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 compl...
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doaj-dc16970d4ec6452ba122e8004b3f08e92020-11-25T02:18:35ZengBMCBMC Bioinformatics1471-21052019-05-012011710.1186/s12859-019-2870-xanamiR: integrated analysis of MicroRNA and gene expression profilingTi-Tai Wang0Chien-Yueh Lee1Liang-Chuan Lai2Mong-Hsun Tsai3Tzu-Pin Lu4Eric Y. Chuang5Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan UniversityGraduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan UniversityGraduate Institute of Physiology, National Taiwan UniversityBioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan UniversityInstitute of Epidemiology and Preventive Medicine, National Taiwan UniversityGraduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan UniversityAbstract 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.http://link.springer.com/article/10.1186/s12859-019-2870-xMicroRNAGene expressionFunctional enrichment analysisR/Bioconductor |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ti-Tai Wang Chien-Yueh Lee Liang-Chuan Lai Mong-Hsun Tsai Tzu-Pin Lu Eric Y. Chuang |
spellingShingle |
Ti-Tai Wang Chien-Yueh Lee Liang-Chuan Lai Mong-Hsun Tsai Tzu-Pin Lu Eric Y. Chuang anamiR: integrated analysis of MicroRNA and gene expression profiling BMC Bioinformatics MicroRNA Gene expression Functional enrichment analysis R/Bioconductor |
author_facet |
Ti-Tai Wang Chien-Yueh Lee Liang-Chuan Lai Mong-Hsun Tsai Tzu-Pin Lu Eric Y. Chuang |
author_sort |
Ti-Tai Wang |
title |
anamiR: integrated analysis of MicroRNA and gene expression profiling |
title_short |
anamiR: integrated analysis of MicroRNA and gene expression profiling |
title_full |
anamiR: integrated analysis of MicroRNA and gene expression profiling |
title_fullStr |
anamiR: integrated analysis of MicroRNA and gene expression profiling |
title_full_unstemmed |
anamiR: integrated analysis of MicroRNA and gene expression profiling |
title_sort |
anamir: integrated analysis of microrna and gene expression profiling |
publisher |
BMC |
series |
BMC Bioinformatics |
issn |
1471-2105 |
publishDate |
2019-05-01 |
description |
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. |
topic |
MicroRNA Gene expression Functional enrichment analysis R/Bioconductor |
url |
http://link.springer.com/article/10.1186/s12859-019-2870-x |
work_keys_str_mv |
AT titaiwang anamirintegratedanalysisofmicrornaandgeneexpressionprofiling AT chienyuehlee anamirintegratedanalysisofmicrornaandgeneexpressionprofiling AT liangchuanlai anamirintegratedanalysisofmicrornaandgeneexpressionprofiling AT monghsuntsai anamirintegratedanalysisofmicrornaandgeneexpressionprofiling AT tzupinlu anamirintegratedanalysisofmicrornaandgeneexpressionprofiling AT ericychuang anamirintegratedanalysisofmicrornaandgeneexpressionprofiling |
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