Sng, Letitia MF;
Thomson, Peter C;
Trabzuni, Daniah;
(2020)
Comparison Between Expression Microarrays and RNA-Sequencing Using UKBEC Dataset Identified a trans-eQTL Associated with MPZ Gene in Substantia Nigra.
Advances in Neurology and Neuroscience Research
, 1
, Article 100001.
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Abstract
In recent years, the advantages of RNA-sequencing (RNA-Seq) have made it the platform of choice for measuring gene expression over traditional microarrays. However, RNA-Seq comes with bioinformatical challenges and higher computational costs. Therefore, this study set out to assess whether the increased depth of transcriptomic information facilitated by RNA-Seq is worth the increased computation over microarrays, specifically at three levels: absolute expression levels, differentially expressed genes identification, and expression QTL (eQTL) mapping in regions of the human brain. Using the United Kingdom Brain Expression Consortium (UKBEC) dataset, there is high agreement of gene expression levels measured by microarrays and RNA-seq when quantifying absolute expression levels and when identifying differentially expressed genes. These findings suggest that depending on the aims of a study, the relative ease of working with microarray data may outweigh the computational time and costs of RNA-Seq pipelines. On the other, there was low agreement when mapping eQTLs. However, a number of eQTLs associated with genes that play important roles in the brain were found in both platforms. For example, a trans-eQTL was mapped that is associated with the MPZ gene in the substantia nigra. These eQTLs that we have highlighted are extremely promising candidates that merit further investigation.
| Type: | Article |
|---|---|
| Title: | Comparison Between Expression Microarrays and RNA-Sequencing Using UKBEC Dataset Identified a trans-eQTL Associated with MPZ Gene in Substantia Nigra |
| Location: | England |
| Open access status: | An open access version is available from UCL Discovery |
| Publisher version: | https://www.emrespublisher.com/open-access-pdf/com... |
| Language: | English |
| Additional information: | This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (https://creativecommons.org/licenses/by/4.0/) |
| Keywords: | MPZ gene, RNA-Seq, expression QTL, human brain, neuroscience |
| UCL classification: | UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology > Neurodegenerative Diseases UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10146041 |
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