DMD Biological Process Map V1.1
Explore DMD as a biological system—not a list of cell cards. An evidence-aware skeletal-muscle process graph connects myofibre injury, immune states, myogenic transitions, FAP/ECM remodeling, vascular context and function. Every node and edge declares question identity plus evidence metadata: origin, context match, unit structure, lifecycle and outcome fields.
Core process nodes 24
Audited relationships 30
Process-model status Not calibrated
Candidate outcome status Not measured yet
Scope DMD skeletal muscle only
Evidence Evidence-contract metadata; no scalar score
Macrophages State-based ontology, not M1/M2
Layout Manual hierarchy · seed 42 · not biology
Biological Process Canvas
Damage → inflammation / clearance → regeneration → remodeling → recurrent damage The feedback loop is a hypothesis-bearing disease system. Arrow existence and evidence metadata matter; node distance does not.
Hand off a missing edge → Biology Evidence Models Experiments
Show process nodes and all evidence-labeled biological relationships.
22 1 1
DMD skeletal muscle biological process map Manual hierarchical process map with 24 nodes and 30 evidence-aware edges. DMD genomic lesion → Dystrophin deficiency · OBSERVED · CROSS_SPECIES · AMBIGUOUS Dystrophin deficiency → Sarcolemmal / mechanical instability · OBSERVED · CROSS_SPECIES · AMBIGUOUS Sarcolemmal / mechanical instability → Ca2+ / cellular stress state · OBSERVED · CROSS_SPECIES · AMBIGUOUS Sarcolemmal / mechanical instability → Myofibre injury · OBSERVED · CROSS_SPECIES · AMBIGUOUS Myofibre injury → Degeneration / necrosis · OBSERVED · TARGET_CONTEXT · AMBIGUOUS Degeneration / necrosis → Damage / inflammatory signalling · OBSERVED · TARGET_CONTEXT · AMBIGUOUS Damage / inflammatory signalling → Monocyte / myeloid recruitment · OBSERVED · TARGET_CONTEXT · AMBIGUOUS Monocyte / myeloid recruitment → Phagocytic / clearance macrophage state · OBSERVED · TARGET_CONTEXT · AMBIGUOUS Monocyte / myeloid recruitment → Repair-associated macrophage state · OBSERVED · TARGET_CONTEXT · AMBIGUOUS Monocyte / myeloid recruitment → Fibrosis-associated macrophage state · OBSERVED · TARGET_CONTEXT · AMBIGUOUS Fibrosis-associated macrophage state → FAP activation · COMPUTATIONAL · TARGET_CONTEXT · AMBIGUOUS Fibrosis-associated macrophage state → Fibrotic stromal / FAP state · COMPUTATIONAL · TARGET_CONTEXT · AMBIGUOUS Degeneration / necrosis → MuSC activation · OBSERVED · TARGET_CONTEXT · AMBIGUOUS MuSC activation → Myogenic proliferation · OBSERVED · SAME_TISSUE · AMBIGUOUS Myogenic proliferation → Myogenic differentiation · OBSERVED · SAME_TISSUE · AMBIGUOUS Myogenic differentiation → Myoblast fusion · OBSERVED · SAME_TISSUE · AMBIGUOUS Myoblast fusion → Regenerated myofibre · MISSING · TARGET_CONTEXT · MISSING_TARGET_CONTEXT_OUTCOME Regenerated myofibre → Myofibre injury · OBSERVED · CROSS_SPECIES · AMBIGUOUS MuSC activation → Regeneration-supportive stromal state · OBSERVED · TARGET_CONTEXT · AMBIGUOUS FAP activation → Regeneration-supportive stromal state · OBSERVED · TARGET_CONTEXT · AMBIGUOUS FAP activation → Fibrotic stromal / FAP state · OBSERVED · TARGET_CONTEXT · AMBIGUOUS Fibrotic stromal / FAP state → ECM deposition / remodeling · OBSERVED · TARGET_CONTEXT · AMBIGUOUS ECM deposition / remodeling → Fibrosis / adipogenic remodeling · OBSERVED · TARGET_CONTEXT · AMBIGUOUS Endothelial / vascular response → Regenerative niche · OBSERVED · TARGET_CONTEXT · AMBIGUOUS Regeneration-supportive stromal state → Regenerative niche · COMPUTATIONAL · TARGET_CONTEXT · AMBIGUOUS Regenerative niche → Myogenic differentiation · COMPUTATIONAL · TARGET_CONTEXT · AMBIGUOUS Myogenic