Genes and pathways affected by LOH of PTPRJ . A) Heatmap of genes differentially expressed between cases with retention (RET) and LOH calls. B) DNA polymerase (HSA03030), TP53 signaling pathway (HSA04115) and Proteasome (HSA03050) were identified as the most enriched gene sets in cases with retention of PTPRJ. C) In cases with LOH, the gene sets VEGF signaling pathway (HSA04370), Melanoma (HSA05218), ERBB signaling pathway (HSA04012), Calcium signaling pathway (HSA04020), FC Epsilon RI signaling pathway (HSA04664) and MAPK signaling pathway (HSA04010) were the most enriched. Despite an FDR (false discovery rate) of 1 for all the enrichments, the results from this gene-set enrichment analysis were analysed based on the P values instead of the FDR scores. The high FDR values obtained in this analysis may be due to the low population size. The lists of all gene sets from this analysis are provided in Additional file 3 and Additional file 4.