Fig. 3: L1 RNA throughout TCGA.
a Estimated expression of L1 RNA in each sample by tumor type, quantified by L1EM. L1 RNA expression per sample is aggregated across all active L1HS and L1PA2 loci, N = 1483. Asterisks (*) indicate significance level of Bonferroni adjusted one-sided Mann–Whitney U test comparing tumor to normal expression (*p < 0.01, **p < 0.001, ***p < 0.0001). Bonferroni-adjusted p-values and effect sizes for the asterisked indications, from left to right in the figure, are as follows. Esophageal: 1.31 × 10−3, 0.69; Colon: 2.88 × 10−19, 0.90; LUSC: 1.14 × 10−27, 0.96; Head & Neck: 5.57 × 10−9, 0.6; Stomach: 1.57 × 10−12, 0.79; Bladder: 2.05 × 10−4, 0.58; UCEC: 9.06 × 10−5, 0.56; Cholangiocarcinoma: 1.80 × 10−4, 0.94; LUAD: 2.30 × 10−20, 0.76; Breast: 5.57 × 10−9, 0.33; KIRC: 1.8 × 10−7, 0.41; Liver: 9.93 × 10−14, 0.67; Rectum: 4.2 × 10−4, 0.79. b Estimated expression of RNA from 121 L1 loci in each sample grouped by tumor type, quantified by L1EM. L1 RNA expression per sample is aggregated across 121 loci with evidence of in vitro activity or transductions (see Methods section, Identifying subsets of L1 elements). Bonferroni-adjusted p-values and effect sizes for the asterisked indications, from left to right in the figure, are as follows. Esophageal: 1.38 × 10−3, 0.69; Colon: 2.47 × 10−18, 0.87; LUSC: 1.26 × 10−26, 0.94; Head & Neck: 5.44 × 10−3, 0.32; Stomach: 7.4 × 10−11, 0.73; Bladder: 9.73 × 10−3, 0.4; Cervical: 3.49 × 10−3, 0.94;UCEC: 2.44 × 10−6, 0.65; Cholangiocarcinoma: 1.42 × 10−3, 0.83; LUAD: 1.12 × 10−20, 0.76; Breast: 4.7 × 10−7, 0.31; Liver: 4.33 × 10−9, 0.54; Rectum: 1.6 × 10−3, 0.73. a, b Total N = 9717 samples; 8998 tumor samples and 719 normal samples. Tumor types are sorted as in Fig. 2, with the addition of Rectal adenocarcinoma and AML. Blue, tumor samples. Orange. normal samples. Center line indicates median. Box indicates interquartile range. Points more than 1.5× IQR away from the IQR box are shown as individual outliers.
