Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan.
Graduate Institute of Physiology, National Taiwan University, Taipei, 10051, Taiwan.
BMC Bioinformatics. 2019 May 14;20(1):239. doi: 10.1186/s12859-019-2870-x.
With advancements in high-throughput technologies, the cost of obtaining expression profiles of both mRNA and microRNA in the same individual has substantially decreased. Integrated analysis of these profiles can help to elucidate the functional effects of RNA expression in complex diseases, such as cancer. However, fundamental discrepancies are observed in the results from microRNA-mRNA target gene prediction algorithms, and few packages can be used to analyze microRNA and mRNA expression levels simultaneously.
To address these issues, an R package, anamiR, was developed. A total of 10 experimental/prediction databases were integrated. Two analytical functions are provided in anamiR, including the single marker test and functional gene set enrichment analysis, and several parameters can be changed by users. Here we demonstrate the potential application of the anamiR package to 2 publicly available microarray datasets.
The anamiR package is effective for an integrated analysis of both RNA and microRNA profiles. By characterizing biological functions and signaling pathways, this package helps identify dysregulated genes/miRNAs from biological and medical experiments. The source code and manual of the anamiR package are freely available at https://bioconductor.org/packages/release/bioc/html/anamiR.html .
随着高通量技术的进步，在同一个体中同时获得 mRNA 和 microRNA 表达谱的成本大大降低。这些谱的综合分析有助于阐明 RNA 表达在复杂疾病（如癌症）中的功能效应。然而，microRNA-mRNA 靶基因预测算法的结果存在根本差异，并且很少有软件包可用于同时分析 microRNA 和 mRNA 表达水平。
为了解决这些问题，开发了一个 R 包 anamiR。总共整合了 10 个实验/预测数据库。anamiR 提供了两个分析功能，包括单个标记测试和功能基因集富集分析，并且用户可以更改几个参数。在这里，我们演示了 anamiR 包在 2 个公开可用的微阵列数据集上的潜在应用。
anamiR 包可有效地对 RNA 和 microRNA 谱进行综合分析。通过对生物功能和信号通路进行特征化，该包有助于从生物和医学实验中识别失调的基因/miRNA。anamiR 包的源代码和手册可在 https://bioconductor.org/packages/release/bioc/html/anamiR.html 上免费获得。
