10.1371/journal.ppat.1007441.g013 Timothy M. Rose Timothy M. Rose A. Gregory Bruce A. Gregory Bruce Serge Barcy Serge Barcy Matt Fitzgibbon Matt Fitzgibbon Lisa R. Matsumoto Lisa R. Matsumoto Minako Ikoma Minako Ikoma Corey Casper Corey Casper Jackson Orem Jackson Orem Warren Phipps Warren Phipps Analysis of the highly expressed genes in the KS tumors. Public Library of Science 2018 Ugandan KS tumors KSHV latency region lytic gene expression profiles quantitate KSHV transcription PCA ORF 75 sequences Quantitative RNAseq analysis KS tumors UCDS KSHV gene expression profiles KSHV transcription HIV microRNAs K 1-9 latency promoter KSHV KSHV gene expression 2018-12-17 18:59:33 Figure https://plos.figshare.com/articles/figure/Analysis_of_the_highly_expressed_genes_in_the_KS_tumors_/7475906 <p>A) The median expression levels of the most highly expressed KSHV genes were compared, with each dot representing the normalized transcript level (TPM) detected by each KSHV UCDS feature. Genes with transcript levels above 5,000 TPM (blue line) are specifically indicated. Genes with transcript levels between 1,000 (red line) and 5,000 TPM are listed together. Genes with transcript levels below 1,000 are grouped as “all other”. Clusters of UCDS features detecting common transcripts are indicated: Red—major T1.7A transcript in the latency region; Blue—K15/ORF75 bicistronic transcript; Green—ORF71/72 bicistronic transcript. An asterisk marks the genes proximal to poly-A sites. B) hierarchical clustering of gene-gene expression correlations for those genes with median transcript levels above 1,000 TPM. Pearson correlation coefficients (R) were calculated for pairs of genes using normalized transcript levels. The negative correlation (R = -1.0) is shown in orange and the positive correlation (R = 1.0) in purple, with the absence of correlation (R = 0) in white. The unsupervised hierarchical clustering is indicated at the top and the major clusters of genes (A-C) are indicated.</p>