differentiation → Functional muscle output · MISSING · TARGET_CONTEXT · MISSING_TARGET_CONTEXT_OUTCOME Fibrotic stromal / FAP state → Functional muscle output · MISSING · TARGET_CONTEXT · MISSING_TARGET_CONTEXT_OUTCOME Functional muscle output → Myofibre injury · MISSING · TARGET_CONTEXT · MISSING_TARGET_CONTEXT_OUTCOME Myoblast fusion → Functional muscle output · MISSING · TARGET_CONTEXT · MISSING_TARGET_CONTEXT_OUTCOME P001 DMD genomic lesion OBSERVED/AMBIGUOUS P002 Dystrophin deficiency OBSERVED/AMBIGUOUS P003 Sarcolemmal / mechanica… OBSERVED/AMBIGUOUS P004 Ca2+ / cellular stress … OBSERVED/AMBIGUOUS P005 Myofibre injury OBSERVED/AMBIGUOUS P006 Degeneration / necrosis OBSERVED/AMBIGUOUS P007 Damage / inflammatory s… OBSERVED/AMBIGUOUS P008 Monocyte / myeloid recr… OBSERVED/AMBIGUOUS P009 Phagocytic / clearance … OBSERVED/AMBIGUOUS P010 Repair-associated macro… OBSERVED/AMBIGUOUS P011 Fibrosis-associated mac… OBSERVED/AMBIGUOUS P012 MuSC activation OBSERVED/AMBIGUOUS P013 Myogenic proliferation OBSERVED/AMBIGUOUS P014 Myogenic differentiation OBSERVED/AMBIGUOUS P015 Myoblast fusion OBSERVED/AMBIGUOUS P016 Regenerated myofibre OBSERVED/AMBIGUOUS P017 FAP activation OBSERVED/AMBIGUOUS P018 Regeneration-supportive… OBSERVED/AMBIGUOUS P019 Fibrotic stromal / FAP … OBSERVED/AMBIGUOUS P020 ECM deposition / remode… OBSERVED/AMBIGUOUS P021 Fibrosis / adipogenic r… OBSERVED/AMBIGUOUS P022 Endothelial / vascular … OBSERVED/AMBIGUOUS P023 Regenerative niche COMPUTATIONAL/AMBIGUOUS P024 Functional muscle output MISSING/MISSING_TARGET_CONTEXT_OUTCOME Reading rule: Node coordinates encode a reproducible reading order only; position and distance are not biological evidence.
Evidence Coverage
Every source has a mapping state and a next gate. Coverage counts map source objects to process nodes and edges; they do not measure effect size, causality or confidence.
9 source objects
9 mapped to the process
3 sources needing a next gate
Traceable mapping policy
Source Mapping state Map links Readiness Next gate Route GSE272233DMD-locus correction transcript reference RELEASED_REFERENCE 3 nodes · 0 edges curated / released No additional intake gate; retain the declared contextual or curated claim ceiling. Source object PRJNA772047Human DMD patient skeletal muscle reference RELEASED_REFERENCE 7 nodes · 2 edges curated / released No additional intake gate; retain the declared contextual or curated claim ceiling. Source object GSE288958Human DMD/BMD/control muscle snRNA-seq and spatial context gse288958_sample_aware_module_context_v01 CONTEXT_READY 9 nodes · 4 edges context ready Use the read-only sample-aware reference with Normal_2, Scrublet and annotation-disagreement sensitivities. Unfiltered droplets or author contamination estimates are needed only to close ambient RNA; exact author artifacts are needed only for an author-exact reprocessing claim. Source object Sample-aware context object · Formal QC gate · Reference audit · Reference audit JSON · Context brief · Stable module table · Candidate context triage GSE277637DMD iPSC-derived skeletal-muscle organoid scRNA-seq gse277637_external_dmd_organoid_validation_v01 CONTEXT_READY 4 nodes · 0 edges context ready Freeze line-aware sample metadata, preserve one-line-one-unit aggregation, publish source checksum and license record before public matrix release. Source object Cross-dataset metrics · Line-aware context object GSE293514Human myoblast fusion CRISPR screen and CROP-seq context IDENTITY_BLOCKED 2 nodes · 2 edges intake gate Recover author-ordered feature table, guide reference, exact cell metadata and processing contract; checksum every returned file before any expression transfer. Source