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Fig. 4 | Genome Medicine

Fig. 4

From: Distinct signatures of codon and codon pair usage in 32 primary tumor types in the novel database CancerCoCoPUTs for cancer-specific codon usage

Fig. 4

Change in codon usage and change in RSCU in breast cancers. A Scatterplot representing codon usage difference between normal breast tissue and aggregate breast cancer based on the median tissue values. Values along the x-axis represent the codon usage per thousand in normal breast tissue. Values along the y-axis represent the percent difference between aggregate breast cancer and normal breast usage. BD Scatterplots representing the correlation between change in relative synonymous codon usage (RSCU) of GGT and its synonymous codons GGA (B), GGC (C), and GGG (D). Each point represents a change in individual patients (n = 107). p-value text appears green where the null hypothesis may be rejected (see the “Methods” section for the explanation of the Wald test used). E Scatterplot representing the codon usage difference between normal breast tissue and invasive ductal carcinoma (IDC) of the breast based on the median tissue values. Values along the x-axis represent the codon usage per thousand in normal breast tissue. Values along the y-axis represent the percent difference between IDC and normal breast usage. FH Scatterplots representing the correlation between change in relative synonymous codon usage (RSCU) of GGT and its synonymous codons GGA (F), GGC (G), and GGG (H). Each point represents a change in individual IDC patients (n = 85). p-value text appears green where the null hypothesis may be rejected (see the “Methods” section for the explanation of the Wald test used). I Scatterplot representing the codon usage difference between normal breast tissue and invasive lobular carcinoma (ILC) based on the median tissue values. JL Scatterplots representing the correlation between change in RSCU of GGT and its synonymous codons GGA (J), GGC (K), and GGG (L). Each point represents a codon change in individual ILC patients (n = 7). p-value text appears green where the null hypothesis may be rejected (see the “Methods” section for the explanation of the Wald test used). M Scatterplots representing the codon usage difference between normal breast tissue and mixed invasive ductal and lobular carcinoma (IDLC) based on the median tissue values. NP Scatterplots representing the correlation between change in RSCU of GGT and its synonymous codons GGA (N), GGC (O), and GGG (P). Each point represents the change in individual IDLC patients (n = 9). p-value text appears green where the null hypothesis may be rejected (see the “Methods” section for the explanation of the Wald test used)

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