1. Peaks are analyzed in two different ways: differential and individual. Individual peaks do not consider the overlap between peaks to be compared and is essentially a peak calling on individual conditions. Differential peaks are compared based on an overlapping peak called in two conditions. In this case all 4 data groups (WT EXP and 2 inputs) are used in the comparison.

2. Peaks are called with two different set of window parameters when SICER is concered. Examples:

`

Shorter window

epic --treatment ../../../bed2/WT1_H3K9.bed ../../../bed2/WT2_H3K9.bed --control ../../../bed2/KO1_H3K9.bed ../../../bed2/KO2_H3K9.bed --number-cores 8 --genome mm10 --fra gment-size 65 --chromsizes ../../../mm10.sizes.txt --window-size 130

Larger window

epic --treatment ../../../bed2/WT1_H3K9.bed ../../../bed2/WT2_H3K9.bed --control ../../../bed2/KO1_H3K9.bed ../../../bed2/KO2_H3K9.bed --number-cores 8 --genome mm10 --fra gment-size 150 --chromsizes ../../../mm10.sizes.txt --window-size 300

`

Repeats, DiffRep

Repeats, Epic

Nr4a2 H3K9

Nr4a2 Input

Akt1 H3K9

Akt1 Input

Other plots

Differential

Genes, Diff. Peaks, p=~1E-9, fold>3

Listing

In-target Genes, Diff. Peaks, unfiltered

Listing

Individual

Genes, Indiv. Peaks, p=~1E-9, fold>3

Listing

In-target Genes, Indiv. Peaks, unfiltered

Listing

All are based on differential peaks

Genes, Diff. Peaks, p=~1E-9, fold>3

Listing

In-target Genes, Diff. Peaks, unfiltered

Listing

Gene level Repeats, Diff. Peaks, p=0.05, fold>1

Listing

All are differential peaks

Genes, Diff. Peaks, p=0.001, fold>2

Listing

Genes, Diff. Peaks, p=0.001, fold>2, in target

Listing

Genes, Diff. Peaks, p=0.05, fold>1

Listing

Genes, Diff. Peaks, p=0.05, fold>1, in target

Listing

All are based on differential peaks

Genes, Diff. Peaks, p=0.05, fold>2

Listing

Genes, Diff. Peaks, p=0.05, fold>1

Venn

Listing

Exons, Diff. Peaks, p=0.05, fold>2

Listing

Exons, Diff. Peaks, p=0.05, fold>1

Venn

Listing

Gene level Repeats, Diff. Peaks, p=0.05, fold>2

Venn

Listing

Gene level Repeats, Diff. Peaks, p=0.05, fold>1

Listing

Exon level Repeats, Diff. Peaks, p=0.05, fold>2

Venn

Listing

Exon level Repeats, Diff. Peaks, p=0.05, fold>1

Listing

Individual

SICER+EPIC (Individual, WT)

SICER+EPIC (Individual, KO)

Differential

SICER+EPIC (Differential, WT UP)

SICER+EPIC (Differential, KO UP)

Individual

SICER+EPIC (Individual, WT)

SICER+EPIC (Individual, KO)

Differential

SICER+EPIC (Differential, WT UP)

SICER+EPIC (Differential, KO UP)

Individual

SICER+EPIC (Individual)

SICER+EPIC (Individual)

Differential

Epic TSS SICER+EPIC (Differential)

Epic PIE SICER+EPIC (Differential)

All are differential peaks

SICER+EPIC (Differential)

SICER+EPIC (Differential)

DiffRep

DiffRep

Homer TSS HOMER+EDGER

Homer PIE HOMER+EDGER

Epic TSS SICER+EPIC (Individual)

Epic PIE SICER+EPIC (Individual)

SICER/EPIC results (diff. peaks)

SICER/EPIC results (diff. peaks, newer, smaller window)

DiffRep results (diff. peaks)

Comparison (overlap) between EPIC and diffRep

SICER/EPIC results (indiv. peaks)

SICER/EPIC results (indiv. peaks, newer, smaller window)

Homer results (diff. peaks)

Repeats from Homer results

Repeats Results

Pathway Enrichment

Genes, Large, UP IN KO

Genes, Large, DOWN IN KO

Exons, Large, UP IN KO

Exons, Large, DOWN IN KO

Genes, Small, UP IN KO

Genes, Small, DOWN IN KO

Exons, Small, UP IN KO

Exons, Small, DOWN IN KO

Older Tables and peaks files

All Differential Tables

All Annotated Peaks (Not Differential)

All Shared Peaks (Differential)