Fig. 4: SVs identified by multiple genome comparisons and their effect on the expression of associated genes (SV genes). | Nature Genetics

Fig. 4: SVs identified by multiple genome comparisons and their effect on the expression of associated genes (SV genes).

From: Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea

Fig. 4

a, Different types of SV genes, based on the ___location of the SV relative to the gene, with data on expression, show a high proportion of SV genes with gene expression changes. b, The expression of SV genes from 6,526 syntenic gene families, with separated expression values for the absence and presence genotype groups (of corresponding SV). The x axis shows two groups, of which 3,536 and 2,990 syntenic gene families associated with suppression and promotion SVs, respectively. The y axis shows the normalized (z score) expression values. The green/yellow lines link the average expression values from each syntenic gene family for their presence and absence of genotype groups. c, Comparison of CpG island density and the ratio of highly methylated CpG islands between different types of SVs in −1.5 kb (n = 484 versus 369 versus 2,794; permutation test for 10,000 times; centerline, median; triangle, mean; box limits, first and third quartiles; whiskers, 1.5× IQR) or −3 kb (n = 153 versus 148 versus 1,391; permutation test for 10,000 times; centerline, median; triangle, mean; box limits, first and third quartiles; whiskers, 1.5× IQR). d, The expression fold changes of SV genes between the presence and absence of genotype groups. The black stars below the term ‘Suppress’ denote DNA methylation modifications. The x axis shows the distance between SV and SV genes.

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