Title

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

Authors

Fereshteh Izadi*, Hamid Najafi Zarrini & Nadali Babaeian Jelodar

Affiliation

1Plant Breeding Department, Sari Agricultural Sciences and Natural Resources, Iran

Email

Fereshteh Izadi - E-mail: izadi1991@yahoo.com; *Corresponding author

Article Type

Hypothesis

Date

Received July 7 2016; Revised August 5, 2016; Accepted August 6, 2016; Published October 12, 2016

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.

Keywords:

gene regulatory network, RNA-Seq, microarray, normalization

Citation

Izadi et al. Bioinformation 12(6): 340-341 (2016)

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

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.