# 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