A dataset of ChIP-seq with antibody against CBX6 (GEO: GSM1295076) was used in the above example. The genomic binding regions were mapped to coding genes using the seq2gene function with UCSC genomic annotation. The Entrez gene IDs were converted into gene symbols using the bitr function implemented in clusterProfiler. To identify and characterize transcript cofactors, we performed functional enrichment analysis using the ENCODE and ChEA transcript factor gene sets. The result was visualized as a category-gene network (Figure 3), which showed that genes associated with CBX6 (obtained by the seq2gene function) significantly overlap with genes regulated by POU5F1, TRIM28, SUZ12, and EZH2. OCT4 (POU5F1)34 and KAP1 (TRIM28)35 have been reported to interact with polycomb repressive complex 1 (PRC1), and CBX6 is a known subunit of PRC1.36 SUZ12 and EZH2 are core components of PRC2 and negatively regulate CBX6.37 These pieces of evidence support the effectiveness of these analyses including the mapping of genomic ROIs to coding genes and functional enrichment, which suggest that this method can be used to identify unknown cofactors (Figure 3) and characterize functions of genomic regions.
