Table 1 Track types and examples
From: Search and comparison of (epi)genomic feature patterns in multiple genome browser tracks
Type | Description | Example |
|---|---|---|
Perfect matching | Matching regions must be present | H3K4me3 histone modification has to be present when looking for the promoter pattern |
Partial matching | Regions that are not mandatory but would improve the result if found in the pattern matching | Co-factors |
Negative matching | Regions that should not appear in the solution; candidate patterns enclosing such regions are removed from the solution search space | H3K27ac histone modification in enhancer pattern. TSS for distal enhancer pattern. The negative matching track can be associated with a distance (the negative regions are extended on both sides to this distance, e.g., 1,000 bp from TSS) |
Valid area | Opposite of negative matching: all regions outside the valid area are removed | TSS neighboring region (e.g., setting a range of 1000 bp around the TSS) in the promoter pattern. Topologically associating domain (TAD) regions |
Loop | Interacting regions. Each region is associated with a second region. All regions from other tracks that overlap with one of the two interacting regions are copied to the location of the other interacting region | DNA contact maps inferred from Hi-C experiments: the loops bring physically together a distal enhancer with its associated TSS |