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Genome by Multidimensional Scaling
The positions of enhancers and promoters on genomic DNA remain poorly understood. Chromosomes cannot be observed during the cell division cycle because the genome forms a chromatin structure and spreads within the nucleus. However, high-throughput chromosome conformation capture (Hi-C) measures the physical interactions of genomes. In previous studies, DNA extrusion loops were directly derived from Hi-C heat maps. By using Multidimensional Scaling (MDS), we can easily locate enhancers and promoters more precisely.
2. Hypothetical Chromosomes
where i and j are coordinates, and dij is the number of Hi-C detections. Pairs with large values in the matrix indicate region pairs with a high contact probability. The inverse of the Hi-C data was used as the distance data because MDS was used for similarity matrices. Then, MDS was applied to the Hi-C data, and the resulting hypothetical chromosomes are shown in Figure 3. The euchromatin region was identified (Figure 2).
3. Enrichment Analysis
4. Comparison with Previous Studies
This entry is adapted from 10.3390/genes12111671
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