SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data.
SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data.
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DOI：
10.3390/ijms18020274
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发表时间：
2017-01-27
影响因子：
5.6
通讯作者：
Castiglioni I
中科院分区：
文献类型：
--
作者：
Cava C;Colaprico A;Bertoli G;Graudenzi A;Silva TC;Olsen C;Noushmehr H;Bontempi G;Mauri G;Castiglioni I
基因调控网络（GRNs）控制着许多生物系统，但这种网络协调是如何形成的仍然是未知的。GRN可以被细分为描述网络成员如何交互的基本连接，共表达、物理相互作用、共定位、遗传影响、途径和共享的蛋白质结构域。这些网络的重要调控机制涉及miRNA。我们开发了一个R/Bioconductor软件包，即SpidermiR，它为最终用户提供了一个容易获得GRNs和miRNA的途径，并将此信息与从癌症基因组图谱中获得的差异表达基因整合在一起。具体来说，SpidermiR允许用户：（i）从验证和预测的库中查询和下载GRNs和miRNA;（ii）将miRNA与GRNs整合，以获得miRNA-基因-基因和miRNA-蛋白质-蛋白质相互作用，并分析miRNA GRNs，以识别miRNA-基因群落;以及（iii）以图形方式可视化分析结果。这些分析可以通过单一界面执行，无需任何下载。然后，全部数据集在当地迅速整合和处理。
Gene Regulatory Networks (GRNs) control many biological systems, but how such network coordination is shaped is still unknown. GRNs can be subdivided into basic connections that describe how the network members interact e.g., co-expression, physical interaction, co-localization, genetic influence, pathways, and shared protein domains. The important regulatory mechanisms of these networks involve miRNAs. We developed an R/Bioconductor package, namely SpidermiR, which offers an easy access to both GRNs and miRNAs to the end user, and integrates this information with differentially expressed genes obtained from The Cancer Genome Atlas. Specifically, SpidermiR allows the users to: (i) query and download GRNs and miRNAs from validated and predicted repositories; (ii) integrate miRNAs with GRNs in order to obtain miRNA–gene–gene and miRNA–protein–protein interactions, and to analyze miRNA GRNs in order to identify miRNA–gene communities; and (iii) graphically visualize the results of the analyses. These analyses can be performed through a single interface and without the need for any downloads. The full data sets are then rapidly integrated and processed locally.