Supplementary Figure 1 Step by step guide

Loading the CpG islands dataset

● Go to the EpiExplorer main page http://epiexplorer.mpi-inf.mpg.de

● The CpG islands dataset, 'CpG islands (specific)', is loaded by default in EpiExplorer

Supplentary Figure 1A

● Press on the dataset name, 'CpG islands (specific)', in the menu on the left

● From Select overlap criterion: select Any overlap● From Select tissue: select H1- hESC

http://epiexplorer.mpi-inf.mpg.de/index.php?analysisLink=a4dde7584a45b947b26a7339e566b1b3

Supplementary Figure 1B

● Press on Histone modifications

● Then on H3K4me3● Then switch to bubble

chart mode

http://epiexplorer.mpi-inf.mpg.de/index.php?analysisLink=093245a47d39a860e9c7c16941d7fd57

Supplementary Figure 1C

● Press on Histone Modifications (ENCODE)● Then on H3K4me3● Finally on Neighborhood● (To obtain the exact picture as below, exclude the "any"

tissue by pressing on it in the figure legend)

http://epiexplorer.mpi-inf.mpg.de/index.php?analysisLink=5031781981e3cf7041a7ec0ca0434a60

Supplementary Figure 1D

● Press on H3K27me3● Then on Neighborhood● (To obain the exact picture as below, exclude the "any"

tissue by pressing on it in the figure legend)

http://epiexplorer.mpi-inf.mpg.de/index.php?analysisLink=4a58d9ff87f7fb08b08020309ac7ddff

Supplementary Figure 1E, 1/3

● Selecting all intergenic CGIs as reference○ Press on Genes and annotations○ Then on Genes○ Finally on Distance to nearest○ Slide the left handle to 20,000○ Press on Filter to this selection

● Press on Compare to select intergenic CGIs as reference dataset (dataset to compare to)

● Selecting all promoter CGIs○ Press on the Remove next to the refinement "The

minimum distance to genes is between 20000 and 3000000 bp"

Supplementary Figure 1E, 2/3

○ Press on Genes and Annotations○ Press on Gene promoters○ Press on Gene promoters (-1kb to 1kb)○ Press on Overlapping ○ Press on the line Gene promoters (-1kb to 1kb) that

appeared just below● (Note: an alternative and more flexible way to define the

same dataset is: ○ Refine to CGIs with maximum distance to TSS of 1kb○ Press the OR button that appeared next to the

above refinement○ Add a refinement for overlapping with gene TSS

● )● Press on Summary

Supplementary Figure 1E, 3/3

http://epiexplorer.mpi-inf.mpg.de/index.php?analysisLink=ce0d580601503697a4b9fe5cad511910

Supplementary Figure 1F, 1/4

● Set up (Reset)○ Press on the Remove next to the Reference regions

listing○ Press on the Remove next to the refinement with gene

promoters. ○ (Alternatively, press on the Back and select the CpG

islands dataset again)

Supplementary Figure 1F 2/4

● Select all consistently methylated CpG islands○ Press on DNA methylation (ROADMAP) ○ For every tissue T

(we used hES_H1_p38, hES_H9_p58, hFib_11_p8, Fetal_lung, Smooth_muscle, Stomach_mucosa, Skeletal_muscle)■ Press on the tissue T■ Press on Number of observed CpGs■ Slide the left handle to 5■ Press Filter to this selection■ Press on Average CpG methylation ratio■ Slide the left handle to 0.6■ Press Filter to this selection

● Press on Compare to select the current dataset as a reference dataset (dataset to compare to)

● Select all consistently unmethylated CpG islands○ From the current selection of methylated cases, remove all

methylation ratio refinements (they should be 7) by pressing the Remove next to each of them

○ For every tissue T (we used hES_H1_p38, hES_H9_p58, hFib_11_p8, Fetal_lung, Smooth_muscle, Stomach_mucosa, Skeletal_muscle)■ Press on the tissue T■ Press on Average CpG methylation ratio■ Slide the right handle to 0.3■ Press Filter to this selection

● Press on Summary

Supplementary Figure 1F 3/4

Supplementary Figure 1F 4/4

http://epiexplorer.mpi-inf.mpg.de/index.php?analysisLink=5d0eedfe15fec0d5a6bd61e5a9037c8b

Supplementary Figure 1G

● Press on Region lengths

http://epiexplorer.mpi-inf.mpg.de/index.php?analysisLink=d4a852e4e976a555c13d87102fa1d59b

Supplementary Figure 1H

● Press on DNA sequence● Then on Frequency of CG

http://epiexplorer.mpi-inf.mpg.de/index.php?analysisLink=3890c330cf45e69372f784413a4cdbee

Supplementary Figure 1I

● Press on DNA sequence● Then on Frequency of TG

http://epiexplorer.mpi-inf.mpg.de/index.php?analysisLink=f0470a63455567979d3c779701708a27

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