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Fig. 3 | BMC Molecular Biology

Fig. 3

From: Genes targeted by the Hedgehog-signaling pathway can be regulated by Estrogen related receptor β

Fig. 3

Pair-wise comparisons for differentially expressed genes within Control, Hedgehog treatment, Esrrb expression and Esrrb expression plus Hedgehog treatment. a Scatter plot of gene expression values in different conditions. 0.001 is added to the RPKM value of each transcript and resulted RPKM + 0.001 values are log2 transformed. For each plot, each point (Xcondition1, Ycondition2) on the plot represents the log2 (RPKM + 0.001) of the gene in indicated conditions. If a certain gene passed the different expression test, that gene is highlighted by blue color, otherwise is red colored. All pair-wise comparisons are plotted, except Hedgehog vs. Esrrb, which lacks biological meaning and b Spearman Ranking Correlation was used to analyze the similarity of mRNA profiles in control, Hh-signaling activation, Esrrb expression and Hh-signaling activation with Esrrb expression. Spearman ranking correlation coefficient was calculated and Hierarchical clustered. Correlation coefficient is color coded as indicated in the figure

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