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Term issue: H3K36me #320

Closed ValWood closed 7 months ago

ValWood commented 7 months ago

InitMet-/K36me hht1 SPAC1834.04 P09988 InitMet-/K36me hht2 SPBC8D2.04 P09988 InitMet-/K36me hht3 SPBC1105.11c P10651

I don't have ECP, but this is conserved global, I will need it to annotate fully heterochromatin formation (causally upstream) ~Will use TAS and~ PMID:37459529 actually there is some EXP data

ValWood commented 7 months ago

I guess I should get the demethylated at this position too...

nataled commented 7 months ago

Hi Val, From the look of it, the authors dealt specifically with the trimethylated version. Shall I make them that way, or do you prefer to have the methylation type unspecified?

Edit: It seems that, for K9 methylation, I made both unspecified and the trimethylated forms.

nataled commented 7 months ago

Here are your terms. The first three are for the 'regular' methylation (that is, not specific to mono-, di-, or tri-methylated) and the last three are specific to trimethylation.

PR:000085717 = Spom-hht1/InitMet-/K36Me PR:000085718 = Spom-hht2/InitMet-/K36Me PR:000085719 = Spom-hht3/InitMet-/K36Me PR:000085720 = Spom-hht1/InitMet-/K36Me3 PR:000085721 = Spom-hht2/InitMet-/K36Me3 PR:000085722 = Spom-hht3/InitMet-/K36Me3

[Term]
id: PR:000085717
name: histone H3.1, initiator methionine removed K36-methylated form (Schizosaccharomyces pombe)
def: "A histone H3.1, initiator methionine removed form (Schizosaccharomyces pombe) that has been methylated on Lys-36. Example: UniProtKB:P09988, 2-136, Lys-37, MOD:00663." [PRO:DAN, PomBase:VW, PMID:37459529]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited the residue number is different because the initial methionine is not counted.
synonym: "Spom-hht1/InitMet-/K36Me" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221366, Lys-37, MOD:00663" RELATED PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P09988, 2-136, Lys-37, MOD:00663" RELATED PRO-proteoform-std [PRO:DNx]
is_a: PR:000027574 ! histone H3.1, initiator methionine removed form (Schizosaccharomyces pombe)
relationship: has_part MOD:00663 ! methylated lysine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000085718
name: histone H3.2, initiator methionine removed K36-methylated form (Schizosaccharomyces pombe)
def: "A histone H3.2, initiator methionine removed form (Schizosaccharomyces pombe) that has been methylated on Lys-36. Example: UniProtKB:P09988, 2-136, Lys-37, MOD:00663." [PRO:DAN, PomBase:VW, PMID:37459529]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited the residue number is different because the initial methionine is not counted.
synonym: "Spom-hht2/InitMet-/K36Me" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221366, Lys-37, MOD:00663" RELATED PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P09988, 2-136, Lys-37, MOD:00663" RELATED PRO-proteoform-std [PRO:DNx]
is_a: PR:000027580 ! histone H3.2, initiator methionine removed form (Schizosaccharomyces pombe)
relationship: has_part MOD:00663 ! methylated lysine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000085719
name: histone H3.3, initiator methionine removed K36-methylated form (Schizosaccharomyces pombe)
def: "A histone H3.3, initiator methionine removed form (Schizosaccharomyces pombe) that has been methylated on Lys-36. Example: UniProtKB:P10651, 2-136, Lys-37, MOD:00663." [PRO:DAN, PomBase:VW, PMID:37459529]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited residue number is different because the initial methionine is not counted.
synonym: "Spom-hht3/InitMet-/K36Me" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221367, Lys-37, MOD:00663" EXACT PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P10651, 2-136, Lys-37, MOD:00663" EXACT PRO-proteoform-std [PRO:DNx]
is_a: PR:000027598 ! histone H3.3, initiator methionine removed form (Schizosaccharomyces pombe)
relationship: has_part MOD:00663 ! methylated lysine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000085720
name: histone H3.1, initiator methionine removed K36-trimethylated form (Schizosaccharomyces pombe)
def: "A histone H3.1, initiator methionine removed K36-methylated form (Schizosaccharomyces pombe) whose methylation type is trimethylation. Example: UniProtKB:P09988, 2-136, Lys-37, MOD:00083." [PRO:DAN, PomBase:VW, PMID:37459529]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited residue number is different because the initial methionine is not counted.
synonym: "Spom-hht1/InitMet-/K36Me3" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221366, Lys-37, MOD:00083" RELATED PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P09988, 2-136, Lys-37, MOD:00083" RELATED PRO-proteoform-std [PRO:DAN]
intersection_of: PR:000027578 ! histone H3.1, initiator methionine removed K36-methylated form (Schizosaccharomyces pombe)
intersection_of: has_part MOD:00083 ! N6,N6,N6-trimethyl-L-lysine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000085721
name: histone H3.2, initiator methionine removed K36-trimethylated form (Schizosaccharomyces pombe)
def: "A histone H3.2, initiator methionine removed K36-methylated form (Schizosaccharomyces pombe) whose methylation type is trimethylation. Example: UniProtKB:P09988, 2-136, Lys-37, MOD:00083." [PRO:DAN, PomBase:VW, PMID:37459529]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited residue number is different because the initial methionine is not counted.
synonym: "Spom-hht2/InitMet-/K36Me3" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221366, Lys-37, MOD:00083" RELATED PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P09988, 2-136, Lys-37, MOD:00083" RELATED PRO-proteoform-std [PRO:DAN]
intersection_of: PR:000027593 ! histone H3.2, initiator methionine removed K36-methylated form (Schizosaccharomyces pombe)
intersection_of: has_part MOD:00083 ! N6,N6,N6-trimethyl-L-lysine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000085722
name: histone H3.3, initiator methionine removed K36-trimethylated form (Schizosaccharomyces pombe)
def: "A histone H3.3, initiator methionine removed K36-methylated form (Schizosaccharomyces pombe) whose methylation type is trimethylation. Example: UniProtKB:P10651, 2-136, Lys-37, MOD:00083." [PRO:DAN, PomBase:VW, PMID:37459529]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited residue number is different because the initial methionine is not counted.
synonym: "Spom-hht3/InitMet-/K36Me3" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221367, Lys-37, MOD:00083" NARROW PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P10651, 2-136, Lys-37, MOD:00083" NARROW PRO-proteoform-std [PRO:DNx]
intersection_of: PR:000027604 ! histone H3.3, initiator methionine removed K36-methylated form (Schizosaccharomyces pombe)
intersection_of: has_part MOD:00083 ! N6,N6,N6-trimethyl-L-lysine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe
nataled commented 7 months ago

