Fig 1.
(a) Data inputs includes Hi-C matrix, accessible chromatin landscapes, and enriched experimental data such as ChIA-PET/HiChIP and Capture Hi-C as positive interactions. (b) Positive samples are generated according to the input data, and negative samples are generated according to the similar distance or greater distance of the positive samples. (c) DLoopCaller includes three convolutional blocks, two fully connected layers and a classification layer, in which each block consists of a convolutional layer, a ReLU layer, a dropout layer, and followed by a global average pooling layer.
Fig 2.
The generation of accessible chromatin matrix.
Fig 3.
The overall performance comparison of DLoopCaller and Peakschu on different cell lines.
(a) The F1-score, PRAUC, Precision and Recall values of RAD ChIA-PET and H3K27ac HiChIP in GM12878. (b)-(c): The F1-score and PRAUC values of CTCF ChIA-PET, H3K27ac HiChIP, SMC1 HiChIP, RAD ChIA-PET, and promoter Capture Hi-C in GM12878, CTCF ChIA-PET in K562 (replicate1) and H1-ESC, and SMC1 HiChIP in mESC.
Fig 4.
Comparison of chromatin loops within individual cell types.
(a) Distance distribution of DLoopCaller identified chromatin loops from Hi-C contact maps by using CTCF ChIA-PET, H3K27ac HiChIP, SMC1 HiChIP, RAD ChIA-PET, and promoter Capture Hi-C data after training on GM12878. (b) Venn diagram of DLoopCaller identified chromatin loops determined by CTCF ChIA-PET and H3K27ac HiChIP experiments in GM12878. (c) The proportion of CTCF ChIA-PET interactions and H3K27ac HiChIP interactions types for GM12878. The proportion of identified chromatin loops types using CTCF ChIA-PET data and H3K27ac HiChIP after training for GM12878.
Fig 5.
Comparison of chromatin loops identified by DLoopCaller, HiCCUPS, Fit-HiC, and Peakachu in GM12878.
(a) Venn diagram of identified chromatin loops determined by DLoopCaller CTCF ChIA-PET, HiCCUPS, Fit-HiC, and Peakachu in GM12878. (b) APA plots for DLoopCaller CTCF ChIA-PET loops, HiCCUPS, Fit-HiC, and Peakachu in GM12878. (c) A visual example of identified loops by different models in a region. The black dots in the upper half of the three diamond-shaped graphs represent the chromatin loops identified by DLoopCaller, and the blue, green, and yellow dots in the lower half represent the chromatin loops identified by Peakachu, Fit-HiC, and HiCCUPS respectively.
Fig 6.
Comparison of chromatin loops among cell types.
(a) Distance distribution of DLoopCaller identified chromatin loops from Hi-C contact maps by using CTCF ChIA-PET data after training on GM12878, H1-ESC, and K562 (replicate1) separately. (b) APA plots of identified chromatin loops in GM12878, H1-ESC, and K562 (replicate1). (c) Venn diagram of DLoopCaller identified chromatin loops determined by CTCF ChIA-PET experiments in GM12878, H1-ESC and K562 (replicate1). (d) The proportion of CTCF ChIA-PET interactions types for H1-ESC and K562. The proportion of identified chromatin loops types using CTCF ChIA-PET data after training for H1-ESC and K562 (replicate1).
Fig 7.
The co-enrichment of transcription factors on identified chromatin loops in H1-ESC with CTCF ChIA-PET training model.