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In molecular biology, genome architecture mapping is a cryosectioning method to map colocalized DNA regions in a ligation independent manner. It overcomes some limitations of Chromosome conformation capture , as these methods have a reliance on digestion and ligation to capture interacting DNA segments. GAM is the first genome-wide method for capturing three-dimensional proximities between any number of genomic loci without ligation.
The sections that are found using the cryosectioning method mentioned above are referred to as “Nuclear Profiles”. The information that they provide relates to their coverage across a genome. A large set of values can be produced that represents the strength of nuclear profiles’ presence within a genome. Based on how large or small the coverage across a genome is, judgements can be made involving chromatin interactions, nuclear profile location within the nucleus being cryosectioned, and chromatin compaction levels.
To be able to visualize this information, certain methods can be implemented using the raw data given by a table that shows whether or not nuclear profiles are detected in a genomic window, the genomic windows being represented within a certain chromosome. With a 1 representing a detection within a window and a 0 representing no detection, subsets of data can be obtained and interpreted by creating graphs, charts, heatmaps, and other visualization methods that allow these subsets to be seen in ways other than binary detection methods. By using a more graphic approach to interpreting the data obtained with cryosectioning, it is possible to see interactions that would have otherwise not been seen before.
Some examples of how these visuals can be interpreted include bar graphs that show the radial position and chromatin compaction levels of nuclear profiles, they can be split into categories to give a generalization of how often nuclear profiles are detected within a genomic window. A radar chart is a circular graph that represents the percentages of occurrence within a number of variables. In the sense of genomic information, radar charts can be used to show how genomic windows are represented within “features” of the genome that are part of certain regions that make it up. These charts can be made to compare groups of nuclear profiles with each other and their differences in how they occur within these features is shown graphically. Heatmaps are another form of visual representation where individual values in a table are shown by cells that take on different colors based on their value. This allows for trends to be seen within a table by the display of groups of similar colors or the lack of.