| # Curated marker-channel input genes per system for PANDA-Marker variant. | |
| # | |
| # These are the SIBLING-DISCRIMINATING genes that PCA(50) tends to discard. | |
| # They are concatenated directly onto PCA(50) as log-normalised expression, | |
| # bypassing the PCA bottleneck for the low-variance signal that separates | |
| # closely-related subtypes. | |
| # | |
| # Set size targets: 20-40 markers per system. Curated for BOTH: | |
| # (a) each class's positive identity marker (recovers within-class) | |
| # (b) sibling-pair contrast markers (e.g. Dkk4 for eccrine vs hair placode) | |
| # | |
| # All symbols are mouse gene symbols (case-fold applied at inference for | |
| # cross-species targets like Veres). | |
| pan_skin: | |
| # eccrine placode / nascent-gland / hair-placode axis | |
| - Dkk4 # eccrine placode > hair placode (Dingwall Fig 2) | |
| - Lgr6 # placode marker (Epi3) | |
| - Trpv6 # nascent eccrine gland (Epi5/Epi8) | |
| - Edar # both placodes; hair > eccrine | |
| - Shh # hair placode discriminator | |
| - Sox9 # hair placode / HF-primary-germ | |
| - Lhx2 # hair placode | |
| - Foxi3 # placode induction | |
| - Wnt6 # placode Wnt program | |
| - Wnt7b # placode Wnt program | |
| - Lef1 # Wnt signalling | |
| - Bmp7 # placode | |
| # eccrine/appendage identity | |
| - En1 # spatial repressor of eccrine outside placode | |
| - Grhl3 # eccrine-duct master TF | |
| - Cldn6 # eccrine tight junction | |
| - Kremen2 # placode / eccrine | |
| # basal / IFE / spinous / granular | |
| - Krt5 # basal | |
| - Krt14 # basal | |
| - Krt10 # spinous differentiation | |
| - Krt1 # spinous differentiation | |
| - Trp63 # basal master | |
| # melanocyte MITF regulon | |
| - Dct # melanocyte | |
| - Mlana # melanocyte | |
| - Tyrp1 # melanocyte | |
| - Pmel # melanocyte | |
| - Sox10 # neural crest / melanocyte | |
| # endothelial / fibroblast / immune | |
| - Pecam1 # endothelial | |
| - Cdh5 # endothelial | |
| - Col1a1 # fibroblast reticular | |
| - Dcn # fibroblast papillary | |
| - Ptprc # immune (CD45) | |
| # dermal niche (EDEN — Dingwall §5) | |
| - S100a4 # EDEN dermal niche | |
| - Pdgfra # dermal mesenchyme | |
| hematopoiesis: | |
| # LT-HSC / stem | |
| - Hlf # LT-HSC canonical (Komorowska 2017) | |
| - Meis1 # HSC/MPP | |
| - Mecom # LT-HSC | |
| - Procr # LT-HSC (EPCR) | |
| - Fgd5 # LT-HSC reporter | |
| - Mllt3 # LT-HSC self-renewal | |
| # MPP substates | |
| - Cd48 # MPP1 vs LT | |
| - Flt3 # MPP4/LMPP | |
| - Sell # ST-HSC / MPP1 (CD62L) | |
| - Slamf1 # SLAM CD150 | |
| # erythroid | |
| - Klf1 # erythroid master TF | |
| - Gata1 # erythroid/mega | |
| - Car1 # erythroblast | |
| - Car2 # erythroblast | |
| - Blvrb # committed erythroid | |
| - Hba-a1 # hemoglobin | |
| # megakaryocyte | |
| - Itga2b # CD41 megakaryocyte | |
| - Pf4 # megakaryocyte | |
| - Gp1bb # megakaryocyte | |
| # lymphoid | |
| - Dntt # pre-B / lymphoid | |
| - Vpreb1 # pre-B lymphoid | |
| - Vpreb3 # pre-B lymphoid | |
| - Il7r # lymphoid progenitor | |
| # myeloid / mast / basophil | |
| - Elane # GMP / granulocyte | |
| - Mpo # myeloid | |
| - Cpa3 # basophil-mast lineage | |
| - Ms4a2 # mast Fc-epsilon-RI | |
| - Csf1r # macrophage | |
| # macrophage antimicrobial (myeloid combinatorial identity per §10.3) | |
| - Wfdc17 | |
| - Mmp8 | |
| - Ctss | |
| pancreas: | |
| # endocrine progenitor (Ngn3 → Fev → hormone axis) | |
| - Neurog3 # Ngn3 endocrine progenitor | |
| - Fev # Fev+ intermediate EP | |
| - Pax4 # alpha/beta bipotential | |
| - Insm1 # endocrine progenitor | |
| - Neurod1 # beta / late endocrine | |
| - Cbfa2t3 # endocrine progenitor | |
| - Btbd17 # endocrine progenitor | |
| # alpha lineage | |
| - Arx # alpha master | |
| - Irx1 # alpha | |
| - Irx2 # alpha (Veres §7 finding) | |
| - Mafb # alpha | |
| - Gcg # glucagon | |
| # beta lineage | |
| - Nkx6-1 # beta master | |
| - Mnx1 # beta | |
| - Ins1 # insulin | |
| - Ins2 # insulin | |
| - Mafa # mature beta | |
| - Pdx1 # pancreatic progenitor + beta | |
| # delta / gamma / epsilon | |
| - Sst # delta | |
| - Hhex # delta | |
| - Ppy # gamma (PP) | |
| - Aqp3 # gamma | |
| - Ghrl # epsilon | |
| # exocrine / stromal | |
| - Prss1 # acinar | |
| - Cel # acinar | |
| - Ptf1a # acinar/pro-endocrine | |
| - Krt19 # ductal | |
| - Sox9 # ductal / progenitor | |
| # embryonic hematopoiesis contamination flag (per §10.3 finding) | |
| - Hbb-bs | |
| - Hba-a1 | |