cumulative distribution function (cdf) or complete spatial random (csr) plots  (GraphPad Software Inc)

Journal: Epigenetics & Chromatin

Article Title: Impact of 3D genome organization, guided by cohesin and CTCF looping, on sex-biased chromatin interactions and gene expression in mouse liver

doi: 10.1186/s13072-020-00350-y

Figure Lengend Snippet: Cohesin and CTCF ChIP-seq binding strength and proximity to genes. a Box plots of normalized ChIP-seq signal for the peak sets indicated on the x -axis. Peaks with sex differential binding for cohesin ( top graph ) and CTCF (b ottom graph ) are shown. Each pair of boxplots represents the male and female ChIP-seq signal for the same set of peaks, defined by their sex bias and peak type (CAC or CNC, for ΔCohesin peaks; and CAC or Lone CTCF, for ΔCTCF peaks), as indicated below the x -axis. Peak scores were calculated by average intra-peak ChIP signal, normalized by total sequence reads per million in peak (RIPM; see “ ”). Female-biased peaks were, on average, stronger than male-biased peaks by M–W test: p ≤ 0.001 for female vs male CAC(ΔCoh), CAC(ΔCTCF), and for CNC, but not for Lone CTCF peaks. b Distance from each indicated set of cohesin and CTCF peaks to the nearest enhancer DHS. Cumulative frequency curves indicate the fraction of each group on the y -axis, within the distance in kb to the nearest enhancer DHS indicated on the x -axis. Enhancer DHS were defined based on their high ratio of the enhancer histone mark H3K4me1 over the promoter mark H3K4me3 at DHS . Sex-biased CNC peaks are closer to enhancer DHS (median distance to eDHS of 0.22 kb for male-biased CNCs and 0.12 kb for female-biased CNCs; KS pval < 0.0001 for all comparisons) than the other CTCF and cohesin peak classes (M CAC(ΔCTCF): 14.98 kb; F CAC(ΔCTCF) 13.76 kb; M Lone ΔCTCF: 13.88 kb; F Lone ΔCTCF: 7.17 kb). Female-biased CNC peaks are significantly closer to enhancer DHS than are male-biased CNC peaks ( p = 0.0351; KS t -test). Male-biased CAC(ΔCohesin) peaks were closer to enhancers than female-biased CAC(ΔCohesin) peaks ( p = 0.002; KS t -test), however, the reverse was found for CAC(ΔCTCF) peaks ( p = 0.0052; KS t -test). Distance to nearest enhancer was not significantly different between male-biased and female-biased Lone CTCF peaks ( p = 0.1068; KS t -test). P values for comparisons between male-biased and female-biased peaks of the same class are shown for each plot (KS t -test). c Distance from each indicated set of cohesin and CTCF peaks to the nearest TSS. Cumulative frequency curves indicate the fraction of each group on the y -axis within the distance in kb to the nearest TSS indicated on the x -axis. TSS for protein coding (RefSeq) and liver lncRNA genes were considered . Female-biased cohesin and CTCF peaks are closer to TSS than male-biased CTCF and cohesin peaks of the same class (significance by KS t-test is indicated at top left of each plot). Distance to the TSS was not significantly different for male-biased versus female-biased CNC peaks ( p = 0.1458; KS t -test). d Proximity of sex-biased cohesin and CTCF binding sites to sex-biased genes. Peak designations were as follows: Proximal, peaks < 20 kb from a sex-biased gene TSS; Intra-TAD, peaks within the same intra-TAD loop as a sex-biased gene; or TAD, peaks in the same TAD as a sex-biased gene. Each of these groups is mutually exclusive. TAD loop and intra-TAD loop coordinates were from the indicated references. A set of 983 sex-biased biased protein-coding genes was used in this analysis (see Additional file : Table S1 of ). e Cumulative frequency curves show the fraction of each group ( y -axis) within the distance in kb to the nearest sex-biased DHS or H3K27ac genomic region ( x -axis), based on a merged list of published sex-biased DHS and sex-biased H3K27ac ChIP-seq peaks for male and female mouse liver. For this analysis, CAC peaks with sex-biased binding of CTCF and cohesin were combined and presented as a single group [CAC (Both)]. Male-biased and female-biased CNC peaks are significantly closer to sex-biased DHS/H3K27ac than the four other peak classes ( p < 0.001; KS t -test). Female-biased CNC peaks were significantly closer to sex-biased DHS/H3K27ac than male-biased CNC peaks ( p = 0.0094; KS)

Article Snippet: Boxplots, cumulative distribution plots, and statistical analyses were implemented using GraphPad Prism 7.

Techniques: ChIP-sequencing, Binding Assay, Sequencing

Journal: Molecular Biology of the Cell

Article Title: Lymphatic endothelial cell calcium pulses are sensitive to spatial gradients in wall shear stress

doi: 10.1091/mbc.E18-10-0618

Figure Lengend Snippet: HLMVEC Ca 2+ pulse durations are sensitive to WSS magnitude and WSSGs in cells that pulse repeatedly. Plots represent the cumulative distribution functions (CDFs) for individual pulse durations (measured as FWHM) for P cells. The initial pulse (first pulse, FP) is shown in red, while all subsequent pulses (second, third, etc., SP) are shown in black. Dotted lines are fits to the Weibull distribution (see text). Pulse duration distributions are portrayed for Rings 1–6 (A–F), spatially uniform WSS (parallel plate chamber, G), and no flow (H). The scale (β) and shape (κ) parameters for fits to the Weibull distribution and the average pulse durations (FWHM; μ) are presented at the bottom of each graph. Experiments were performed in triplicate. Asterisks indicate statistically significant differences in CDFs as determined using the Kolmogorov–Smirnov test ( n.s. , not significant; *, p < 0.05; **, p < 10 –4 ; ***, p < 10 –7 ).

Article Snippet: Cumulative distribution function plots and modeling of the distributions of experimental data were performed using MATLAB.

Techniques: