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Fig. 1 | BMC Evolutionary Biology

Fig. 1

From: Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus

Fig. 1

Comparison and clustering of developmental transcriptomes. a Correlation of expression values and numbers of significantly differentially expressed genes across all pairwise comparisons. The upper left triangle of the matrix indicates the number of genes (×103) that were predicted to be significantly differentially expressed by Cuffdiff and the lower right triangle shows Spearman correlations of expression values. b Principal component analysis of expression values as measured by Cufflinks, indicates that the transcriptomes can be grouped into three clusters. c Hierarchical clustering of transcriptomes based on the pairwise comparisons of all samples using Cuffdiff. df Violin plot of expression values in all samples for genes clustered in bicluster 4 (panel d), 12 (e) and 24 (f) respectively. Color code indicates the rough grouping of samples into three developmental stages. The statistical significance of expression differences across stages is shown as the maximum p-value (Wilcoxon test) between any pairwise comparisons of samples across stages. gi Enrichment of Pfam domains in bicluster 4 (g), 12 (h) and 24 (i) respectively. The plots show the enrichment factor vs. the significance (−l o g 10 P). The most significant protein families are highlighted in the individual plots

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