Fig. 3

FAN-C analysis features. All analyses performed on GM12878 cells [25] on the 10 kb resolution matrix, unless otherwise noted. a Schematic representation of the analysis types available for FAN-C, Cooler, and Juicer matrices. b Hi-C matrix plot of a sample region with 10 kb resolution. c Log-log “Distance decay” plot of the expected normalised contact frequency against locus distance. d Log2-observed/expected (O/E) matrix for the same region as in a. e 500 kb resolution correlation matrix/A/B compartment plot of chromosome 1 (top) and its first eigenvector (EV) (bottom). f “Saddle plot” showing preferential interactions of active/active and inactive/inactive regions (top), and bar plot showing the cutoffs used for binning regions by the corresponding EV entry magnitude (bottom). Note the outlier on the far right. g Aggregate TAD plot showing the average log2-O/E in and around arrowhead domains [25]. h Aggregate loop plot showing the average log2-O/E at peaks called by HICCUPS [25]. i–n Example region on chromosome 18 highlighting additional analyses available in FAN-C and the possibility of “genome browser” style plotting. i Triangular Hi-C matrix plot. j Line plot showing CTCF occupancy (fold-change over input) as measured by ChIP. Data from GEO:GSM733752. k Heatmap showing insulation scores calculated using different window sizes. l Insulation score track for a window size of 100 kb. m Heatmap showing directionality index results for multiple window sizes. n Directionality index track for a window size of 1 Mb. o Gene plot using data from Gencode (v19) [57]