Will make the non-methylated forms next.

nataled commented 7 months ago

Without K36 methylation:

[Term]
id: PR:000085723
name: histone H3.1, initiator methionine removed K36-unmethylated form (Schizosaccharomyces pombe)
def: "A histone H3.1, initiator methionine removed form (Schizosaccharomyces pombe) that is not methylated on Lys-36. Example: UniProtKB:P09988, 2-136, Lys-37, PR:000026291." [PRO:DAN, PomBase:VW, PMID:37459529]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited the residue number is different because the initial methionine is not counted.
synonym: "Spom-hht1/InitMet-/K36unMe" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221366, Lys-37, PR:000026291" RELATED PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P09988, 2-136, Lys-37, PR:000026291" RELATED PRO-proteoform-std [PRO:DNx]
is_a: PR:000027574 ! histone H3.1, initiator methionine removed form (Schizosaccharomyces pombe)
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000085724
name: histone H3.2, initiator methionine removed K36-unmethylated form (Schizosaccharomyces pombe)
def: "A histone H3.2, initiator methionine removed form (Schizosaccharomyces pombe) that is not methylated on Lys-36. Example: UniProtKB:P09988, 2-136, Lys-37, PR:000026291." [PRO:DAN, PomBase:VW, PMID:37459529]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited the residue number is different because the initial methionine is not counted.
synonym: "Spom-hht2/InitMet-/K36unMe" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221366, Lys-37, PR:000026291" RELATED PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P09988, 2-136, Lys-37, PR:000026291" RELATED PRO-proteoform-std [PRO:DNx]
is_a: PR:000027580 ! histone H3.2, initiator methionine removed form (Schizosaccharomyces pombe)
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000085725
name: histone H3.3, initiator methionine removed K36-unmethylated form (Schizosaccharomyces pombe)
def: "A histone H3.3, initiator methionine removed form (Schizosaccharomyces pombe) that is not methylated on Lys-36. Example: UniProtKB:P10651, 2-136, Lys-37, PR:000026291." [PRO:DAN, PomBase:VW, PMID:37459529]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited residue number is different because the initial methionine is not counted.
synonym: "Spom-hht3/InitMet-/K36unMe" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221367, Lys-37, PR:000026291" EXACT PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P10651, 2-136, Lys-37, PR:000026291" EXACT PRO-proteoform-std [PRO:DNx]
is_a: PR:000027598 ! histone H3.3, initiator methionine removed form (Schizosaccharomyces pombe)
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe