Bivalent Promoter
Flag promoter bivalency from activating and repressive mark signals.
Description
Two histone-mark signals can support a bivalent-promoter screen under a chosen floor.
Two histone-mark signals can support a bivalent-promoter screen under a chosen floor.1
Flag promoter bivalency from activating and repressive mark signals.
When to use Bivalent Promoter
Use this tool to flag promoter bivalency from activating and repressive mark 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 Bivalent Promoter 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 h3k4me3Signal, h3k27me3Signal, minimumSignal using the field table and calculation rules, then run the tool.
- Read h3k4Present, h3k27Present, bivalent. 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 |
|---|---|---|---|
| h3k4me3Signal | H3K4me3 signal | number; minimum: 0 | Required |
| h3k27me3Signal | H3K27me3 signal | number; minimum: 0 | Required |
| minimumSignal | Minimum mark signal | number; minimum: 0 | Required |
Enter nonnegative marks/minimum; return separate gates and conjunction.
bivalent=H3K4me3≥minimum AND H3K27me3≥minimum Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| h3k4Present | H3K4me3 present | boolean |
| h3k27Present | H3K27me3 present | boolean |
| bivalent | Bivalent promoter | boolean |
{
"input": {
"h3k4me3Signal": 10,
"h3k27me3Signal": 12,
"minimumSignal": 8
},
"output": {
"h3k4Present": true,
"h3k27Present": true,
"bivalent": true
}
}Limitations and assumptions
No promoter location, same-cell co-occupancy or functional state 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. A successfully returned false flag is an evaluated outcome; its meaning is explained above.
Alternative or Complementary methods
Use Promoter–Enhancer State: Resolve promoter-enhancer state from H3K4 methylation signals. For a complementary task, use H2A.Z Enrichment: Calculate H2A.Z enrichment relative to H2A.
References
-
Bivalent Promoter — tool.io
Similar or alternative tools
- Promoter–Enhancer State
Resolve promoter-enhancer state from H3K4 methylation signals.
- H2A.Z Enrichment
Calculate H2A.Z enrichment relative to H2A.