wiki:AntoniasCuratedPapers

Version 493 (modified by antonialock, 9 years ago) (diff)

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https://sourceforge.net/apps/trac/pombase/wiki/CuratorTrainingPapers

Papers needing ODA conversions
Papers with WT info or no annotations


21727087Antonia
dmr1 (ppr3)mitochondrial translation phenotype, less translation of mt proteinsallele=deletion
variousadd missing phenotype alleles


21745468Antonia
lkh1, dsk1((phenotype)) slow cell growth (cell growth assay)allele=Δdsk1Δlkh1
lkh1, dsk1((phenotype)) slow cell growth (cell growth assay)allele=Δdsk1,lkh1-K391A


17369611Antonia
rtt109Delta rtt109/Histone H3 K56R double-mutant phenotypeasynthetic sensitivity to DNA damage


2900761Antonia
mat2-P...or mat2-Pc/Pi?Silenced (waiting for GeneDB to update cassette info so this can be annotated)IMP mat1-
mat3-M...or mat3-Mc/Mi?Silenced (waiting for GeneDB to update cassette info so this can be annotated)IMP mat1-
mat1-MiPhenotype: can conjugate but not undergo meiosis/sporulateallele=Mifs15(del_nt43-129)
mat1-PiPhenotype: can conjugate but not undergo meiosis/sporulateallele=Piop7(del_nt19-357)
mat1-PcPhenotype: can't conjugateallele=Pcop5(del_nt17-480)
mat1-McPhenotype: can't conjugateallele=Mcop7(del_nt19-546)
mat1-Pcsevere reduction in spore formationallele=deletion
mat1-Pcprocess: required for efficient meiosisIMP, allele=deletion
mat1-Mcprocess: required for efficient meiosisIMP, allele=deletion
mat1-Pcexpression: constitutively expressed (low levels) (rich media)IMP, allele=SP272(h+/h- meiotically competent diploid)
mat1-Pcexpression: constitutively expressed (low levels) (rich media)IMP, allele=SP720(fus1 deletion...capture as WT?)
mat1-Mcexpression: constitutively expressed (low levels) (rich media)IMP, allele=SP272(h+/h- meiotically competent diploid)
mat1-Mcexpression: constitutively expressed (low levels) (rich media)IMP, allele=SP720(fus1 deletion...capture as WT?)
mat1-Piexpression: not expressed (rich media)IMP, allele=SP272(h+/h- meiotically competent diploid)
mat1-Piexpression: not expressed (rich media)IMP, allele=SP720(fus1 deletion...capture as WT?)
mat1-Miexpression: not expressed (rich media)IMP, allele=SP272(h+/h- meiotically competent diploid)
mat1-Miexpression: not expressed (rich media)IMP, allele=SP720(fus1 deletion...capture as WT?)
All 4 are upregulated in response to nitrogen starvation. In diploid; downregulation at 6h compared to 4h, in haploid; no downregulation


2328719Antonia
map1transcription phenotype, target is not upregulated in response to nitrogen starvationallele=deletion,annotation_extension=has_regulation_target(GeneDB_Spombe:mat1-PC,(strain is H90))
mat1-Pcpositive autoregulation of transcription in response to nitrogen starvationallele=mat1-Pc-161()
map1transcription phenotype, target is not expressed in response to nitrogen starvationallele=deletion,annotation_extension=has_regulation_target(GeneDB_Spombe:mat1-Pm,(strain is H90))
mat1-Pctranscription phenotype, target is not expressed in response to nitrogen starvationallele=mat1-Pc-161(),annotation_extension=has_regulation_target(GeneDB_Spombe:mat1-Pm,(strain is H90))
mat1-Pclow constitutive expression in rich mediaallele=H90(fus1 deletion)
mat1-Pmno constitutive expression in rich mediaallele=H90(fus1 deletion)
mat1-Pmexpression in response to nitrogen starvation is dependent on the presence of CL:0002674annotation_extension=occurs_in(CL:0002675)
mat1-Pcupregulation in response to nitrogen starvation is not dependent on the presence of CL:0002674annotation_extension=occurs_in(CL:0002675)
ran1process: negative regulation of transcription from RNA polymerase II promoter during mitosis (IMP evidence code)allele=pat1-114,annotation_extension=has_regulation_target(GeneDB_Spombe:mat1-Pm, mat1-Mc and Mat1-Pc


17452352
sequence feature annotate AACCCT as a GATA transcription factor binding site, seq 5'-ATCA(C/A)AACCCTAACCCT-3'do we annotate this on the genome sequence?


