Fig. 2

Local gene copy number alteration.a-b GISTIC analysis of recurrent amplification (left, red) and deletion (right, blue) in LMS (a) and DDLPS (b). The y-axes represent genomic position of altered regions (left axis: chromosome; right axis: cytoband) and the x-axes represent normalized amplification signal (top axis) and significance by Q value (bottom axis). The vertical green line represents the significance cutoff at Q value = 0.25. The most prominent amplification is seen around 12q14 in DDLPS. c GSEA by position. Gene sets of chromosomal neighbors are used as the input in GSEA which gives an ES = 0.784 (nominal p-value 0.0177, FDR q-value 0.447) at Chr12q15. MDM2 is located at the junction of Chr12q14 and Chr12q15 and on the side of Chrq15