. We highlighted several oncogenic and tumor suppressor microRNAs that were cancer-specific and common in several cancer types. Our method substantially outperformed the five state-of-art methods in selecting significantly known microRNA-gene interactions in multiple cancer types. Several microRNAs and genes were found to be associated with tumor survival and progression. Selected target genes were found to be significantly enriched in cancer-related pathways, cancer hallmark and Gene Ontology (GO) terms. Furthermore, subtype-specific potential gene signatures were discovered in multiple cancer types.
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影响因子：
14.9
作者：
Colaprico A;Silva TC;Olsen C;Garofano L;Cava C;Garolini D;Sabedot TS;Malta TM;Pagnotta SM;Castiglioni I;Ceccarelli M;Bontempi G;Noushmehr H
通讯作者：
Noushmehr H
影响因子：
5.2
作者：
Jin C;Rajabi H;Kufe D
通讯作者：
Kufe D
影响因子：
16.6
作者：
Foglizzo, Martina;Middleton, Adam J.;Mace, Peter D.
通讯作者：
Mace, Peter D.
DOI：
10.1073/pnas.0800121105
发表时间：
2008-04-01
影响因子：
11.1
作者：
Calin, George A.;Cimmino, Amelia;Croce, Carlo M.
通讯作者：
Croce, Carlo M.
影响因子：
16.6
作者：
Dhawan, Andrew;Scott, Jacob G.;Buffa, Francesca M.
通讯作者：
Buffa, Francesca M.