PanomiR: a systems biology framework for analysis of multi-pathway targeting by miRNAs.
PanomiR: a systems biology framework for analysis of multi-pathway targeting by miRNAs.
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DOI：
10.1093/bib/bbad418
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发表时间：
2023-09-22
影响因子：
9.5
通讯作者：
中科院分区：
文献类型：
--
作者：
绘制跨通路的microRNA（miRNA）调控是表征其功能的关键。然而，目前还没有方法可以量化miRNA如何调节多个相互关联的通路，或者根据它们调节协调转录程序的能力来优先考虑它们。现有的方法主要是利用差异表达的基因来推断miRNAs和通路之间的一对一关系。我们介绍PanomiR，这是一个用于研究miRNA与疾病功能相互作用的计算机框架。PanomiR整合了基因表达，mRNA-miRNA相互作用和已知的生物学途径，以揭示miRNA的协调多途径靶向作用。PanomiR利用通路活性分析方法、通路共表达网络和网络聚类算法来优先考虑靶向大规模转录疾病表型的miRNA。它直接解决途径的差异调节，而不管它们的差异基因表达，并捕获共活性以建立功能途径分组和可能调节它们的miRNA。PanomiR使用系统生物学方法来提供对miRNA调节的功能程序的广泛但精确的见解。可在https://bioconductor.org/packages/PanomiR上查阅。
Charting microRNA (miRNA) regulation across pathways is key to characterizing their function. Yet, no method currently exists that can quantify how miRNAs regulate multiple interconnected pathways or prioritize them for their ability to regulate coordinate transcriptional programs. Existing methods primarily infer one-to-one relationships between miRNAs and pathways using differentially expressed genes. We introduce PanomiR, an in silico framework for studying the interplay of miRNAs and disease functions. PanomiR integrates gene expression, mRNA–miRNA interactions and known biological pathways to reveal coordinated multi-pathway targeting by miRNAs. PanomiR utilizes pathway-activity profiling approaches, a pathway co-expression network and network clustering algorithms to prioritize miRNAs that target broad-scale transcriptional disease phenotypes. It directly resolves differential regulation of pathways, irrespective of their differential gene expression, and captures co-activity to establish functional pathway groupings and the miRNAs that may regulate them. PanomiR uses a systems biology approach to provide broad but precise insights into miRNA-regulated functional programs. It is available at https://bioconductor.org/packages/PanomiR.
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影响因子：
1
作者：
Brandes, U
通讯作者：
Brandes, U
影响因子：
--
作者：
Alaimo S;Giugno R;Acunzo M;Veneziano D;Ferro A;Pulvirenti A
通讯作者：
Pulvirenti A
影响因子：
64.5
作者：
Cancer Genome Atlas Research Network. Electronic address: wheeler@bcm.edu;Cancer Genome Atlas Research Network
通讯作者：
Cancer Genome Atlas Research Network
影响因子：
5.2
作者：
Eun JW;Seo CW;Baek GO;Yoon MG;Ahn HR;Son JA;Sung S;Kim DW;Kim SS;Cho HJ;Cheong JY
通讯作者：
Cheong JY
影响因子：
12.3
作者：
Altschuler GM;Hofmann O;Kalatskaya I;Payne R;Ho Sui SJ;Saxena U;Krivtsov AV;Armstrong SA;Cai T;Stein L;Hide WA
通讯作者：
Hide WA