18077559|Antonia
ams2 hip1slow cell growthallele=dbl mutant


20230746Antonia
ams2 remove NAS and TAS from artemis
ams2protein is unstable during G2 and M phase, partially stable during G1 and stable during S
ams2protein stability: is stable during S phase, level increased
ams2protein stability: is unstable during G2 phase, level decreased OR possibly only synthesised during S phase?
ams2protein stability: is unstable during G1/M phase, level increased OR possibly only synthesised during S phase?
ams2protein stability: is degraded by the SCF ubiquitin ligase pathway


18158900Antonia
double mutantsim3 mutants (allele=143(G81E),allele=205(E207K)) + overexpressed cnp1 = normal phenotype
double mutantsim3 mutants (allele=143(G81E),allele=205(E207K)) + overexpressed H4 = normal phenotype
double mutantsim3 mutants (allele=143(G81E),allele=205(E207K)) + overexpressed H3 = reduced viability (inviable ok)


cnb1,ppb1dbl deletion mutant same phenotype as each single mutant (branched,elongated multi-septate cells + slow growth in presence of mgcl2worth annotating? i.e. shows may be linked perhaps? dbl mutant not more severe
cnb1,ppb1,pmp1dbl del + overexpressed = normal cell growth
cnb1,ppb1deletion,overexpr. slow growth in presence of mgcl2i.e. large amounts of catalytic domain is not functional without regulatory subunit. is this interesting to capture?
cnb1,ppb1∆C(L445->STOPdeletion,overexpressed. slow growth in presence of mgcl2constitutively active mutant is not active without regulatory subunit
cnb1,ppb1∆C(L445->STOPoverexpressed,overexpressed. phenotype growth arrest, round small bent pear-shaped cells. depolarized distr of cortical F-actin patchesnormal phenotype in presence of CHEBI:61049
cnb1,ppb1∆C(L445->STOP,prz1overexpressed,overexpressed, deleted. no growth arrest


20018864Antonia
deletion(prz1), overexpression(ncs1)slow growthcell growth assay
deletion(ncs1), overexpression(prz1)slow growthcell growth assay
deletion(prz1), overexpression(ncs1)inviable in_response_to(CHEBI:29108)IMP
deletion(ncs1), overexpression(prz1)inviable in_response_to(CHEBI:29108)IMP
deletion(ncs1),deletion(yam8)normal cell growth in_presence_of(CHEBI:33120cell growth assay
ncs1promoter region lies in -1-130 region caact esp important
ncs1promoter for upregulation in response to calcium lies in -101-130 region
ncs1promoter for basal expression lies in -1-130 region
prz1binds caact in promoter region of ncs1


19606215Antonia
cnx1dbl mutant phenotype: abnormal cell wall morphologyallele=lumenal_cnx1p(aa_del488-560),allele=C-termTM_Cnx1p_cmyc(aa_del1-415)
cnx1some confusing data regarding apoptosis. Notes in hardcopy paperallele=lumenal_cnx1p(aa_del488-560)
cnx1allele specifications may not be 100% correct


18621924Antonia
cyr1,cgs1 dbl deletionnuclear export abolishedallele=deletion,annotation_extension=localizes(GeneDBSpombe:SPBC106.10)


map3/mam2diploid strain (CL:0000415) cannot sporulate if both receptors expressed at the same time


1563351Antonia
MatPi?expressed in response to nitrogen starvation and M factor in PcellsIDA
ste6MatPi? not expressed during N starvation and in presence of M factor in P cellsallele=deletion
ras1MatPi? not expressed during N starvation and in presence of M factor in P cellsallele=deletion
ras1MatPi? expressed during N starvation and in presence of M factor in P cells, not constitutively expressedallele=ras1val17
pat1/ras1mat1-Pm transcribedallele=pat1-114/deletion, at high temp
pat1/ste6mat1-Pm transcribedallele=pat1-114/deletion, at high temp

[BR]