object GSE52529Human myogenic differentiation time course RELEASED_REFERENCE 3 nodes · 5 edges curated / released No additional intake gate; retain the declared contextual or curated claim ceiling. Source object DMD-MUSCLE-REVIEWDMD skeletal-muscle disease mechanism anchor CURATED_CONTEXT 5 nodes · 5 edges curated / released No additional intake gate; retain the declared contextual or curated claim ceiling. Source object DMD-SPATIAL-CONTEXTDMD spatial degeneration, regeneration and fibrosis context CURATED_CONTEXT 15 nodes · 17 edges curated / released No additional intake gate; retain the declared contextual or curated claim ceiling. Source object STUDY-CARD-MANIFEST21 governed DMD Study Card drafts REGISTRY_HANDOFF 1 nodes · 5 edges curated / released No additional intake gate; retain the declared contextual or curated claim ceiling. Source object
Current actionable gap: GSE277637 maps to four target-context process nodes. GSE288958 is now CONTEXT_READY with a sample-aware context object, read-only QC, donor-wise Scrublet and independent annotation-disagreement audits; its 1,967-cell raw-to-object gap, ambient-RNA boundary and author-exact reprocessing gap remain visible. Neither source establishes a cell-state transition, macrophage/FAP communication, candidate perturbation response or function.
Evidence Inspector
Click a node or edge to inspect its claim ceiling. Spatial co-localization, ligand–receptor inference and trajectory references retain explicit evidence metadata. They never silently become causal edges.
Node inspector · DMD-P017
FAP activation OBSERVED · TARGET_CONTEXT · AMBIGUOUS
Evidence axes OBSERVED · TARGET_CONTEXT · AMBIGUOUS
Biological meaning FAP activation
Cell / compartment FAP · stromal
Scale / time cell_state · repair_regeneration
Readouts FAP state markers · ECM programme · secretome
Model readiness NOT_CALIBRATED
Claim ceiling Disease-associated FAP state; macrophage-to-FAP causality is not established.
Next discriminating experiment Macrophage-conditioned or SPP1 perturbation study with DMD FAP fibrotic readouts. Source objects: GSE288958 · DMD-SPATIAL-CONTEXT
Edge inspector · DMD-E011
Fibrosis-associated macrophage state → FAP activation COMPUTATIONAL · TARGET_CONTEXT · AMBIGUOUS · NOT_ESTABLISHED
Evidence axes COMPUTATIONAL · TARGET_CONTEXT · AMBIGUOUS
Relationship signal_to · macrophage_to_fap
Support dimensions Human ✓ · Animal ✓ · Spatial ✓ · Temporal — · Computational ✓
Direct perturbation support NOT ESTABLISHED
Claim ceiling Association, spatial co-localization and candidate communication only; causal status not established.
Next test Macrophage-conditioned or SPP1 perturbation study on DMD FAP.
Recommended line COMPUTATIONAL_INFERENCE Source objects: DMD-SPATIAL-CONTEXT
State transition contract
The first computable transition layer is myogenic; DMD-conditioned transitions remain NOT ESTIMABLE. Open measured trajectory → Observed reference MuSC → proliferation → differentiation → fusion GSE52529 and GSE293514 provide unperturbed time and healthy-myoblast context.
Missing DMD outcome DMD myogenic perturbation → regenerated fibre → function Candidate-level DMD outcomes have not yet been measured; missing is not negative.
Future output P(state A → B) + uncertainty + abstention Only after donor, time, perturbation and functional outcomes are frozen and measured.
Claim boundary
Mechanism → experiment → outcome → claim update DMD Biological Process Map V1.0 is an evidence-aware mechanistic map. It is not a causal network, perturbation-conditioned virtual-cell prediction, patient simulation, treatment ranking or clinical decision system. Missing is not negative, and layout is not biology.