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Fig. 3 | BMC Biology

Fig. 3

From: The transcriptional trajectories of pluripotency and differentiation comprise genes with antithetical architecture and repetitive-element content

Fig. 3

Repetitive-element density biases in gene expression changes during preimplantation development. Heatmaps of enrichment and depletion scores of the repetitive density in genes that are up-regulated or down-regulated in the blastocyst as compared to early embryo in human (a, b) and mouse (c, d) embryos. The heatmaps visualize the Z-score of the observed mean density in each repetitive-element family with respect to an expected distribution constructed with Monte Carlo simulations. A positive Z-score (colored orange) represents a density more than expected by chance, while a negative Z-score (colored purple) shows that the observed density is lower than expected. Z-scores were computed independently for intron and exons and for the sense and antisense orientation of these genomic regions. For each panel (a–d), only the repetitive families with at least one significant enrichment or depletion (absolute Z-score larger than 2) are shown. Additional file 4: Supplemental Table S3 includes the values used for plotting the heatmaps as well as the respective FDR scores

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