8196631Antonia
mfm1/mfm2FYPO:0000584 decreased sporulationallele=deletion (both)
mfm1/mfm3FYPO:0000584 decreased sporulationallele=deletion (both)
mfm2/mfm3FYPO:0000584 decreased sporulationallele=deletion (both)
mfm1/mfm2/mfm3FYPO:0000583 sporulation abolishedallele=deletion (all 3)
mfm1/mfm2/mfm3FYPO:0000583 sporulation abolishedallele=deletion (all 3),annotation_extension=in_presence_of(M-factor - externally added),annotation_extension=occurs_in:CL0002674
mfm1/mfm2/mfm3FYPO:0000590 normal sporulationallele=deletion (all 3),annotation_extension=occurs_in:CL0002674


7975894Antonia
gpa1phenotype: increased expression of MatPi? during nitrogen starvation; constitutively active. Pheromone doesn't influence transcriptionQ244L
ras1phenotype: increased expression of Matpi during nitrogen starvation in the presence of pheromoneG17V
mat1Pm/pipromoter element mapped in paper -61- -41 (ccctctttctttgttccttat


8314086Antonia
sxa2expressed in presence of p-factor
map2expressed in H- cells
cyr1/sxa2phenotype G1 arrest in presence of P-factor in rich mediaallele=deletion
cyr1/sxa2abnormal/increased shmoo formation in presence of P-factor in rich mediaallele=deletion


18059475Antonia
fkh2/fhl1reduced zygote formationallele=deletion
fkh2/mei4reduced zygote formationallele=deletion
fkh2/fhl1/mei4reduced zygote formationallele=deletion
ste11annotate promoter proximal element FLEX1 and FLEXL1 to ste11, artemis
cig2/fkh2increased zygote formationallele=deletion,happens_during(GO:0006995 - cellular response to nitrogen starvation)
cig2/fkh2/fhl1reduced zygote formationallele=deletion,happens_during(GO:0006995 - cellular response to nitrogen starvation)
cig2/fkh2/mei4reduced zygote formationallele=deletion,happens_during(GO:0006995 - cellular response to nitrogen starvation)
cig2/fkh2/fhl1/mei4reduced zygote formationallele=deletion,happens_during(GO:0006995 - cellular response to nitrogen starvation)


10867006Antonia
ste11Unable to bind DNA region outside of the consensus motifste91


15580593Antonia
mam2negative regulation of pheromone INDEPENDENT signal transduction. TG: neg reg of GO:0038034. If I can't get this term from GO then use negative regulation of signal transduction involved in conjugation with cellular fusion + add the extension "in absence of P-factor" (occurs in M-cells)
Mam2 mutantsphenotype: constitutively active (if term goes inM cells


15659165Antonia
mam2negative regulation of pheromone INDEPENDENT signal transduction. TG: neg reg of GO:0038034. Sequesters G alpha. If I can't get this term from GO then use negative regulation of signal transduction involved in conjugation with cellular fusion + add the extension "in absence of P-factor" (occurs in M-cells)
mam2/gpa1interaction evidence is wrong, but it's the best fit....should I not curate this? I think the evidence is pretty strong


21118960
srw1 ectopically expressed | reb1 deletionnormal cell cycle arrest in response to pheromonephenotype
reb1|wee1phenotype: slow growth at high temperatureallele=deletion(reb1)/wee1-50
reb1|wee1phenotype: multiseptate (0000118)allele=deletion(reb1)/wee1-50
reb1|wee1phenotype: weeallele=deletion(reb1)/wee1-50
reb1|wee1phenotype: spheroid cellsallele=deletion(reb1)/wee1-50
reb1|wee1phenotype: DNA content increasedallele=deletion(reb1)/wee1-50
reb1|wee1phenotype: normal cell growth at high temperaturein_presence_of:CHEBI:44423, allele=deletion(reb1)/wee1-50
reb1|cdc10phenotype: slow growth at high temperatureallele=deletion(reb1)/cdc10-129
reb1|cdc10phenotype: abnormal? cell cycle arrestqualifier=at_high_temperature,allele=deletion(reb1)/cdc10-129


9427748
deletion ppb1|overexpression pmp1suppresses salt stress sensitivity
deletion pmp1|expression of const. active ppb1deltaC (C-term truncated)suppresses salt stress sensitivity
deletion pmp1|expression of const. active ppb1deltaC (C-term truncated)suppresses FK506 sensitivity
deletion pmp1|expression of ppb1 overexpressedsensitive to salt stress and FK506
deletion pmp1|deletion ppb1|deletion pmk1normal cell growth
deletion ppb1|deletionpmk1filamentous and multiseptateallele=deletion
deletion ppb1|overexpression pmp1normal morphology


