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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