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A comparative analytical assay of gene regulatory networks inferred using microarray and RNA-seq datasets

Izadi, F; Zarrini, HN; Kiani, G; Jelodar, NB; (2016) A comparative analytical assay of gene regulatory networks inferred using microarray and RNA-seq datasets. Bioinformation , 12 (6) pp. 340-346. 10.6026/97320630012340. Green open access

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Abstract

A Gene Regulatory Network (GRN) is a collection of interactions between molecular regulators and their targets in cells governing gene expression level. Omics data explosion generated from high-throughput genomic assays such as microarray and RNA-Seq technologies and the emergence of a number of pre-processing methods demands suitable guidelines to determine the impact of transcript data platforms and normalization procedures on describing associations in GRNs. In this study exploiting publically available microarray and RNA-Seq datasets and a gold standard of transcriptional interactions in Arabidopsis, we performed a comparison between six GRNs derived by RNA-Seq and microarray data and different normalization procedures. As a result we observed that compared algorithms were highly data-specific and Networks reconstructed by RNA-Seq data revealed a considerable accuracy against corresponding networks captured by microarrays. Topological analysis showed that GRNs inferred from two platforms were similar in several of topological features although we observed more connectivity in RNA-Seq derived genes network. Taken together transcriptional regulatory networks obtained by Robust Multiarray Averaging (RMA) and Variance-Stabilizing Transformed (VST) normalized data demonstrated predicting higher rate of true edges over the rest of methods used in this comparison.

Type: Article
Title: A comparative analytical assay of gene regulatory networks inferred using microarray and RNA-seq datasets
Location: Singapore
Open access status: An open access version is available from UCL Discovery
DOI: 10.6026/97320630012340
Publisher version: https://doi.org/10.6026/97320630012340
Language: English
Additional information: This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)
Keywords: RNA-Seq, gene regulatory network, microarray, normalization
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: http://discovery.ucl.ac.uk/id/eprint/10058319
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