Promoter–Enhancer State
Resolve promoter-enhancer state from H3K4 methylation signals.
Description
H3K4me1 and H3K4me3 can inform regulatory-state review; this tool assigns coarse labels using thresholds.
H3K4me1 and H3K4me3 can inform regulatory-state review; this tool assigns coarse labels using thresholds.1
Resolve promoter-enhancer state from H3K4 methylation signals.
When to use Promoter–Enhancer State
Use this tool to resolve promoter-enhancer state from H3K4 methylation signals.
Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
How to use Promoter–Enhancer State and understand its results
- Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
- Enter h3k4me1Signal, h3k4me3Signal, minimumSignal using the field table and calculation rules, then run the tool.
- Read me1ToMe3Ratio, state. The explanation below defines the units, signs, ordering and any flags or placeholder values.
- If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.
| Input field | Meaning | Value type; see rules below | Requirement |
|---|---|---|---|
| h3k4me1Signal | H3K4me1 signal | number; minimum: 0 | Required |
| h3k4me3Signal | H3K4me3 signal | number; minimum: 0 | Required |
| minimumSignal | Minimum mark signal | number; minimum: 0 | Required |
Enter nonnegative marks/minimum. Return ratio; me1 alone gives poised, me3 alone promoter, neither unmarked.
both above minimum: ratio>1→enhancer, else promoter Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| me1ToMe3Ratio | H3K4me1-to-H3K4me3 ratio | number; minimum: 0 |
| state | Regulatory state | string; one of "promoter", "enhancer", "poised", "unmarked" |
{
"input": {
"h3k4me1Signal": 20,
"h3k4me3Signal": 10,
"minimumSignal": 5
},
"output": {
"me1ToMe3Ratio": 2,
"state": "enhancer"
}
}Limitations and assumptions
Zero me3 returns me1 as a ratio placeholder. No activation mark, annotation or regulatory function is established.
Numeric inputs, where present, must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.
Alternative or Complementary methods
Use Bivalent Promoter: Flag promoter bivalency from activating and repressive mark signals. For a complementary task, use ABC Linkage Rank: Rank enhancer-gene links by activity-by-contact score.
References
-
Promoter–Enhancer State — tool.io
Similar or alternative tools
- Bivalent Promoter
Flag promoter bivalency from activating and repressive mark signals.
- ABC Linkage Rank
Rank enhancer-gene links by activity-by-contact score.