Stable server-rendered gene record · v1.2.0-measured-dmd-evidence
DNAAF3
Verify expression
G3 · non-DMD perturbation evidenceR1 · non-DMD perturbation substrateSupported · L2 observed same context perturbationAssessed · L2 observed same context perturbation
What this meansDNAAF3 has been experimentally perturbed in HepG2 cells, but it has not been independently perturbed in a DMD muscle model. The available DMD source summaries should still be treated as contextual evidence rather than perturbation truth. The next useful step is verify expression—not a therapeutic claim.
通俗解释DNAAF3已经在HepG2细胞中做过扰动，但尚未在DMD肌肉模型中独立验证。现有DMD来源信息仍只是背景证据，不是扰动真值。下一步应完成能弥补当前证据缺口的受控实验，而不能把它直接称为治疗靶点。
Design the next experiment →Prediction readinessR1 · non-DMD perturbation substrate
Current evidenceObserved perturbation in the same HepG2 context
Additional contextNo qualifying external myogenic screen
Historical DMD prior (legacy)up
Source agreement1/1 sources
Gene Entity Page 2.1 · quantitative layer
Dataset-level evidence for DNAAF3
Every row keeps its original context, metric and denominator. Empty fields remain explicit; no cross-source meta-effect is computed.
| Dataset / evidence | Context and endpoint | Observed value | Denominator / support | State and source |
|---|---|---|---|---|
| HEPG2_CRISPRI_FROZEN_AGGREGATEperturbation observation | Eligible cells contributing to the frozen target-level aggregateHepG2; CRISPRi; non-muscle, non-DMD context | 115 cells | 115 cells | measuredOpen sourceObserved perturbation coverage in HepG2. The cells are not independent biological replicates and do not establish a DMD effect. |
| GTEX_V8_SKELETAL_MUSCLEexpression context | Expression feasibility contextHuman skeletal muscle tissue | 0.075556 TPM | 1 contexts · row count unavailable | context onlyOpen sourceTissue expression supports assay feasibility only; it does not establish cell-type expression, function or perturbation response. |
| DEPMAP_CONTEXT_METRICdependency context | Median gene-effect context metricDepMap cell-line dependency context; not muscle-specific | 0.059827 DepMap gene-effect score | Denominator not carried | context onlyOpen sourceA broad dependency context metric. It is not a safety result and is not evidence of disease-selective dependency. |
| HEPG2_CONTEXT_RELATIONSHIP_V06context relationship | Contextual signature relationshipSame processed HepG2 perturbation substrate | 0.034438 unitless score | 115 cells contributing to the target aggregate | context onlyOpen sourceA descriptive relationship within the same processed context; it is not therapeutic rescue or an independently validated effect. |
| SEMA3C DESeq2 source-statedisease context effect | Source-specific differential expressionDMD skeletal-muscle source-state analysis | 0.869128 source-specific effect scaleMedian signed score 0.04232681 | 8 contexts · 8 rows0 significant rows | context onlyOpen sourceObserved-expression source summary; contextual evidence rather than candidate perturbation truth. |
Source-specific effect display
DMD source-effect forest
Position is scaled to the largest absolute effect shown for this gene. Values remain on source-specific scales and are not pooled.
DESeq2 source-state+0.8691288 contexts · 0/8 significant rows
Dataset rows preserve their original context and scale. They are not pooled into a causal effect, therapeutic rank or calibrated DMD prediction.
Frozen candidate bridge · PCB-v0.2-20260804
Cross-context DMD statistical bridge
Measured HepG2 response is compared with three separately measured DMD pathway axes. Individual source results come first; pooled values are exploratory descriptive summaries only.
Measured candidate DMD perturbations0/21
Validated candidate-level predictions0
Cross-context projection is not a measured DNAAF3 response in DMD muscle and does not establish rescue, efficacy, or a target rank.
| Measured DMD source | Direct projection ρ | Cascade projection ρ | Statistical unit and ceiling |
|---|---|---|---|
| GSE233606 | -0.20491,360 pathways | -0.146611,360 pathways | one line per condition3566 cells · descriptive unselected gene-axis concordance |
| GSE272233 | 0.057161,320 pathways | 0.070641,320 pathways | 3 reported biological repeats per group21 samples · background-specific correction response |
| GSE277637 | 0.067241,360 pathways | 0.154231,360 pathways | 4 lines with one shared WT10480 cells; 4 pseudobulks · line-specific descriptive effects |
Why the workflow abstains
- weak split half measurement
- skeletal muscle tpm le 1
- correction alignment not positive
- target engagement coordinate missing or not suppressed
Pathways overlap and the three source vectors are not independent studies. HepG2 cell-level statistics support source-context exploration only. The disease-matched functional-validation gate remains open.
