In CharlesJB/metageneVignettes: Vignette for the metagene paper

Comparison of H3K27ac profile and H3K4me1 profile in region chr7:61968807-61969730

Introduction

Highly active enhancer regions are thought to be important for the cell fate (Andersson et al. 2014, FANTOM5 consortium, Hnisz et al. 2013). Highly active enhancers regions have been selected in GM12878 cells. Similarity of ChIP-seq profiles has been tested using two histone post-transcriptional modifications linked to highly active enhancers H3K27ac (DCC accession: ENCFF000ASG) and H3K4me1 (DCC accession: ENCFF000ARY) from the Encyclopedia of DNA Elements (ENCODE) data (Dunham I et al. 2012). Accordingly with the literature, similarity between the profiles of these two histone marks has been identified.

1. Loading similaRpeak package

First, the similaRpeak package must be loaded.

library(similaRpeak)

2. Loading profiles data

A region, chr7:61968807-61969730, shows interesting profiles for both histones. Let's load the data for this region.

data(chr7Profiles)
str(chr7Profiles)

H3K27ac and H3K4me1 profiles have those shapes:

plot(chr7Profiles$chr7.61968807.61969730$H3K27ac, type="l", col="blue", 
        xlab="", ylab="", ylim=c(0, 700), main="chr7:61968807-61969730")
par(new=TRUE)
plot(chr7Profiles$chr7.61968807.61969730$H3K4me1, type="l", col="darkgreen", 
        xlab="Position", ylab="Reads per million (RPM)", 
        ylim=c(0, 700))
legend("topleft", c("H3K27ac","H3K4me1"), cex=1.2, 
        col=c("blue","darkgreen"), lty=1)

Figure S8. H3K27ac profile versus H3K4me1 profile

3. Calculating metrics with similaRpeak

The metrics are calculated using the similarity function which takes as arguments the two ChIP-Seq profiles vectors and the threshold values.

metrics <- similarity(chr7Profiles$chr7.61968807.61969730$H3K27ac, 
                            chr7Profiles$chr7.61968807.61969730$H3K4me1, 
                            ratioAreaThreshold=5, 
                            ratioMaxMaxThreshold=2, 
                            ratioIntersectThreshold=5, 
                            ratioNormalizedIntersectThreshold=2,
                            diffPosMaxThresholdMinValue=10, 
                            diffPosMaxThresholdMaxDiff=100, 
                            diffPosMaxTolerance=0.01)

The similarity function returns a list which contains the general information about both ChIP-Seq profiles and a list of all calculated metrics.

metrics

Each specific information can be directly accessed. Some examples:

metrics$areaProfile1
metrics$areaProfile2
metrics$metrics$RATIO_INTERSECT

The RATIO_INTERSECT value of r round(metrics$metrics$RATIO_INTERSECT, 2) and the RATIO_MAX_MAX value of r round(metrics$metrics$RATIO_MAX_MAX, 2) are quite low. Both values can be explained by the large difference in coverage between profiles. Those values could be interpreted as two profiles with low level of similarity. However, the RATIO_NORMALIZED_INTERSECT of r round(metrics$metrics$RATIO_NORMALIZED_INTERSECT, 2) is much closer to 1. It could be a sign that the profiles, once normalized, are quite similar. This hypothesis can be validated by looking at a graph of the normalized profiles :

plot(chr7Profiles$chr7.61968807.61969730$H3K27ac*
        length(chr7Profiles$chr7.61968807.61969730$H3K27ac)/
        sum(chr7Profiles$chr7.61968807.61969730$H3K27ac, na.rm=TRUE), 
        type="l", col="blue", xlab="", ylab="", ylim=c(0, 3.5))
par(new=TRUE)
plot(chr7Profiles$chr7.61968807.61969730$H3K4me1*
        length(chr7Profiles$chr7.61968807.61969730$H3K4me1)/
        sum(chr7Profiles$chr7.61968807.61969730$H3K4me1, na.rm=TRUE), 
        type="l", col="darkgreen", xlab="Position", 
        ylab="Normalized Coverage (Coverage/Mean Coverage)", 
        ylim=c(0, 3.5))
legend("topleft", c("H3K27ac","H3K4me1"), cex=1.2, 
        col=c("blue","darkgreen"), lty=1)

Figure S9. Normalized H3K27ac profile versus normlized H3K4me1 profile

References

Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, et al. (2014) An atlas of active enhancers across human cell types and tissues. Nature, 507(7493), 455-461.

Dunham I, Kundaje A, Aldred SF, et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74.

Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, et al. (2014) A promoter-level mammalian expression atlas. Nature, 507(7493):462-470.

Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-André V, et al. (2013) Super-enhancers in the control of cell identity and disease. Cell, 155(4), 934-947.

CharlesJB/metageneVignettes documentation built on May 6, 2019, 9:58 a.m.