Differential Methylation

Introduction: Differential Methylation of Sample Groups

Differential methylation analysis was conducted on site and region level according to the sample groups specified in the analysis.

Comparisons

The following comparisons were made:

The table below summarizes information on the comparisons.

comparison adjustment covariateTable
1 CMP vs. GMP (based on cmp_ct_CMPvGMP) csv
2 CLP vs. CMP (based on cmp_ct_CMPvCLP) csv
3 CLP vs. MLP0 (based on cmp_ct_CLPvMLP0) csv
4 HSC vs. MPP (based on cmp_ct_HSCvMPP) csv
5 CMP vs. MPP (based on cmp_ct_MPPvCMP) csv
6 MLP0 vs. MPP (based on cmp_ct_MPPvMLP0) csv
7 CLP vs. MPP (based on cmp_ct_MPPvCLP) csv
8 HSC vs. ML (based on cmp_ct_HSCvML) donorId,flowcell csv

P-values

In the following anlyses, p-values on the site level were computed using the limma method. I.e. hierarchical linear models from the limma package were employed and fitted using an empirical Bayes approach on derived M-values.

Region Level

Differential methylation on the region level was computed based on a variety of metrics. Of particular interest for the following plots and analyses are the following quantities for each region: the mean methylation difference in a region of the two groups being and of quotient of mean methylation levelsas well as a p-value obtained from statistical testing (limma or t-test; depending on parameter settings). Additionally each region was assigned a rank based on each of these three criteria. A combined rank is computed as the maximum (i.e. worst) value among the three ranks. The smaller the combined rank for a region, the more evidence for differential methylation it exhibits. Regions were defined based on the region types specified in the analysis. This section includes scatterplots of the region group means as well as volcano plots of each pairwise comparison colored according to the combined rank of a given region.

The following rank cutfoffs have been automatically selected for the analysis of differentially methylated regions:

tiling cpgislands genes promoters ensembleRegBuildBPall ensembleRegBuildBPallMerged
CMP vs. GMP (based on cmp_ct_CMPvGMP) 0 0 0 0 0 0
CLP vs. CMP (based on cmp_ct_CMPvCLP) 0 0 0 0 0 0
CLP vs. MLP0 (based on cmp_ct_CLPvMLP0) 0 0 0 0 0 0
HSC vs. MPP (based on cmp_ct_HSCvMPP) 0 0 0 0 0 0
CMP vs. MPP (based on cmp_ct_MPPvCMP) 0 0 0 0 0 0
MLP0 vs. MPP (based on cmp_ct_MPPvMLP0) 0 0 0 0 0 0
CLP vs. MPP (based on cmp_ct_MPPvCLP) 0 0 0 0 0 0
HSC vs. ML (based on cmp_ct_HSCvML) 0 0 0 0 0 0
comparison
regions
differential methylation measure

Figure 1

Figure 1

Scatterplot for differential methylation (regions). If the selected criterion is not rankGradient: The transparency corresponds to point density. The 1% of the points in the sparsest populated plot regions are drawn explicitly. Additionally, the colored points represent differentially methylated regions (according to the selected criterion). If the selected criterion is rankGradient: median combined ranks accross hexagonal bins are shown as a gradient according to the color legend.

comparison
regions
difference metric
significance metric

Figure 2

Figure 2

Volcano plot for differential methylation quantified by various metrics. Color scale according to combined ranking.

Differential Methylation Tables

A tabular overview of measures for differential methylation on the region level for the individual comparisons are provided in this section.

