CL and Intracellular Markers: Difference between revisions

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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.
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):
Three examples (from the OBO translation of cl.owl) are given below. 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.
<nowiki>
 
[Term]
 
'''[Term]
 
id: CL:0000545
id: CL:0000545
name: T-helper 1 cell
 
name: T-helper 1 cell'''
 
namespace: 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]
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: "helper T cell type 1" EXACT []
synonym: "T helper cells type 1" EXACT [PMID:9419219]
synonym: "T helper cells type 1" EXACT [PMID:9419219]
synonym: "T(H)-1 cell" EXACT []
synonym: "T(H)-1 cell" EXACT []
synonym: "Th1 cell" EXACT []
synonym: "Th1 cell" EXACT []
synonym: "Th1 T cell" EXACT []
synonym: "Th1 T cell" EXACT []
synonym: "Th1 T lymphocyte" EXACT []
synonym: "Th1 T lymphocyte" EXACT []
synonym: "Th1 T-cell" EXACT []
synonym: "Th1 T-cell" EXACT []
synonym: "Th1 T-lymphocyte" EXACT []
synonym: "Th1 T-lymphocyte" EXACT []
xref: BTO:0001678
xref: BTO:0001678
xref: FMA:84382
xref: FMA:84382
is_a: CL:0000492 {is_inferred="true"} ! CD4-positive helper T cell
is_a: CL:0000492 {is_inferred="true"} ! CD4-positive helper T cell
intersection_of: CL:0000492 ! 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: has_part PR:000001835 ! T-box transcription factor TBX21
intersection_of: RO:0002215 GO:0032609 ! capable_of interferon-gamma production
intersection_of: RO:0002215 GO:0032609 ! capable_of interferon-gamma production


[Term]
 
'''[Term]
 
id: CL:0000546
id: CL:0000546
name: T-helper 2 cell
 
name: T-helper 2 cell'''
 
namespace: 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]
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: "helper T cell type 2" EXACT []
synonym: "T helper cells type 2" EXACT [PMID:9419219]
synonym: "T helper cells type 2" EXACT [PMID:9419219]
synonym: "T(H)-2 cell" EXACT []
synonym: "T(H)-2 cell" EXACT []
synonym: "Th2 cell" EXACT []
synonym: "Th2 cell" EXACT []
synonym: "Th2 T cell" EXACT []
synonym: "Th2 T cell" EXACT []
synonym: "Th2 T lymphocyte" EXACT []
synonym: "Th2 T lymphocyte" EXACT []
synonym: "Th2 T-cell" EXACT []
synonym: "Th2 T-cell" EXACT []
synonym: "Th2 T-lymphocyte" EXACT []
synonym: "Th2 T-lymphocyte" EXACT []
xref: BTO:0001679
xref: BTO:0001679
xref: FMA:84385
xref: FMA:84385
is_a: CL:0000492 {is_inferred="true"} ! CD4-positive helper T cell
is_a: CL:0000492 {is_inferred="true"} ! CD4-positive helper T cell
intersection_of: CL:0000492 ! 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: has_part PR:000001941 ! trans-acting T-cell-specific transcription factor GATA-3
intersection_of: RO:0002215 GO:0032633 ! capable_of interleukin-4 production
intersection_of: RO:0002215 GO:0032633 ! capable_of interleukin-4 production
relationship: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell
relationship: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell


[Term]
 
'''[Term]
 
id: CL:0000902
id: CL:0000902
name: induced T-regulatory cell
name: induced T-regulatory cell
'''
namespace: 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]
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: "adaptive Treg" RELATED []
synonym: "aTreg" RELATED []
synonym: "aTreg" RELATED []
synonym: "induced regulatory T cell" EXACT []
synonym: "induced regulatory T cell" EXACT []
synonym: "induced regulatory T lymphocyte" EXACT []
synonym: "induced regulatory T lymphocyte" EXACT []
synonym: "induced regulatory T-cell" EXACT []
synonym: "induced regulatory T-cell" EXACT []
synonym: "induced regulatory T-lymphocyte" EXACT []
synonym: "induced regulatory T-lymphocyte" EXACT []
synonym: "induced Treg" EXACT []
synonym: "induced Treg" EXACT []
synonym: "iTreg" EXACT []
synonym: "iTreg" EXACT []
is_a: CL:0000792 {is_inferred="true"} ! CD4-positive, CD25-positive, alpha-beta regulatory T cell
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: 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: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell
intersection_of: has_part PR:000001350 ! forkhead box protein P3
intersection_of: has_part PR:000001350 ! forkhead box protein P3
intersection_of: has_plasma_membrane_part PR:000001852 ! cytotoxic T-lymphocyte protein 4</nowiki>


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.
intersection_of: has_plasma_membrane_part PR:000001852 ! cytotoxic T-lymphocyte protein 4

Latest revision as of 15:47, 5 June 2013

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.

Three examples (from the OBO translation of cl.owl) are given below. 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.


[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

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