Stable server-rendered gene record · v1.2.0-measured-dmd-evidence
GFOD2
Provisional hold · external report not yet audited
G3 · non-DMD perturbation evidenceR1 · non-DMD perturbation substrateSupported · L2 observed same context perturbationAssessed · L2 observed same context perturbation
What this meansGFOD2 has been experimentally perturbed in HepG2 cells, but it has not been independently perturbed in a DMD muscle model. Different DMD datasets do not completely agree on its disease-associated direction. The next useful step is provisional hold · external report not yet audited—not a therapeutic claim.
通俗解释GFOD2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。不同DMD数据集对它的疾病相关方向并不完全一致。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 agreement2/4 sources
Gene Entity Page 2.1 · quantitative layer
Dataset-level evidence for GFOD2
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 | 127 cells | 127 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 | 2.94732 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 | -0.076846 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 | 0.074113 unitless score | 127 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. |
| DMD single-cell baseline pseudobulkdisease context effect | Disease-associated baseline expressionDMD skeletal-muscle single-cell source; baseline pseudobulk summaries | 0.127772 source-specific effect scaleMedian signed score 0.00000145 | 16 contexts · 16 rows0 significant rows | context onlyOpen sourceObserved-expression source summary; contextual evidence rather than candidate perturbation truth. |
| DMD single-cell delta / DIDdisease context effect | Disease-associated change across declared contextsDMD skeletal-muscle single-cell source; final-label delta / DID summaries | 0.006615 source-specific effect scaleMedian signed score 0.00000056 | 17 contexts · 17 rows0 significant rows | context onlyOpen sourceObserved-expression source summary; contextual evidence rather than candidate perturbation truth. |
| SEMA3C DESeq2 source-statedisease context effect | Source-specific differential expressionDMD skeletal-muscle source-state analysis | -0.06002 source-specific effect scaleMedian signed score -0.00000026 | 9 contexts · 9 rows0 significant rows | context onlyOpen sourceObserved-expression source summary; contextual evidence rather than candidate perturbation truth. |
| SEMA3C NicheNet target-statedisease context effect | Inferred target-state relationshipDMD skeletal-muscle regulatory-inference context | -0.090854 source-specific effect scaleMedian signed score -0.00672882 | 2 contexts · 2 rows0 significant rows | context onlyOpen sourceRegulatory-inference channel; displayed separately and not pooled as an independent expression cohort. |
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.
sc baseline pseudobulk+0.12777216 contexts · 0/16 significant rows
sc delta/DID+0.00661517 contexts · 0/17 significant rows
DESeq2 source-state-0.060029 contexts · 0/9 significant rows
NicheNet target-state-0.0908542 contexts · 0/2 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 GFOD2 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 | -0.351011,360 pathways | -0.350271,360 pathways | one line per condition3566 cells · descriptive unselected gene-axis concordance |
| GSE272233 | -0.198931,320 pathways | -0.196211,320 pathways | 3 reported biological repeats per group21 samples · background-specific correction response |
| GSE277637 | 0.081321,360 pathways | 0.048741,360 pathways | 4 lines with one shared WT10480 cells; 4 pseudobulks · line-specific descriptive effects |
Why the workflow abstains
- disease source projection inconsistent
- correction alignment not positive
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
Can the reported external GFOD2 evidence be reproduced from traceable quantitative data and provenance?
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?
SupportiveReassign the candidate through the evidence-transition rules only if the quantitative result and provenance reproduce.
NullKeep the hold and retain the failed audit as evidence if the report cannot be reproduced.
Inconclusive / QC failureKeep the report unassessed when essential files or metadata are unavailable.
Gene Entity Page 2.1
Entity graph: identity, evidence and prospective objects
This chain shows which objects exist for GFOD2, 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:GFOD2HGNCHGNC:28159
EnsemblENSG00000141098
NCBI Gene81577
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 GFOD2
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
sc baseline pseudobulkPositive source directionMedian effect +0.127772 · signed score 0.00000145observed expression · 16 contexts · 0/16 significant rows
sc delta/DIDPositive source directionMedian effect +0.006615 · signed score 0.00000056observed expression · 17 contexts · 0/17 significant rows
DESeq2 source-stateNegative source directionMedian effect -0.06002 · signed score -0.00000026observed expression · 9 contexts · 0/9 significant rows
NicheNet target-stateNegative source directionMedian effect -0.090854 · signed score -0.00672882regulatory inference · 2 contexts · 0/2 significant rows
Observed-expression and regulatory-inference channels are displayed side by side and are not pooled as independent cohorts.
Context gauges
Source agreement2/4 sources
This measures agreement among source pipelines; it is not biological ground truth.Muscle expression2.947 TPM
Visual guide; ≥1 TPM is the current triage threshold.Cells contributing to the aggregate127
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-09External quantitative evidence has not been imported and audited
- Current actionProvisional hold · external report not yet audited
- 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-09 · External quantitative evidence has not been imported and audited
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 | conflicted |
|---|---|
| Variant stability | sign varied across variants |
| Evidence modules | direction conflicted |
| Statistical support | direction only no significant context rows |
| Coverage | 4 of 4 sources |
| Uncertainty | direction conflict retained |
Identifiers and context
Machine-resolvable core
| HGNC | HGNC:28159 |
|---|---|
| Ensembl | ENSG00000141098 |
| NCBI Gene | 81577 |
| HepG2 perturbation | assessed |
| HepG2 observed cells | 127 |
| Observed counteralignment | 0.07411341 |
| Myoblast screen | not assessed |
| Myoblast fusion-screen effect | Not available |
| Myoblast fusion-screen FDR | Not available |
| Skeletal-muscle expression | 2.94732 TPM |
| DepMap median gene effect | -0.07684586 |
Cite this record
Stable identity
Object ID: GENE:v1.2.0-measured-dmd-evidence:GFOD2
NMD-VCell. GFOD2 evidence record. Resource v1.2.0-measured-dmd-evidence; evidence freeze 2026-08-03; schema 1.1; build EA-20260817-57. DOI pending.