11461899
stm1|ras1absence of G1 arrest in response to nitrogen starvationallele+deletion (both) flow cytometry
stm1|ras1slow cell growth in minimal media containing ammonia nitrogen sourceallele=deletion (both) cell growth assay
stm1|gpa2normal cell growth in minimal media containing ammonia nitrogen sourceannotation_extension=condition(overexpression - stm1)allele=deletion (gpa2) cell growth assay
stm1|gpa2normal septationannotation_extension=condition(overexpression - stm1)allele=deletion (gpa2) cell growth assay


21960007
mag1structure PDB ID 3S61according to authors, does not appear to match however


1448087
pyp2552 bp 5' UTR
pyp1|pyp2inviable germinating sporeallele=deletion (both)
pyp1 cdc25cell cycle arrestannotation_extension=condition(overexpression, pyp1), allele=cdc25-22, anotation_extension=condition(at_normal_temperature)
pyp2 cdc25cell cycle arrestannotation_extension=condition(overexpression, pyp1), allele=cdc25-22, anotation_extension=condition(at_normal_temperature)
pyp1 cdc25cell cycle arrestannotation_extension=condition(overexpression, pyp1), allele=cdc25-22, anotation_extension=condition(at_high_temperature)
pyp2 cdc25cell cycle arrestannotation_extension=condition(overexpression, pyp1), allele=cdc25-22, anotation_extension=condition(at_high_temperature)
pyp1 cdc2normal cell length (cell division/cell cycle)annotation_extension=condition(overexpression, pyp1), allele=cdc2-1w
pyp2 cdc2normal cell length (cell division/cell cycle)annotation_extension=condition(overexpression, pyp1), allele=cdc2-1w
pyp1 wee1elongated cellsannotation_extension=condition(overexpression, pyp1), allele=wee1-50, anotation_extension=condition(at_normal_temperature)
pyp2 wee1elongated cellsannotation_extension=condition(overexpression, pyp1), allele=wee1-50, anotation_extension=condition(at_normal_temperature)
pyp1 wee1normal cell length (possibly could use normal cell growth or normal cell division/mitotic cell cycleannotation_extension=condition(overexpression, pyp1), allele=wee1-50, anotation_extension=condition(at_high_temperature)
pyp2 wee1normal cell length (possibly could use normal cell growth or normal cell division/mitotic cell cycleannotation_extension=condition(overexpression, pyp1), allele=wee1-50, anotation_extension=condition(at_high_temperature)
pyp1 cdc25normal cell lengthallele=deletion, pyp1), allele=cdc25-22, annotation_extension=condition(at_normal_temperature)
pyp2 cdc25elongated cellsallele=deletion, pyp1), allele=cdc25-22, annotation_extension=condition(at_normal_temperature)
pyp1 cdc25elongated cellsallele=deletion, pyp1), allele=cdc25-22, annotation_extension=condition(at_high_temperature)


11470243
fas2increased accumulation of see belowallele=H201(I1276T),annotation_extension=condition(at_high_temperature)
fas2increased accumulation of see belowallele=H265(Q4Y),annotation_extension=condition(at_high_temperature)
fas2increased accumulation of see belowallele=H518(I600N),annotation_extension=condition(at_high_temperature)
fas2decreased accumulation of see belowallele=H201(I1276T),annotation_extension=condition(at_high_temperature)
fas2decreased accumulation of see belowallele=H265(Q4Y),annotation_extension=condition(at_high_temperature)
fas2decreased accumulation of see belowallele=H518(I600N),annotation_extension=condition(at_high_temperature)

For the 3 mutants above:
increased accumulation of at high temp: N-monomethyldioleoyl-PE (N-monomethyl-C18:1-C18:1-PE) N,N-dimethyl-C18:1-C18:1-PE N,N-monomethyl-C18:1-C18:1-PE N,N-dimethyl-C16:1-C18:1-PE 1-melissoyl-oleolyl-sn-glycero-3-phosphoethanolamine (C30:0-C18:1-PE) 1-melissoyl-2-oleolyl-sn-glycero-3-phosphocholine (C30:0-C18:1-PC) CHEBI:16337 CHEBI:36711


decreased accumulation of at high temp: (NOT in mutant 518) 1-oleolyl-2-caproyl-sn-glycero-3-phosphocholine (C18:1-C10:0-PC) C18:0-C10:0-PC C18:0-C8:0-PC CHEBI:18303 CHEBI:17517