The tables for the individual comparisons can be found here:

tiling cpgislands genes promoters ensembleRegBuildBPall ensembleRegBuildBPallMerged
CMP vs. GMP (based on cmp_ct_CMPvGMP) csv csv csv csv csv csv
CLP vs. CMP (based on cmp_ct_CMPvCLP) csv csv csv csv csv csv
CLP vs. MLP0 (based on cmp_ct_CLPvMLP0) csv csv csv csv csv csv
HSC vs. MPP (based on cmp_ct_HSCvMPP) csv csv csv csv csv csv
CMP vs. MPP (based on cmp_ct_MPPvCMP) csv csv csv csv csv csv
MLP0 vs. MPP (based on cmp_ct_MPPvMLP0) csv csv csv csv csv csv
CLP vs. MPP (based on cmp_ct_MPPvCLP) csv csv csv csv csv csv
HSC vs. ML (based on cmp_ct_HSCvML) csv csv csv csv csv csv

Enrichment Analysis

Enrichment Analysis was conducted. The wordclouds and tables below contains significant GO terms as determined by a hypergeometric test.

comparison
Hypermethylation/hypomethylation
ontology
regions
differential methylation measure

Figure 3

Figure 3

Wordclouds for GO enrichment terms.

comparison
Hypermethylation/hypomethylation
ontology
regions
differential methylation measure

