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Fig. 3 | BMC Bioinformatics

Fig. 3

From: 3D: diversity, dynamics, differential testing – a proposed pipeline for analysis of next-generation sequencing T cell repertoire data

Fig. 3

The dynamics from PBMC to tissue for prostate cancer subjects (NeoACT study). a The proportion of overlap between PBMC and RP tissue. The traditional formula was used to calculate the overlap proportion of T-cell clonotypes between RP tissue and PBMC at each time point (PBMC.0- > tissue, PBMC.2- > tissue, PBMC.4- > tissue) for the treated prostate cancer subjects and untreated subjects (PBMC- > tissue). b The intraclass correlation coefficient (ICC) between RP tissue and PBMC. The ICC was calculated based on the clones present at both RP tissue and PBMC from the untreated prostate cancer subjects (PBMC- > tissue), or between RP tissue and PBMC at each time point of the treated prostate cancer subjects (PBMC.0- > tissue, PBMC.2- > tissue, PBMC.4- > tissue). c The binned analysis of fold change in clonal frequency from PBMC to RP tissue. This fold change analysis only included the clones that present at both tissue and PBMC for the untreated subjects (PBMC- > tissue) or present at both tissue and PBMC at each week (PBMC.0- > tissue, PBMC.2- > tissue, PBMC.4- > tissue), respectively, for the treated prostate cancer subjects. From top to the bottom, each panel presents the fraction of the decrease, unchanged and increase clones which correspond to the adjusted FC of tissue vs. PBMC is less than 0.25, between 0.25 and 4 and greater than 4, respectively. The median and interquartiles are shown

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