Loading Annotations (Web)

Loading 1D Annotations

Let's load some ChIP-Seq tracks from ENCODE.

  1. Click the Load Tracks button on the top panel

  2. Click ENCODE.

The first time the tracks are loaded, it may take 10-15 seconds.

All the ENCODE tracks available for this genome appear. We are going to filter in order to find the tracks we want to load.

  1. Type GM12878 CTCF Bernstein

  2. Select the combined signal p-value track.

  3. Click Go.

  1. Now click Load Tracks → ENCODE again

  2. Search for GM12878 H3K36me3 Bernstein

  3. Select the signal p-value track.

  4. Click Go.

We can edit how these 1D annotations appear in the visualization using the Gear icon next to the track.

  1. Use Set track name to relabel the annotations to CTCF and H3K36me3 respectively.

  2. Use Set track color to change the colors for both 1D tracks.

Loading 2D Annotations

Select Load Tracks in the top menu bar and click ENCODE.

Search for GM12878 domains. Select the one with all the replicates.

Repeat the steps above and search for GM12878 long range for this map. Select the one with all the replicates.

Here is a link to the current state: https://tinyurl.com/ybcawels

You will see a series of yellow boxes and cyan points loaded. The yellow boxes denote contact domains. The cyan points denote chromatin loops, and as such, are small. These are the contact domains and loops that we found when analyzing this map. These calls were made with the automated Juicer pipeline.

You can edit the 2D annotations by selecting the 3 bars icon and then clicking 2D Annotations. This panel allows you to selectively hide 2D annotations (eye icon), change the color of annotations (color box), change the drawing order of overlapping annotations (up/down arrows), or remove an annotation (trash icon).

Putting together 1D and 2D Annotations

You can line up what you see in the heat map with the tracks. Hold the Shift key to enable the straight edge as you click and drag the mouse to pan around the map.

You’ll notice that the CTCF peaks seem to line up with the focal cyan loops in the map, and that the H3K36me3 track seems to line up with domain boundaries. These are two key findings from the Rao and Huntley, et al. Cell 2014 paper. This discovery was made using Juicebox by qualitatively visualizing the data in just the same way. Further technical analyses then showed that CTCF does appear to mediate loop formation and domains are decorated by differing epigenetic markers. See the Sanborn and Rao, et al. PNAS 2015 paper for more details!