Dataset Information

AnamiR: integrated analysis of MicroRNA and gene expression profiling.

ABSTRACT:

Background

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.

Results

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.

Conclusion

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 .

SUBMITTER: Wang TT

PROVIDER: S-EPMC6518761 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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Publications

anamiR: integrated analysis of MicroRNA and gene expression profiling.

Wang Ti-Tai TT Lee Chien-Yueh CY Lai Liang-Chuan LC Tsai Mong-Hsun MH Lu Tzu-Pin TP Chuang Eric Y EY

BMC bioinformatics 20190514 1

<h4>Background</h4>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 mR ...[more]

PMID: 31088348

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