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Fig. 6 | BMC Genomics

Fig. 6

From: A survey of tandem repeat instabilities and associated gene expression changes in 35 colorectal cancers

Fig. 6

Schematic illustration of the expression analysis of genes with and without repeat instability. A gene (A, B, C and so on, where n = 18,439) is shown in solid black, if it does not contain any repeat instability (repeat copy number variation, repeat gain, or repeat loss) in its promoter or its exons between tumor and matched normal genomes of a patient (n = 35). It is shown cross-hatched if it contains at least one of these repeat instability types. Only genes with a repeat instability in at least one of the patients are considered for this expression analysis (n = 11,016 genes for promoter repeats, and n = 7531 genes for exonic repeats). For each gene, we computed (i) the mean of its expression level in tumors where the gene shows repeat instability (cross-hatched arrow indicating transcription) and (ii) the mean of its expression in tumors where the gene does not show repeat instability (solid black arrow indicating transcription). We then performed a WSR test to compare the mean expression values between these two groups of genes, the null hypothesis being that the expression level of a gene is not associated with mutations in its tandem repeat in a tumor tissue

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