Figure 4.
Properties of vTR ChIP-Seq Datasets
(A) Overlap of vTR ChIP-seq peaks. Each entry indicates the overlap (number of intersecting peaks divided by the number of peaks in the smaller peak set) between the given pair of vTR ChIP-seq datasets. Rows and columns were hierarchically clustered using the Unweighted Pair Group Method With Arithmetic Mean (UPGMA) algorithm.
(B) Distribution of vTR ChIP-seq peaks relative to human gene transcription start sites (TSSs). Transcript-related features were obtained from the UCSC “Known Genes” database table (Haeussler et al., 2019). The plot was created using the ChIPseeker package (Yu et al., 2015).
(C) Human TF binding site motifs enriched in vTR ChIP-seq peaks. TF binding site motif enrichment was calculated using HOMER (Heinz et al., 2010). Motifs shown are among the top five motif families (based on HOMER p value) in any individual ChIP-seq dataset. Heatmap color indicates the normalized –log p value. A value of 100 means that the motif has the best –log p value for the given vTR, with 50% indicating half of the best –log p value.