Pollara, G;
Murray, MJ;
Heather, JM;
Byng-Maddick, R;
Guppy, N;
Ellis, M;
Turner, CT;
... Noursadeghi, M; + view all
(2017)
Validation of Immune Cell Modules in Multicellular Transcriptomic Data.
PLOS One
, 12
(1)
, Article e0169271. 10.1371/journal.pone.0169271.
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Abstract
Numerous gene signatures, or modules have been described to evaluate the immune cell composition in transcriptomes of multicellular tissue samples. However, significant diversity in module gene content for specific cell types is associated with heterogeneity in their performance. In order to rank modules that best reflect their purported association, we have generated the modular discrimination index (MDI) score that assesses expression of each module in the target cell type relative to other cells. We demonstrate that MDI scores predict modules that best reflect independently validated differences in cellular composition, and correlate with the covariance between cell numbers and module expression in human blood and tissue samples. Our analyses demonstrate that MDI scores provide an ordinal summary statistic that reliably ranks the accuracy of gene expression modules for deconvolution of cell type abundance in transcriptional data.
| Type: | Article |
|---|---|
| Title: | Validation of Immune Cell Modules in Multicellular Transcriptomic Data |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1371/journal.pone.0169271 |
| Publisher version: | http://doi.org/10.1371/journal.pone.0169271 |
| Language: | English |
| Additional information: | Copyright © 2017 Pollara et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
| Keywords: | T cells, Covariance,B cells, Transcriptome analysis, Immune cells, Biopsy, Gene expression, DNA transcription |
| UCL classification: | UCL 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 Brain Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Infection and Immunity |
| URI: | https://discovery.ucl.ac.uk/id/eprint/1534577 |
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