15075260
pdf1dbl mutant normal growth in presence of sodium orthovanadateallele=S106A(S106A),allele=H478A(H478A) (2 plasmids)
pdf1dbl mutant normal growth in presence of sodium orthovanadateallele=D226A(D226A),allele=H478A(H478A) (2 plasmids)
pdf1dbl mutant normal growth in presence of 'near alkaline/high' pH (=condition?)allele=S106A(S106A),allele=H478A(H478A) (2 plasmids)
pdf1dbl mutant normal growth in presence of 'near alkaline/high' pH (=condition?)allele=D226A(D226A),allele=H478A(H478A) (2 plasmids)


9017391http://curation.pombase.org/pombe/curs/40aa30b33b608f68
gcs1 + ade6sensitive to cadmiumallele=apd1-1(unknown),allele=ade6-210(unknown)
gcs1 + ade6sensitive to cadmiumallele=deletion,allele=ade6-210(unknown))
gcs1 + ade6normal growth in presence of either ions: Ca|Na|Mgallele=apd1-1(unknown),allele=ade6-210(unknown)
gcs1 + ade6normal cell growthannotation_extension=condition(in_rich_media),allele=apd1-1(unknown),allele=ade6-210(unknown)
gcs1 + ade6resistant to MNNG (N-methyl-N'-nitro-N-nitrosoguanidine)allele=deletion,allele=ade6-210(unknown))|
gcs1 + ade6slow cell growthannotation_extension=condition(in_minimal_media),allele=apd1-1(unknown),allele=ade6-210(unknown)
gcs1 + ade6slow cell growthannotation_extension=condition(in_minimal_media),allele=deletion,allele=ade6-210(unknown)
gsh2 + ade6slow cell growthannotation_extension=condition(in_minimal_media),allele=deletion,allele=ade6-210(unknown)
hmt1 + ade6normal cell growthannotation_extension=condition(in_minimal_media),allele=deletion,allele=ade6-210(unknown)
gcs1 + ade6normal cell growthannotation_extension=condition(in_minimal_media),annotation_extension=in_presence_of(CHEBI:16856),allele=apd1-1(unknown),allele=ade6-210(unknown)
gcs1 + ade6normal cell growthannotation_extension=condition(in_minimal_media),annotation_extension=in_presence_of(CHEBI:16856),allele=deletion,allele=ade6-210(unknown)
gsh2 + ade6normal cell growthannotation_extension=condition(in_minimal_media),annotation_extension=in_presence_of(CHEBI:16856),allele=deletion,allele=ade6-210(unknown)
gcs1 + ade6sporulation abolishedallele=apd1-1(unknown),allele=ade6-210(unknown)
gcs1 + ade6normal sporulationannotation_extension=in_presence_of(CHEBI:16856),allele=apd1-1(unknown),allele=ade6-210(unknown)
hmt1 + ade6red pigmentation of coloniesallele=deletion,allele=ade6-210(unknown)
gcs1 + ade6absent/reduced red pigmentation of coloniesallele=apd1-1(unknown),allele=ade6-210(unknown)
gcs1 + ade6absent/reduced red pigmentation of coloniesallele=deletion,allele=ade6-210(unknown)
gsh2 + ade6reduced red pigmentation of coloniesallele=deletion,allele=ade6-210(unknown)
gcs1 + ade6absent/reduced red pigmentation of coloniesannotation_extension=condition(in_minimal_media),annotation_extension=in_presence_of(CHEBI:16856),allele=apd1-1(unknown),allele=ade6-210(unknown)


1448066
ade2/ade6dbl mutant sensitive to cadmiumallele=ade6-216(unknown),allele=ade2(deletion), growth assay
ade2/ade7dbl mutant sensitive to cadmiumallele=ade7-50(unknown),allele=ade2(deletion), growth assay
-asked for a term to describe HMW complex. Link to it
ade2/ade6dbl mutant can't accumulate HMW PC-Cd-S2- complexallele=ade6-216(unknown),allele=ade2(deletion)
ade2/ade7dbl mutant can't accumulate HMW PC-Cd-S2- complexallele=ade7-50(unknown),allele=ade2(deletion)
-asked for a term to describe HMW complex. Link to it - GO:0090424


