Genetics: Interpreting Hi-C Maps

Hi-C maps can be hard to understand. I make it more simple.

Julian Willett, MD
Feb 26 · 3 min read
Hi-C Map. Source: Wikipedia. Author: Yardimci et. al.

While Hi-C maps can be pleasing to look at, it can take time to learn how to read them. This article will focus on enabling one to interpret these data-rich figures. A summary of Hi-C is here, from another one of my articles.

Hi-C Map. Source: Wikipedia. Author: Yardimci et. al.

“Cis-Trans Interaction Ratio”¹

Cis interactions are between genetic elements on the same chromosome, and trans interactions are between genetic factors on different chromosomes¹. Given how Hi-C matrices often plot chromosomes against one another, a signal that veers from the diagonal can be interpreted as interactions between different chromosomes¹. This measure is typically used to evaluate data quality¹. Background noise from random processes would affect cis and trans interactions, decreasing the ratio¹. An ideal ratio is between 0.40 and 0.60¹.

Hi-C Map. Source: Wikipedia. Author: Yardimci et. al.

“Distance-Dependent Interaction Frequency”¹

Generally, cis components' interaction decreases with the genomic distance represented on the map as reducing intensity away from the diagonal¹. This is thought to be due to random chromosome movement¹. We can study this using either interpolation by creating a function modelling the findings or segregating data based on genomic distances and averaging it (binning)¹.

Hi-C Map. Source: Wikipedia. Author: Yardimci et. al.

Genomic Compartments¹

These compartments, as I have described in my introductory article to Hi-C, refer to regions that can or cannot bind to other components with active more likely to match with active and inactive with inactive¹. They are represented on the map as checkboard-like patterns and tend to be the first principal component for PCA¹. They represent broader trends versus more focused changes¹.

Hi-C Map. Source: Wikipedia. Author: Yardimci et. al.

Topological Domains¹

While genomic compartments typically represent broader trends, topological domains can represent more narrow trends¹. Enhanced square boxes represent them along the diagonal¹. Various methods can quantitatively evaluate these by focusing on bins, which I will not cover here¹.

Point Interactions¹

This is a more complex topic that I will not be discussing in this article.

The Startup

Get smarter at building your thing. Join The Startup’s +787K followers.

Sign up for Top 10 Stories

By The Startup

Get smarter at building your thing. Subscribe to receive The Startup's top 10 most read stories — delivered straight into your inbox, once a week. Take a look.

By signing up, you will create a Medium account if you don’t already have one. Review our Privacy Policy for more information about our privacy practices.

Check your inbox
Medium sent you an email at to complete your subscription.

Julian Willett, MD

Written by

Loving husband. Physician scientist who enjoys spreading his knowledge with the world whether related to medicine, technology, or science.

The Startup

Get smarter at building your thing. Follow to join The Startup’s +8 million monthly readers & +787K followers.

Julian Willett, MD

Written by

Loving husband. Physician scientist who enjoys spreading his knowledge with the world whether related to medicine, technology, or science.

The Startup

Get smarter at building your thing. Follow to join The Startup’s +8 million monthly readers & +787K followers.

Medium is an open platform where 170 million readers come to find insightful and dynamic thinking. Here, expert and undiscovered voices alike dive into the heart of any topic and bring new ideas to the surface. Learn more

Follow the writers, publications, and topics that matter to you, and you’ll see them on your homepage and in your inbox. Explore

If you have a story to tell, knowledge to share, or a perspective to offer — welcome home. It’s easy and free to post your thinking on any topic. Write on Medium

Get the Medium app

A button that says 'Download on the App Store', and if clicked it will lead you to the iOS App store
A button that says 'Get it on, Google Play', and if clicked it will lead you to the Google Play store