Comparing Maps (Desktop)

Load a Second Map

Continuing with the previously loaded GM12878 map, let’s load another Hi-C map and see if we can discover differences between cell lines!

  1. Go to chromosome 21

  2. Click twice to zoom in

  3. Draw a box while holding down the Alt key so that you’re looking at 28,000 KB to 30,000 KB. Make sure the resolution is 5KB.

  4. Click File → Open Control

  5. Load the ENCODE IMR90 MboI MAPQ 30 map

  6. Go to Show on the toolbar and select Control

  7. Change the Normalization on the right to be Balanced.

You can press F1 to toggle between Observed and Control.

As you can see, the regions look quite different!

VS Mode

Another way to examine the data is the VS mode view.

  1. Go to Show on the toolbar

  2. Select Observed vs Control

Observed (first loaded map - GM12878) is below the diagonal; control (second loaded map - IMR90) is above the diagonal.

You can see in the Show list that there are several different ways to compare two maps visually.

Let's explore these differences by bringing in additional ENCODE data.

  1. Click the Show Annotation Panel in the lower right corner

  2. Click the 1D Annotations tab

  3. Click Load Basic Annotations...

  4. Load the Genes track

  5. Back in the 1D Annotations tab, click Load ENCODE...

  6. Load RNA-seq, H3K4me3, and CTCF tracks for both GM12878 and IMR-90

You’ll notice that there is a peak in the RNA-seq track for IMR-90 on the gene ADAMTS1, and that there’s a peak in the IMR-90 H3K4me3 track; neither of these are present on the respective GM12878 tracks. H3K4me3 is an activation mark. ADAMTS1 encodes a protein involved in fibroblast migration and is inactive in GM12878 but active in IMR90.