FusionPathway: Prediction of pathways and therapeutic targets associated with gene fusions in cancer
Fig 2
Evaluation of p210 BCR-ABL1 prediction using known BCR-ABL1 pathways and benchmark gene sets.
(A) Bar plot of some statistically significant pathways that are associated with BCR-ABL1 in our prediction. A bar in the graph represents the statistically significance of a given pathway in GSEA association analysis, GSEA deregulation analysis, or combination analysis using the truncated product method. The statistically significances are presented in the graph as–log10(p-value). (B) GSEA association plot of the Gleevec pathway in our prediction. GSEA evaluates the genes of the pathway for their distribution in the ordered gene list generated by our association prediction. (C) ROC curves for five benchmark gene sets: 26 Wnt/Ca+/NFAT pathway genes (denoted WNT_CA+_NFAT genes), 1150 genes cited with BCR-ABL1 in the literature (denoted BCR-ABL genes), 1240 genes cited with CML in the literature (denoted CML genes), 328 genes categorized in the KEGG cancer pathways (denoted cancer pathway genes), and 68 target genes of compounds that have been tested in clinical trials or used for the treatment of imatinib-resistant CML (denoted drug targets). Genes in these five gene sets were treated as positive instances, and the remaining genes were treated as negative instances. TPR indicates true positive rate; FPR, false positive rate; and AUC, area under the ROC curve.