Skip to main content
. 2018 Aug 28;7:e38358. doi: 10.7554/eLife.38358

Figure 6. Many HLA-restricted TCR clusters contain TCRβ chains annotated as pathogen-responsive.

Each point represents one of the 78 significant HLA-restricted TCR clusters, plotted based on a normalized cluster size score (Ssize, x-axis) and an aggregate TCR co-occurrence score for the member TCRs (ZCO, y-axis). Markers are colored by the locus of the restricting HLA allele and sized based on the strength of the association between cluster member TCRs and the HLA allele. The database annotations associated to TCRs in each cluster are summarized with text labels using the following abbreviations: B19 = parvovirus B19, INF = influenza, EBV = Epstein Barr Virus, RA = rheumatoid arthritis, MS = multiple sclerosis, MELA = melanoma, T1D = type one diabetes, CMV = cytomegalovirus. Clusters labeled ‘coCMV’ are significantly associated (P<1×10−5) with CMV seropositivity (see main text discussion of cluster #3). Clusters labeled 1–5 are discussed in the text and examined in greater detail in Figure 7 and Figure 8.

Figure 6—source data 1. Paired TCRα chain sequences from the pairSEQ dataset of (Howie et al., 2015) for all clusters with at least 2 matched TCRβ chains, along with a score for each cluster that assesses the degree of sequence similarity among the partner chains.
elife-38358-fig6-data1.tds (8.3KB, tds)
DOI: 10.7554/eLife.38358.021

Figure 6.

Figure 6—figure supplement 1. Distributions of cluster co-occurrence scores on the two validation cohorts.

Figure 6—figure supplement 1.

Smoothed distributions of cluster co-occurrence scores on the two validation cohorts. Gaussian kernel density estimation (KDE)-smoothed distributions of the cluster member TCR co-occurrence scores (ZCO) for the two validation cohorts. A standard normal distribution is shown as an approximate null expectation for these Z-scores.