Fig. 4

Overlapping human ERV-ORFs with functional data in various tissues and cell lines. a PCA plot illustrating the ERV-ORFs expressed during the four stages of human primary myoblast differentiation (three replicates in each stage) for the first two principal components (PC1 and PC2). Differentiation status was indicated by color. D0: undifferentiated myoblasts, D1–3: 1–3 days after myoblast differentiation began. The proportion of contributing variables for a given PC are shown on the axes. b Expression levels for ERV-ORFs with ≥10 normalized read counts during human primary myoblast differentiation. ERV classes and domain categories are displayed on the left. The regularized logarithm (rlog) transformed read counts for ERV-ORFs are color-coded from blue (low expression) to red (high expression). Differentiation status is presented in the same color as in panel a. c Human ERV-ORFs overlapping with H3K36me marks. The fractions of samples of histone marks are shown in heat color scales. ERV classes and domain categories on the top are the same as in the panel b. d Top 10 ERV groups in ERV-ORFs detected by functional data (chi-squared test, p -value < 0.05, FDR corrected). The different ERV sets for all ERV-ORFs in this study (gray bar), detected from the CHESS datasets (pink circle), histone datasets (yellow circle), Myoblast RNA-Seq datasets (blue circle) are indicated. ERV classes on the left are the same in the panel b. e Overlaps of human ERV-ORFs with transcription potential detected by different functional datasets. Fractions of ERV-ORFs located near TSSs (< 5kbp) in each functional datasets are presented under the name of functional data. f Pairwise dN/dS ratios for ERV-ORFs with transcriptional potential (tp) and without tp in human are shown in pink and gray, respectively. Dots and error bars represent average rates and standard deviation, respectively