Extended Data Fig. 6: Comparison of loops predicted by FitHiC2 and NeoLoopFinder in SV regions. | Nature Methods

Extended Data Fig. 6: Comparison of loops predicted by FitHiC2 and NeoLoopFinder in SV regions.

From: Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes

Extended Data Fig. 6

a–c, Neo-loops predicted by NeoLoopFinder and FitHiC2 in LNCaP cells. a, Global view of the Hi-C map of chromosomes 7 and 14 shows that there is an inter-chromosomal translocation (marked by arrow). b, High-resolution Hi-C map showing contact frequencies between ETV1 and its hijacked enhancers on chr14. Blue circles indicate neo-loops identified by NeoLoopFinder. c, Significant interactions (blue circles) identified by FitHiC2. d–g, For this analysis, we used all the loops from ten cancer cell lines with DNase-Seq data available in ENCODE data portal (MCF7, A549, LNCaP, T47D, HL-60, KBM7, RPMI 8226, SK-N-MC, SW480 and K562). d, Upset plot of chromatin loops detected by NeoLoopFinder and FitHiC2 within SV regions. e, Chromatin accessibility around anchors of NeoLoopFinder-unique loops and FitHiC2-unique loops. f-g, Aggregate Peak Analysis (APA) for NeoLoopFinder-unique loops (f) or FitHiC2-unique loops (g).

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