Comparison of alternative approaches for analysing multi-level RNA-seq data

Mohorianu, Irina, Bretman, Amanda, Smith, Damian T., Fowler, Emily K., Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Chapman, Tracey (2017) Comparison of alternative approaches for analysing multi-level RNA-seq data. PLoS One, 12 (8). ISSN 1932-6203

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Abstract

RNA sequencing (RNA-seq) is widely used for RNA quantification in the environmental, biological and medical sciences. It enables the description of genome-wide patterns of expression and the identification of regulatory interactions and networks. The aim of RNA-seq data analyses is to achieve rigorous quantification of genes/transcripts to allow a reliable prediction of differential expression (DE), despite variation in levels of noise and inherent biases in sequencing data. This can be especially challenging for datasets in which gene expression differences are subtle, as in the behavioural transcriptomics test dataset from D. melanogaster that we used here. We investigated the power of existing approaches for quality checking mRNA-seq data and explored additional, quantitative quality checks. To accommodate nested, multi-level experimental designs, we incorporated sample layout into our analyses. We employed a subsampling without replacement-based normalization and an identification of DE that accounted for the hierarchy and amplitude of effect sizes within samples, then evaluated the resulting differential expression call in comparison to existing approaches. In a final step to test for broader applicability, we applied our approaches to a published set of H. sapiens mRNA-seq samples, The dataset-tailored methods improved sample comparability and delivered a robust prediction of subtle gene expression changes. The proposed approaches have the potential to improve key steps in the analysis of RNA-seq data by incorporating the structure and characteristics of biological experiments.

Item Type:	Article
Faculty \ School:	Faculty of Science > School of Computing Sciences Faculty of Science > School of Biological Sciences
UEA Research Groups:	Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation Faculty of Science > Research Groups > Organisms and the Environment Faculty of Science > Research Groups > Plant Sciences
Depositing User:	Pure Connector
Date Deposited:	15 Aug 2017 05:07
Last Modified:	13 May 2023 00:13
URI:	https://ueaeprints.uea.ac.uk/id/eprint/64492
DOI:	10.1371/journal.pone.0182694

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