Differential Accessibility



Comparisons

Differential Accessibility was quantified for the following comparisons:

Comparison name Annotation column Group 1 N1 Group 2 N2
1 TeffMem_U vs Th1prec_U [sampleGroup] sampleGroup TeffMem_U 4 Th1prec_U 4
2 TeffMem_U vs Th2prec_U [sampleGroup] sampleGroup TeffMem_U 4 Th2prec_U 4
3 TeffMem_U vs Th17prec_U [sampleGroup] sampleGroup TeffMem_U 4 Th17prec_U 4
4 TeffMem_U vs Tfh_U [sampleGroup] sampleGroup TeffMem_U 4 Tfh_U 5
5 TCD8_U vs TCD8naive_U [sampleGroup] sampleGroup TCD8_U 4 TCD8naive_U 4
6 Bnaive_U vs Bmem_U [sampleGroup] sampleGroup Bnaive_U 4 Bmem_U 4
7 TeffNaive_U vs TeffMem_U [sampleGroup] sampleGroup TeffNaive_U 4 TeffMem_U 4
8 TCD8naive_U vs TCD8EM_U [sampleGroup] sampleGroup TCD8naive_U 4 TCD8EM_U 4
9 TregNaive_U vs TregMem_U [sampleGroup] sampleGroup TregNaive_U 4 TregMem_U 4

Tables containing differential accessibility results can be found below.

.peaks.cons t10k promoters_gc_protein_coding ERB_BP_distal ERB_BP_dnase ERB_BP_proximal ERB_BP_tfbs ERB_BP_tss
TeffMem_U vs Th1prec_U [sampleGroup] TSV TSV TSV TSV TSV TSV TSV TSV
TeffMem_U vs Th2prec_U [sampleGroup] TSV TSV TSV TSV TSV TSV TSV TSV
TeffMem_U vs Th17prec_U [sampleGroup] TSV TSV TSV TSV TSV TSV TSV TSV
TeffMem_U vs Tfh_U [sampleGroup] TSV TSV TSV TSV TSV TSV TSV TSV
TCD8_U vs TCD8naive_U [sampleGroup] TSV TSV TSV TSV TSV TSV TSV TSV
Bnaive_U vs Bmem_U [sampleGroup] TSV TSV TSV TSV TSV TSV TSV TSV
TeffNaive_U vs TeffMem_U [sampleGroup] TSV TSV TSV TSV TSV TSV TSV TSV
TCD8naive_U vs TCD8EM_U [sampleGroup] TSV TSV TSV TSV TSV TSV TSV TSV
TregNaive_U vs TregMem_U [sampleGroup] TSV TSV TSV TSV TSV TSV TSV TSV
Comparison
Region type
Differential method

Figure 1

Open PDF Figure 1

MA plot

LOLA enrichment analysis

LOLA enrichment analysis [1] for differentially accessible regions.

Comparison
Region type
Differential method

Figure 2

Open PDF Figure 2

LOLA bar plot for enrichment of region annotations. Bar height denotes log2(odds-ratio). Bars are ordered according to the combined ranking in the LOLA result. Up to 200 most enriched categories (q-value < 0.01; Fisher's Exact Test) are shown for each comparison.

References

  1. Sheffield, & Bock (2016). LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor. Bioinformatics, 32(4), 587-589.