12905027
SPAC3H1.10MOD requested: cadmium containing modified residueresidue=C173|


9016341
ade2 + ade7sensitive to cisplatinallele=deletion (ade2) allele=ade7.50
ade2 + ade6sensitive to cisplatinallele=deletion (ade2) allele=ade6.216


16928959
perhaps should use +ve reg of transcr instead of calcium response for the var agentsgo over again


19646873
gef1delta + orb6-25 normal morphology at high tempmicroscopy
rga4 overexpressed + orb6-25 normal morphology at high tempmicroscopy
Gef1 overexpression + orb6-as2stubby PCO:0000005 at normal temp
orb6-25 + rga4deltastubby at normal temp PCO:0000005


19285552
rgs1decreased transcriptional response in response to pheromoneallele=noname(overexpression),​​annotation_extension=occurs_in(CL:0002674)
gpa1can probably migrate some terms to abnormal decrease in transcription/increase, see what midori says


20396879
dak1/dak2 dbl mutnormal cell growthallele=dak1-delta(deletion),allele=dak2-delta(deletion),condition=PCO:0000014
dak1/dak2decreased glycerol dehydrogenase activityallele=dak1-delta(deletion),allele=dak2-delta(deletion),condition=PCO:0000072
dak1/dak2increased accumulation of DHAallele=dak1-delta(deletion),allele=dak2-delta(deletion),condition=PCO:0000072
dak1/dak2slow aerobic cell growthallele=dak1-delta(deletion),allele=ak2-delta(deletion),condition=PCO:0000072
dak1/dak2/gld1abolished glycerol dehydrogenase activityallele=dak1-delta(deletion),allele=dak2-delta(deletion),allele=gld1-delta(deletion),condition=PCO:0000072
dak1/dak2slow aerobic cell growthallele=dak1-delta(deletion),allele=ak2-delta(deletion),condition=PCO:0000073
dak1/dak2slow aerobic cell growthallele=dak1-delta(deletion),allele=ak2-delta(deletion),condition=PCO:0000076,condition=PCO:0000014
tup11/tup12increased glycerol dehydrogenase activityallele=tup11-delta(deletion),allele=tup12-delta(deletion),condition=PCO:0000014
gld1/dak1/dak2slow cell growthallele=noname(overexpression),condition=PCO:0000077


9585505
atf1 + pap1sensitive to cisplatinallele=atf1-delta(deletion), allele=pap1-delta(deletion), condition=PCO:0000012, CGA


1448080
crm1 + pap1normal growth at cold /or/ normal cell growth condition=low tempallele=crm1-809(unknown),allele=pap1-delta(deletion),PCO:0000012
crm1 + pap1sensitive to staurosporineallele=crm1-809(unknown),allele=pap1-delta(deletion),PCO:0000012
crm1 + pap1normal protein accumulationallele=crm1-809(unknown),allele=pap1-delta(deletion),annotation_extension=has_regulation_target(PomBase:SPAC3C7.14c)


7642144
rpn11| pmd1resistant to K-252aallele=pmd1-delta(deletion),allele=noname(overexpression),​condition=PCO:0000012
rpn11| pmd1resistant to staurosporineallele=pmd1-delta(deletion),allele=noname(overexpression),​condition=PCO:0000012
rpn11| pmd1resistant to vanadateallele=pmd1-delta(deletion),allele=noname(overexpression),​condition=PCO:0000012
rpn11| pmd1resistant to cycloheximideallele=pmd1-delta(deletion),allele=noname(overexpression),​condition=PCO:0000012
rpn11| pmd1resistant to actinomycin Dqualifier=NOT, allele=pmd1-delta(deletion),allele=noname(overexpression),​condition=PCO:0000012
rpn11| pmd1resistant to thiabendazolequalifier=NOT, allele=pmd1-delta(deletion),allele=noname(overexpression),​condition=PCO:0000012


