Table 1.

Functional characteristics of cell types

Cluster (cellular subtype)	Brief characteristics	Upregulated spots	High population in	Activated gene signaturesa	Activated genesb
C1	Neural crest-like	C	S	Antigen-presenting cells, transitory neural-crest signature	MAJIN, NME9, CD74, ERBB3, RAMP1, HLA-DRA, SOX10, KRT23
C2	High cycling G1S-arrest biased	A	RV	Proliferating cells, high-cell-cycle activity, DREAM targets	UBE2S, KRT81, KRT17, HMGN2, ANKRD1, FOSL1, KRT18, RANBP1, STMN1, CENPU, CDK1, CDK4, MYC
C3	Slow cycling, stromal-like	D (B)	RV > (RVT > RVC)	Hallmark p53 targets stroma-like, epithelial-to-mesenchymal transition, cell cycle inhibition by CDKN1A	NEAT1, CDKN1A, KDM5B, IL1B, H1-2, GSN, FAM3C, MTOR, MDM2
C4	High cycling, G2M-arrest biased	A	RVC (> RV, RVT, S)	Proliferating cells, cell cycle activity in G2/M arrest	See C2
C5	Translation	B	RVT (> RV, RVC, S)	Ribosome, translation, low proliferation, melanoma housekeeping genes	S100A6, RPL7A, RPL31, RACK1, EEF1A1
C6	Stressed, pluripotency-resembling	F, H, I	RVC (> RVT)	Unconventional PI3K/Akt activators, KLF4 activation	UTS2, COX2, NTS, MMP1, EGR1, MALAT1, SUCNR1, PCSK6, NEAT1, OCT4, SETD1A, KLF4
C7	MAPK reactivating	E, G	RVT	Alternative MAPK pathway, stress-induced signaling, cGMP activity to MAPK, invasiveness	EPO, MARCKS, TSPAN8, GUCY1B1, PDE6B, DDX10, BRAF, WDR63, SPANXD

^aGene sets were taken from an number of earlier reports^8,21,46–48 as part of the gene sets implemented in the R package oposSOM used for analysis¹⁴.

^bGenes were taken from spot lists (Supplementary Table S1).