Fig. 6
From: Peak analysis of cell-free RNA finds recurrently protected narrow regions with clinical potential
CfRNA peaks in plasma are informative of cancer and cancer types. A AUROC bar plot by different peak matrices in the CRC plasma small RNA-seq cohort (PRJNA540919). B Scatter plot showed the relation between peak abundance and classification importance in the CRC plasma cohort (PRJNA540919). X axis means log-transformed absolute coefficient in the LR models (higher value means more importance). Y axis means log-transformed CPM value. CRC highly expressed (relative to primary blood cell) peaks were highlighted in orange. C Left: expression profiles of CRC plasma-enriched RBP set across several human tissue types from GTEx. Right: expression profiles (GSVA score) of CRC plasma-enriched RBP set were overexpressed compared with those of randomly shuffled background RBP set across GTEx colon tissue data (n = 779). D Left: expression profiles of CRC plasma-enriched RBP set across several human cancer types from TCGA. Right: expression profiles (GSVA score) of CRC plasma-enriched RBP set were overexpressed compared with those of randomly shuffled background RBP set across TCGA COAD cancer tissue data (n = 469). CRC plasma-enriched RBP set: 16 RBPs enriched from high abundant peaks (top 500 P value ranked) in the CRC relative to NC plasma (PRJNA540919). Background RBP set: randomly shuffled RBP set with the same number (n = 16, permutation = 2000). Wilcoxon’s rank sum test, two-sided. The centers of the boxplots are median values; the bounds of the boxes are 25% and 75% quantiles. The minima are 25% quantile − 1.5*interquartile range (IQR) and the maxima are 75% quantile + 1.5*IQR. E 3D t-SNE plot showed the top 500 P value ranked cfRNA peaks identified by cfPeak in plasma are informative of cancer types in the three-cancer plasma small RNA-seq discovery cohort (GSE71008). Significance of group distance fraction below was calculated by permutation, same as right. F 3D t-SNE plot showed the top 500 P value ranked cfRNA peaks from plasma are informative of cancer types in the three-cancer tissue small RNA-seq validation cohort (TCGA)