miRkit: R framework analyzing miRNA PCR array data

Maria Tsagiopoulou; Anastasis Togkousidis; Nikolaos Pechlivanis; Maria Christina Maniou; Aristea Batsali; Angelos Matheakakis; Charalampos Pontikoglou; Fotis Psomopoulos

doi:10.1186/s13104-021-05788-1

miRkit: R framework analyzing miRNA PCR array data

BMC Res Notes. 2021 Sep 26;14(1):376. doi: 10.1186/s13104-021-05788-1.

Authors

Maria Tsagiopoulou¹, Anastasis Togkousidis¹, Nikolaos Pechlivanis^{1

2}, Maria Christina Maniou¹, Aristea Batsali³, Angelos Matheakakis^{3

4}, Charalampos Pontikoglou^{3

4}, Fotis Psomopoulos⁵

Affiliations

¹ Institute of Applied Biosciences, Centre of Research and Technology Hellas, 57001, Thessaloniki, Greece.
² Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
³ Haemopoiesis Research Laboratory, School of Medicine, University of Crete, 71003, Heraklion, Greece.
⁴ Department of Hematology, School of Medicine, University of Crete, 71003, Heraklion, Greece.
⁵ Institute of Applied Biosciences, Centre of Research and Technology Hellas, 57001, Thessaloniki, Greece. fpsom@certh.gr.

Abstract

Objective: The characterization of microRNAs (miRNA) in recent years is an important advance in the field of gene regulation. To this end, several approaches for miRNA expression analysis and various bioinformatics tools have been developed over the last few years. It is a common practice to analyze miRNA PCR Array data using the commercially available software, mostly due to its convenience and ease-of-use.

Results: In this work we present miRkit, an open source framework written in R, that allows for the comprehensive analysis of RT-PCR data, from the processing of raw data to a functional analysis of the produced results. The main goal of the proposed tool is to provide an assessment of the samples' quality, perform data normalization by endogenous and exogenous miRNAs, and facilitate differential and functional enrichment analysis. The tool offers fast execution times with low memory usage, and is freely available under a ΜΙΤ license from https://bio.tools/mirkit . Overall, miRkit offers the full analysis from the raw RT-PCR data to functional analysis of targeted genes, and specifically designed to support the popular miScript miRNA PCR Array (Qiagen) technology.

Keywords: GO; KEGG; PCR array; RT-PCR; miRNA; qPCR.

MeSH terms

Computational Biology
Gene Expression Profiling
Gene Expression Regulation
MicroRNAs* / genetics
Polymerase Chain Reaction
Software

Substances

MicroRNAs

Abstract

MeSH terms

Substances

Grants and funding