CL and Intracellular Markers
There are some references to intracellular proteins, mostly transcription factors, in the CL. These are expressed in a stable manner in particular cell types and generally have been identified as master gene switches that are crucial for differentiation into and maintenance of particular cell types.
For instance (from the OBO translation of cl.owl):
[Term] id: CL:0000545 name: T-helper 1 cell namespace: cell def: "A CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive and produces interferon-gamma." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19375293, PMID:20303875] synonym: "helper T cell type 1" EXACT [] synonym: "T helper cells type 1" EXACT [PMID:9419219] synonym: "T(H)-1 cell" EXACT [] synonym: "Th1 cell" EXACT [] synonym: "Th1 T cell" EXACT [] synonym: "Th1 T lymphocyte" EXACT [] synonym: "Th1 T-cell" EXACT [] synonym: "Th1 T-lymphocyte" EXACT [] xref: BTO:0001678 xref: FMA:84382 is_a: CL:0000492 {is_inferred="true"} ! CD4-positive helper T cell intersection_of: CL:0000492 ! CD4-positive helper T cell intersection_of: has_part PR:000001835 ! T-box transcription factor TBX21 intersection_of: RO:0002215 GO:0032609 ! capable_of interferon-gamma production
[Term] id: CL:0000546 name: T-helper 2 cell namespace: cell def: "A CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive and produces interleukin-4." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19375293, PMID:20103781] synonym: "helper T cell type 2" EXACT [] synonym: "T helper cells type 2" EXACT [PMID:9419219] synonym: "T(H)-2 cell" EXACT [] synonym: "Th2 cell" EXACT [] synonym: "Th2 T cell" EXACT [] synonym: "Th2 T lymphocyte" EXACT [] synonym: "Th2 T-cell" EXACT [] synonym: "Th2 T-lymphocyte" EXACT [] xref: BTO:0001679 xref: FMA:84385 is_a: CL:0000492 {is_inferred="true"} ! CD4-positive helper T cell intersection_of: CL:0000492 ! CD4-positive helper T cell intersection_of: has_part PR:000001941 ! trans-acting T-cell-specific transcription factor GATA-3 intersection_of: RO:0002215 GO:0032633 ! capable_of interleukin-4 production relationship: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell
[Term] id: CL:0000902 name: induced T-regulatory cell namespace: cell def: "CD4-positive alpha-beta T cell with the phenotype CD25-positive, CTLA-4-positive, and FoxP3-positive with regulatory function." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19464985] synonym: "adaptive Treg" RELATED [] synonym: "aTreg" RELATED [] synonym: "induced regulatory T cell" EXACT [] synonym: "induced regulatory T lymphocyte" EXACT [] synonym: "induced regulatory T-cell" EXACT [] synonym: "induced regulatory T-lymphocyte" EXACT [] synonym: "induced Treg" EXACT [] synonym: "iTreg" EXACT [] is_a: CL:0000792 {is_inferred="true"} ! CD4-positive, CD25-positive, alpha-beta regulatory T cell intersection_of: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cell intersection_of: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell intersection_of: has_part PR:000001350 ! forkhead box protein P3 intersection_of: has_plasma_membrane_part PR:000001852 ! cytotoxic T-lymphocyte protein 4
These are not the only examples, but there aren't that many more. Certainly there is more information known about particular intracellular proteins that are expressed in a cell type specific manner than we are currently capturing in the CL.
