1 Overview

The UCSC Table Browser is a good source of genomic annotations of many different kinds. It has a clear, easily navigated user interface. It is a good complement to igvR.

The H3K4Me3 post-translational modification is frequently found in active promoters near transcription start sites. Here we obtain H3K4Me3 methylation marks in K562 cells in and around GATA2.

These are the steps involved:

  1. in igvR, display a genomic region of interest
  2. use your mouse to copy the resulting chrom:start-end genomic region string
  3. in the Table Browser, select your genome and dataset of interest
  4. paste the genomic region string into the UCSC Table Browser
  5. click get output to examine the specified data
  6. once you are satisfied that the data are of interest, fill in the output filename and save to a local tsv file
  7. back in R, use read.table to create a data.frame from that file
  8. construct and display an igvR DataFrameAnnotationTrack or DataFrameQuantitativeTrack

All these steps are shown below.

2 Display a genomic region of interest in igvR

igv <- igvR()
setBrowserWindowTitle(igv, "H3K4Me3 GATA2")
setGenome(igv, "hg38")
showGenomicRegion(igv, "GATA2")

3 Obtain the coordinates

[1] "chr3"

[1] 128454762

[1] 128517865

[1] 63104

[1] "chr3:128,454,762-128,517,865"