Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses
Results from unique-read TFBSs are shown. A) The heatmap with hierarchical clustering, which shows statistical enrichment of respective TFBSs in each type of HERV/LTRs. Color in heatmap (from blue to red) indicates enrichment significance (z score) to random expectation. The row indicates TFBSs from a ChIP-Seq analysis. The column indicates a HERV/LTR type. The dendrograms were cut at heights denoted by broken lines. Fourteen clusters were identified for HERV/LTRs and TFBSs. Of these, characteristic clusters of TFBSs (TF_1–8) and HERV/LTRs (HERV_1–9) are shown. The cut heights and the characteristic clusters were manually chosen according to dendrograms and color patterns in heatmap. The number of HERV/LTR types highly enriched in each TFBS dataset (z score >5) is shown on the right side of the heatmap. B) Characteristic clusters of TFBSs (TF_1–8). Ectoderm, endoderm, mesoderm, and mesendoderm were differentiated from HUES64 cells. C) Characteristic clusters of HERV/LTRs (HERV_1–9). Classification of the HERV/LTR family is based on RepeatMasker (20-Mar-2009) (http://www.repeatmasker.org/).