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. 2015 Apr 20;43(10):4833–4854. doi: 10.1093/nar/gkv370

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© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 6. — Gene expression profiles during RA-induced PrE differentiation of mouse F9 EC cells. (A) Identification of differentially expressed genes at different time points after RA stimulation relative to their untreated expression level. Results are shown as a volcano plot representing Benjamini-Hochberg adjusted P-value versus log₂ fold change on the y- and x-axes, respectively. Up- and down-regulated genes are shown in red and green, respectively. (B) Proportion of genes in the indicated set that exhibit an RAR/RXR target regions within the indicated distance range from their closest annotated TSS. Blue bars correspond to the percentage of genes exhibiting an RAR/RXR target region at less than 20 kb upstream or downstream of their annotated TSS. (C) Same as (B) panel for gene up- or down-regulated at the indicated time point after RA stimulation. (D) Clustering of differentially expressed gene expression profiles. Gene associated to Primitive Endoderm differentiation or pluripotency maintenance are indicated in the corresponding annotated boxes. (E) Boxplot representing the distance distribution of the closest RAR/RXR target region relative to annotated TSS of differentially expressed genes for the previously defined (D) expression clusters.