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Identification of cell-type-specific marker genes from co-expression patterns in tissue samples

Yixuan Qiu, Jiebiao Wang, Jing Lei, Kathryn Roeder
doi: https://doi.org/10.1101/2020.11.07.373043
Yixuan Qiu
1Department of Statistics and Data Science, Carnegie Mellon University, USA
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Jiebiao Wang
2Department of Biostatistics, University of Pittsburgh, USA
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Jing Lei
1Department of Statistics and Data Science, Carnegie Mellon University, USA
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Kathryn Roeder
1Department of Statistics and Data Science, Carnegie Mellon University, USA
3Computational Biology Department, Carnegie Mellon University, USA
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  • For correspondence: roeder@andrew.cmu.edu
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Abstract

Motivation Marker genes, defined as genes that are expressed primarily in a single cell type, can be identified from the single cell transcriptome; however, such data are not always available for the many uses of marker genes, such as deconvolution of bulk tissue. Marker genes for a cell type, however, are highly correlated in bulk data, because their expression levels depend primarily on the proportion of that cell type in the samples. Therefore, when many tissue samples are analyzed, it is possible to identify these marker genes from the correlation pattern.

Results To capitalize on this pattern, we develop a new algorithm to detect marker genes by combining published information about likely marker genes with bulk transcriptome data in the form of a semi-supervised algorithm. The algorithm then exploits the correlation structure of the bulk data to refine the published marker genes by adding or removing genes from the list.

Availability and implementation We implement this method as an R package markerpen, hosted on https://github.com/yixuan/markerpen.

Contact roeder{at}andrew.cmu.edu

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 08, 2020.
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Identification of cell-type-specific marker genes from co-expression patterns in tissue samples
Yixuan Qiu, Jiebiao Wang, Jing Lei, Kathryn Roeder
bioRxiv 2020.11.07.373043; doi: https://doi.org/10.1101/2020.11.07.373043
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Identification of cell-type-specific marker genes from co-expression patterns in tissue samples
Yixuan Qiu, Jiebiao Wang, Jing Lei, Kathryn Roeder
bioRxiv 2020.11.07.373043; doi: https://doi.org/10.1101/2020.11.07.373043

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