GOMFID Pvalue OddsRatio ExpCount Count Size Term
GO:0043456 0 359.6782 0.0099 2 5 regulation of pentose-phosphate shunt
GO:0006006 1e-04 14.0704 0.427 5 216 glucose metabolic process
GO:0010675 3e-04 14.8091 0.3143 4 159 regulation of cellular carbohydrate metabolic process
GO:0005996 3e-04 10.1494 0.5852 5 296 monosaccharide metabolic process
GO:0043101 3e-04 89.8678 0.0277 2 14 purine-containing compound salvage
GO:0009310 4e-04 77.0197 0.0316 2 16 amine catabolic process
GO:0014912 4e-04 77.0197 0.0316 2 16 negative regulation of smooth muscle cell migration
GO:0001708 6e-04 20.0938 0.17 3 86 cell fate specification
GO:0019682 7e-04 59.8889 0.0395 2 20 glyceraldehyde-3-phosphate metabolic process
GO:0051156 0.0012 44.8994 0.0514 2 26 glucose 6-phosphate metabolic process
GO:1901575 0.0014 3.8114 3.4559 10 1748 organic substance catabolic process
GO:0019439 0.0015 6.8227 0.858 5 434 aromatic compound catabolic process
GO:0019362 0.0016 14.4727 0.2333 3 118 pyridine nucleotide metabolic process
GO:1901564 0.0016 3.5485 4.1735 11 2111 organonitrogen compound metabolic process
GO:0043603 0.0017 4.7406 1.807 7 914 cellular amide metabolic process
GO:0006739 0.0019 34.7453 0.0652 2 33 NADP metabolic process
GO:0006148 0.002 Inf 0.002 1 1 inosine catabolic process
GO:0006168 0.002 Inf 0.002 1 1 adenine salvage
GO:0006738 0.002 Inf 0.002 1 1 nicotinamide riboside catabolic process
GO:0019428 0.002 Inf 0.002 1 1 allantoin biosynthetic process
GO:0019628 0.002 Inf 0.002 1 1 urate catabolic process
GO:0034356 0.002 Inf 0.002 1 1 NAD biosynthesis via nicotinamide riboside salvage pathway
GO:0034418 0.002 Inf 0.002 1 1 urate biosynthetic process
GO:0035262 0.002 Inf 0.002 1 1 gonad morphogenesis
GO:0050983 0.002 Inf 0.002 1 1 deoxyhypusine biosynthetic process from spermidine
GO:0070637 0.002 Inf 0.002 1 1 pyridine nucleoside metabolic process
GO:1904205 0.002 Inf 0.002 1 1 negative regulation of skeletal muscle hypertrophy
GO:0060795 0.0022 32.6353 0.0692 2 35 cell fate commitment involved in formation of primary germ layer
GO:0009058 0.0023 2.9921 11.7337 20 5935 biosynthetic process
GO:0006144 0.0024 30.9762 0.0727 2 38 purine nucleobase metabolic process
GO:0042278 0.003 7.5286 0.605 4 306 purine nucleoside metabolic process
GO:0043470 0.0032 26.254 0.085 2 43 regulation of carbohydrate catabolic process
GO:0007519 0.0037 10.6408 0.3143 3 159 skeletal muscle tissue development
GO:0009119 0.0039 6.9634 0.6524 4 330 ribonucleoside metabolic process
GO:0002302 0.004 521.6 0.004 1 2 CD8-positive, alpha-beta T cell differentiation involved in immune response
GO:0044209 0.004 521.6 0.004 1 2 AMP salvage
GO:0046083 0.004 521.6 0.004 1 2 adenine metabolic process
GO:0060809 0.004 521.6 0.004 1 2 mesodermal to mesenchymal transition involved in gastrulation
GO:1902732 0.004 521.6 0.004 1 2 positive regulation of chondrocyte proliferation
GO:0051196 0.004 23.3928 0.0949 2 48 regulation of coenzyme metabolic process
GO:0071320 0.004 23.3928 0.0949 2 48 cellular response to cAMP
GO:0051186 0.0046 6.6307 0.6841 4 346 cofactor metabolic process
GO:2001238 0.0049 21.0926 0.1048 2 53 positive regulation of extrinsic apoptotic signaling pathway
GO:0019748 0.0055 19.917 0.1107 2 56 secondary metabolic process
GO:0006576 0.0055 9.2077 0.3618 3 183 cellular biogenic amine metabolic process
GO:1901657 0.0058 6.1862 0.7315 4 370 glycosyl compound metabolic process
GO:0019674 0.0058 19.2032 0.1147 2 58 NAD metabolic process
GO:0021912 0.0059 260.7833 0.0059 1 3 regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification
GO:0033512 0.0059 260.7833 0.0059 1 3 L-lysine catabolic process to acetyl-CoA via saccharopine
GO:0097168 0.0059 260.7833 0.0059 1 3 mesenchymal stem cell proliferation
GO:2001022 0.0069 17.6235 0.1246 2 63 positive regulation of response to DNA damage stimulus
GO:0006082 0.007 3.6094 2.327 7 1177 organic acid metabolic process
GO:0006096 0.0073 17.0619 0.1285 2 65 glycolytic process
GO:0001707 0.0075 16.7942 0.1305 2 66 mesoderm formation
GO:0014812 0.0075 16.7942 0.1305 2 66 muscle cell migration
GO:0006598 0.0079 173.8444 0.0079 1 4 polyamine catabolic process
GO:0008612 0.0079 173.8444 0.0079 1 4 peptidyl-lysine modification to peptidyl-hypusine
GO:0010917 0.0079 173.8444 0.0079 1 4 negative regulation of mitochondrial membrane potential
GO:0019477 0.0079 173.8444 0.0079 1 4 L-lysine catabolic process
GO:0021913 0.0079 173.8444 0.0079 1 4 regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification
GO:1902093 0.0079 173.8444 0.0079 1 4 positive regulation of sperm motility
GO:0044270 0.0081 5.6182 0.8057 4 421 cellular nitrogen compound catabolic process
GO:0046700 0.0081 5.6182 0.8057 4 421 heterocycle catabolic process
GO:0044275 0.0086 15.5722 0.1404 2 71 cellular carbohydrate catabolic process
GO:0055086 0.0089 4.4022 1.3048 5 660 nucleobase-containing small molecule metabolic process
GO:0048608 0.0091 5.4115 0.8323 4 421 reproductive structure development
GO:0046031 0.0094 14.9205 0.1463 2 74 ADP metabolic process
GO:0072526 0.0098 130.375 0.0099 1 5 pyridine-containing compound catabolic process
GO:0097052 0.0098 130.375 0.0099 1 5 L-kynurenine metabolic process
GO:1903898 0.0098 130.375 0.0099 1 5 negative regulation of PERK-mediated unfolded protein response
GO:1903912 0.0098 130.375 0.0099 1 5 negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation