Hello everyone! I am quite confused by a heatmap (like fig a in the following picture), cause I don't understand what does it's coordinates means, could someone help me out? Thank you!
Chromatin Topological Domain structure and epigenetic and transcriptional features of the region around rs55705857 and MYC. Normalized Hi–C interaction frequency displayed as a two-dimensional heat map showing the topologic domain that includes the glioma risk allele rs55705857 as well as the MYC oncogene (Adapted from21). The frequency of interaction between two 40-kb genomic regions is indicated by the color intensity at their diagonal intersection.
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The plot shows the interactions between genomic regions (as determined by Hi-C) more intense (more red) means stronger interaction.
You need to read it in triangles - making diagonal projections on the axis.
copy/pasted from OP:
The frequency of interaction between two 40-kb genomic regions is indicated by the color intensity at their diagonal intersection.
Is Frequency of interaction = strength of interaction? IMHO, Frequency of interaction != strength of interaction
Stronger ~= more frequent, or more often, or more likely.
Hey Belgium, thank you for your reply. I have a further question -- Does the three coordinates means the same thing? For example, in the give picture, does all of them means the chromosome sequence ranging from cMYC to rs55705857?
That's a weird picture. Perhaps you could also add the source?
Almost as weird as using one's location instead of name.
Well, in fact, it is the fig I pasted in my former question (a)), the modification is that I copied the original x-axis to another axes.
No, then you are not ready it correctly. I have added some lines to the heatmap, see below.
The blue lines are the lines for the interaction between cMYC and rs55705857, their interaction strength (which is a frequency) is in the blue circle. It's not a very strong interaction, hence the light colour. Similarly, when checking the interaction between cMYC and the element X I added you will see that it's a far redder triangle, follow the green lines.
These maps are also used to visualize pairwise linkage disequilibrium (LD), an explanation about them can be found here. The idea is the same. Here are some interaction matrices of Hi-C discussed, you may be more familiar with those. Well, the heatmap you asked about is exactly the same idea as those matrices, but cut through the diagonal and turned. You can easily cut through the diagonal as the information is redundant (A interacts as strong with B as B interacts with A).
Thank you very much! I'm not confused with this kind of heat map now.
Glad to help. If my answer resolved your question you should mark it as accepted, as such this thread is marked as solved.
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