A reanalysis of mouse ENCODE comparative gene expression data [v1; ref status: indexed, http://f1000r.es/5ez]

Recently, the Mouse ENCODE Consortium reported that comparative gene expression data from human and mouse tend to cluster more by species rather than by tissue. This observation was surprising, as it contradicted much of the comparative gene regulatory data collected previously, as well as the commo...

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Bibliographic Details
Main Authors: Yoav Gilad, Orna Mizrahi-Man
Format: Article
Language:English
Published: F1000 Research Ltd 2015-05-01
Series:F1000Research
Subjects:
Online Access:http://f1000research.com/articles/4-121/v1
Description
Summary:Recently, the Mouse ENCODE Consortium reported that comparative gene expression data from human and mouse tend to cluster more by species rather than by tissue. This observation was surprising, as it contradicted much of the comparative gene regulatory data collected previously, as well as the common notion that major developmental pathways are highly conserved across a wide range of species, in particular across mammals. Here we show that the Mouse ENCODE gene expression data were collected using a flawed study design, which confounded sequencing batch (namely, the assignment of samples to sequencing flowcells and lanes) with species. When we account for the batch effect, the corrected comparative gene expression data from human and mouse tend to cluster by tissue, not by species.
ISSN:2046-1402