What this candidate is for
Is DNAAF3 detectably expressed at RNA and protein level in the intended human muscle model?
A candidate record authorizes a bounded question and next experiment. It does not authorize a therapeutic or clinical claim.
How would the result change the decision?
SupportiveMove to a bounded perturbation design if the frozen detectability threshold is met in independent biological replicates.
NullStop or redesign the assay if the target stays below the threshold; this does not establish no biological role.
Inconclusive / QC failureResolve assay specificity or state dependence if RNA, protein or replicates disagree.
Gene Entity Page 2.1
Entity graph: identity, evidence and prospective objects
This chain shows which objects exist for DNAAF3, which are still drafts and which registries are empty. Empty is not a negative experimental result.
Object ID
GENE:v1.2.0-measured-dmd-evidence:DNAAF3HGNCHGNC:30492
EnsemblENSG00000167646
NCBI Gene352909
Disease scopeDMD evidence context
01 · Gene objectRELEASEDStable identity and typed core record
→02 · Evidence objectObserved · context-boundedNo DMD perturbation truth is implied
→03 · Model gateR1 · R1 · non-DMD perturbation substratePredictionReadiness governance state
→04 · Study objectDRAFT · editableCandidate Study Card available
→05 · Prediction objectEMPTYNo immutable prospective prediction
→06 · Outcome objectEMPTYNo linked measured outcome
Claim boundary: object connectivity improves traceability; it does not raise the evidence tier or authorize a therapeutic claim.
Gene visual profile · 基因证据剖面
One-page evidence profile for DNAAF3
A four-panel, descriptive view of the same bounded gene record: evidence depth, DMD source matrix, context gauges and the current decision gap. No score, target rank or prediction claim is computed.
Evidence profile
- L1 resourceStable record released
- L2 HepG2 perturbationassessed
- L3a external screenNot assessed
- L3b independent replicationNot assessed
- L4 DMD / muscle validationMissing
- L5 therapeutic / clinicalUnsupported
DMD source matrix
DESeq2 source-statePositive source directionMedian effect +0.869128 · signed score 0.04232681observed expression · 8 contexts · 0/8 significant rows
Observed-expression and regulatory-inference channels are displayed side by side and are not pooled as independent cohorts.
Context gauges
Source agreement1/1 sources
This measures agreement among source pipelines; it is not biological ground truth.Muscle expression0.076 TPM
Visual guide; ≥1 TPM is the current triage threshold.Cells contributing to the aggregate115
Coverage count, not a power calculation.External screenNot assessed
No qualifying evidence is available in this release; this is not a negative result.Gap ladder
GAP-06Expression feasibility is not verified in the intended model
- Current actionVerify expression
- Highest missing layerL4 dmd functional validation
- Claim boundaryNo P1/P2 prediction claim unlocked
Interpretation boundary: this visual profile reorganizes frozen fields for inspection. It does not create a source-balanced successor result, a causal conclusion, a therapeutic direction or a clinical decision-support claim.
Decision boundary
What must be resolved next
Decision-blocking gapGAP-06 · Expression feasibility is not verified in the intended model
Highest missing layerL4 dmd functional validation
Readiness upgrade requiredAdd a muscle-context or DMD-background perturbation endpoint with frozen analysis rules.
The decision-blocking gap is the next missing layer that prevents the current action from advancing. The highest missing layer is the longer-term evidence ceiling; it is not necessarily the next experiment.
DMD context
Source-state record
| Direction state | consistent up |
|---|---|
| Variant stability | sign varied across variants |
| Evidence modules | source limited |
| Statistical support | direction only no significant context rows |
| Coverage | 1 of 4 sources |
| Uncertainty | incomplete source coverage |
Identifiers and context
Machine-resolvable core
| HGNC | HGNC:30492 |
|---|---|
| Ensembl | ENSG00000167646 |
| NCBI Gene | 352909 |
| HepG2 perturbation | assessed |
| HepG2 observed cells | 115 |
| Observed counteralignment | 0.03443818 |
| Myoblast screen | not assessed |
| Myoblast fusion-screen effect | Not available |
| Myoblast fusion-screen FDR | Not available |
| Skeletal-muscle expression | 0.0755557 TPM |
| DepMap median gene effect | 0.05982749 |
Cite this record
Stable identity
Object ID: GENE:v1.2.0-measured-dmd-evidence:DNAAF3
NMD-VCell. DNAAF3 evidence record. Resource v1.2.0-measured-dmd-evidence; evidence freeze 2026-08-03; schema 1.1; build EA-20260817-57. DOI pending.