Figure 3

CpG sites selected by the Boruta method. Local importance (a) and M values (b) of the 216 CpG sites grouped into deciles. The CpG sites shown were selected by the Boruta method as being differential between the seven sarcoma clusters identified by random forest clustering. The seven sarcoma clusters are given in columns and CpG sites are given in rows. A characteristic set of CpG sites was identified for sarcoma cluster 2 (LMS samples), cluster 5 (MLS samples), cluster 6 (MPNST samples) and cluster 7 (SS samples including one MPNST sample). The sarcoma clusters 1, 3 and 4 (mainly DDLS, UPS, MFS and PLS samples) had different patterns of the same set of CpGs and composed CpG cluster 3. The order of the CpG sites is listed in Additional file 1: Table S6. The color code for DNA methylation level is given at the bottom of each graph. For local importance (a), yellow indicates low and purple indicates high importance. DDLS, dedifferentiated liposarcoma; LMS, leiomyosarcoma; MFS, myxofibrosarcoma; MLS, myxoid liposarcoma; MPNST, malignant peripheral nerve sheath tumor; PLS, pleomorphic liposarcoma; SS, synovial sarcoma; UPS, undifferentiated pleomorphic sarcoma.