5. DEG analysis

5.1. DEG_boundary_analysis

DEG_boundary_analysis is designed to carry out TAD-boundary proximity analysis as suggested in Ghavi-Helm et al., Nat Genet. 2019. It utilizes a permutation test to estimate the significance of the proximity of differentially expressed genes (DEGs) or differential peaks, to the perturbed TAD boundaries resulting from protein depletion.

DEG_boundary_analysis [-h] [--border_test BORDER_TEST]
                      [--border_control BORDER_CONTROL]
                      [--gene_test GENE_TEST]
                      [--gene_control GENE_CONTROL] [-o OUTPUT] [-n N]
                      [--maxdistance MAXDISTANCE] [--step STEP]

optional arguments:
-h, --help            show this help message and exit
--border_test BORDER_TEST
                        <TAD boundary to be tested (BED format)>
--border_control BORDER_CONTROL
                        <TAD boundary as background (BED format)>
--gene_test GENE_TEST
                        <Genes to be tested (BED format)>
--gene_control GENE_CONTROL
                        <Genes as background (BED format)>
-o OUTPUT, --output OUTPUT
                        Output name (*.pdf or *.png, default: output.pdf)
-n N                  Number of permutation (default: 1000)
--maxdistance MAXDISTANCE
                        Max distance (bp, default: 300000)
--step STEP           Step of distance (bp, default: 10000)

The function requires four BED files as input data:

  • Test TAD boundaries (e.g., boundaries lost due to depletion)

  • Background TAD boundaries (i.e., all boundaries)

  • Test gene loci (e.g., DEGs resulting from depletion)

  • Background gene loci (i.e., all genes)

Using this input, DEG_boundary_analysis calculates the proportion of genes that overlap with TAD boundaries, extending the distance incrementally (--step) up to the defined maximum distance (--maxdistance). The output data is represented graphically:

Alternate

Fig. 5.1 DEG_boundary_analysis

The purple line illustrates the observed fraction of tested DEGs against the tested boundaries. If this line deviates from the shaded region, it indicates a significant enrichment or depletion of the DEGs.