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Table 1 Codon usage differences between each cancer and its respective normal tissue

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

Cancer name Higher in cancer or normal Codon % difference
Aggregate transitional cell carcinoma—bladder Cancer CGG 5.42
Aggregate transitional cell carcinoma—Bladder Normal TGT 5.23
Transitional cell carcinoma—bladder Cancer CGG 4.76
Transitional cell carcinoma—bladder Normal TGT 5.03
Papillary transitional cell carcinoma—bladder Cancer CGG 8.26
Papillary transitional cell carcinoma—bladder Normal CCT 9.28
Aggregate carcinoma—breast Cancer GGT 15.83
Aggregate carcinoma—breast Normal TGT 7.44
Ductal carcinoma—breast Cancer GGT 15.06
Ductal carcinoma—breast Normal TGT 7.60
Lobular carcinoma—breast Cancer GGT 19.60
Lobular carcinoma—breast Normal TTA 8.93
Duct and lobular carcinoma—breast Cancer GGT 28.12
Duct and lobular carcinoma—breast Normal TGT 5.01
Colorectal adenocarcinoma Cancer CGT 11.28
Colorectal adenocarcinoma Normal TGC 8.23
Left colorectal adenocarcinoma Cancer CGT 11.39
Left colorectal adenocarcinoma Normal TGC 7.55
Right colorectal adenocarcinoma Cancer CGT 12.23
Right colorectal adenocarcinoma Normal TGC 10.40
Adenocarcinoma—endometrium Cancer GCG 6.06
Adenocarcinoma—endometrium Normal CAA 8.52
Endometrioid adenocarcinoma Cancer GCG 6.07
Endometrioid adenocarcinoma Normal CAA 9.01
Serous cystadenocarcinoma—endometrium Cancer GCG 6.86
Serous cystadenocarcinoma—endometrium Normal CAA 7.22
Squamous cell carcinoma—head and neck Cancer TCC 6.20
Squamous cell carcinoma—head and neck Normal CAC 4.78
Squamous cell carcinoma—esophagus Cancer CGC 19.16
Squamous cell carcinoma—esophagus Normal TAT 22.41
Esophageal adenocarcinoma Cancer CGG 17.63
Esophageal adenocarcinoma Normal TAT 18.16
Clear cell renal cell carcinoma Cancer CGC 6.67
Clear cell renal cell carcinoma Normal ATA 6.57
Papillary renal cell carcinoma Cancer CGC 11.36
Papillary renal cell carcinoma Normal TTA 13.01
Chromophobe renal cell carcinoma Cancer CGC 10.11
Chromophobe renal cell carcinoma Normal TGC 10.03
Hepatocellular carcinoma Cancer CGG 24.19
Hepatocellular carcinoma Normal TGT 28.55
Cholangiocarcinoma Cancer CGG 47.48
Cholangiocarcinoma Normal TGT 61.40
Adenocarcinoma—lung Cancer CGT 11.77
Adenocarcinoma—lung Normal TGC 13.07
Squamous cell carcinoma—lung Cancer CGT 16.52
Squamous cell carcinoma—lung Normal TGC 17.95
Adenocarcinoma with mixed subtypes—lung Cancer CGT 11.86
Adenocarcinoma with mixed subtypes—lung Normal TGT 12.38
Bronchioloalveolar carcinoma Cancer TTA 12.15
Bronchioloalveolar carcinoma Normal TGC 10.07
Papillary adenocarcinoma—lung Cancer CGT 10.82
Papillary adenocarcinoma—lung Normal TGT 11.76
Mucinous adenocarcinoma—lung Cancer CGG 8.76
Mucinous adenocarcinoma—lung Normal CCT 8.90
Prostate adenocarcinoma Cancer GGT 3.74
Prostate adenocarcinoma Normal ATA 3.57
Adenocarcinoma—stomach Cancer TTA 12.74
Adenocarcinoma—stomach Normal TGC 5.62
Intestinal type adenocarcinoma—stomach Cancer TTA 12.45
Intestinal type adenocarcinoma—stomach Normal TGC 5.82
Diffuse type carcinoma—stomach Cancer TTA 13.49
Diffuse type carcinoma—stomach Normal GTC 5.68
Tubular adenocarcinoma—stomach Cancer TTA 13.51
Tubular adenocarcinoma—stomach Normal TGC 6.88
  1. This table describes the most pronounced codon usage differences for each cancer type based on median transcriptome-weighted codon usage comparison between each cancer type and its respective normal tissue type. For each cancer type, one codon with higher usage in primary tumor tissue and one codon with higher usage in normal tissue are listed. More codon differences can be found in Additional File 4: Table S3
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Genome Medicine

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