21324894
cia1 | mts2increased protein level allele=asf1-30(F24S,​G120S,​D173G), allele=mts2-1(unknown), condition=PCO:0000004,annotation_extension=has_regulation/downstream_target(PomBase:SPCC663.05c), western
cia1 | mts2slow growth allele=asf1-30(F24S,​G120S,​D173G), allele=mts2-1(unknown), condition=PCO:0000005, condition=PCO:0000012, CGA
cia1 | mts2slow growth at high temp allele=asf1-30(F24S,​G120S,​D173G), allele=mts2-1(unknown), condition=PCO:0000012, CGA
cia1 | ubc4slow growth allele=asf1-30(F24S,​G120S,​D173G), allele=ubc4ts(P61S), condition=PCO:0000005, condition=PCO:0000012, CGA
cia1 | ubc4slow growth at high temp allele=asf1-30(F24S,​G120S,​D173G), allele=ubc4ts(P61S), condition=PCO:0000012, CGA
cia1 + mts2FYPO:0000783, cia1 normally found in nucleus, but here found in cytoplasmallele=asf1-30(F24S,​G120S,​D173G),allele=mts2-1(unknown), condition=PCO:0000004, specify cia in annex? has_target cia1?
cia1 | ubc4increased protein level allele=asf1-30(F24S,​G120S,​D173G), allele=ubc4ts(P61S), condition=PCO:0000004,annotation_extension=has_regulation/downstream_target(PomBase:SPCC663.05c), western
cia1 | SPBC2A(.04Cincreased protein level allele=asf1-30(F24S,​G120S,​D173G), allele=san1-delta(deletion), condition=PCO:0000004,annotation_extension=has_regulation/downstream_target(PomBase:SPCC663.05c), western
cia1 | hrd1 slow growth at normal temp allele=asf1-30(F24S,​G120S,​D173G),allele=hrd1-delta(deletion), condition=PCO:0000012
cia1 | hrd1 slow growth at high temp allele=asf1-30(F24S,​G120S,​D173G),allele=hrd1-delta(deletion), condition=PCO:0000012
cia1 | doa10 slow growth at normal temp allele=asf1-30(F24S,​G120S,​D173G),allele=doa10-delta(deletion), condition=PCO:0000012
cia1 | doa10 slow growth at high temp allele=asf1-30(F24S,​G120S,​D173G),allele=doa10-delta(deletion), condition=PCO:0000012
cia1 | san1 normal cell growth allele=asf1-30(F24S,​G120S,​D173G),allele=san1-delta(deletion), condition=PCO:0000012, condition=PCO:0000006
cia1 | san1 slow growth at high temp allele=asf1-30(F24S,​G120S,​D173G),allele=san1-delta(deletion), condition=PCO:0000012
cia1 | ubr1 normal cell growth allele=asf1-30(F24S,​G120S,​D173G),allele=ubr1-delta(deletion), condition=PCO:0000012, condition=PCO:0000006
cia1 | ubr1 slow growth at high temp allele=asf1-30(F24S,​G120S,​D173G),allele=ubr1-delta(deletion), condition=PCO:0000012
cia1 | ubr11 normal cell growth allele=asf1-30(F24S,​G120S,​D173G),allele=ubr11-delta(deletion), condition=PCO:0000012, condition=PCO:0000006
cia1 | ubr11 slow growth at high temp allele=asf1-30(F24S,​G120S,​D173G),allele=ubr11-delta(deletion), condition=PCO:0000012
SPBC2A9.04c | mis12 normal cell growth at high tempallele=san1-delta(deletion),allele=mis12-537(unknown), condition=PCO:0000012, condition=PCO:0000012
SPBC2A9.04c | pim1 normal cell growth at high tempallele=san1-delta(deletion),allele=pim1-46(unknown), condition=PCO:0000012, condition=PCO:0000012
SPBC2A9.04c | cnp1 normal cell growth at high tempallele=san1-delta(deletion),allele=cnp1-1(unknown), condition=PCO:0000012, condition=PCO:0000012


9191271
mfm1dbl check annotations, allele descr for phenotype annotationhas_regulation_target(PomBase:SPMTR.02))


19366728
SF ITEM https://sourceforge.net/tracker/?func=detail&aid=3521043&group_id=65526&atid=2096431
end4normal nuclear / medial cortex morphology during nitrogen starvation allele=end4-507(G73D), condition=PCO:0000098, microscopy
end4abnormal nuclear / medial cortex morphology during nitrogen starvation allele=end4-507(G73D), condition=PCO:0000097, microscopy


8321236http://oliver0.sysbiol.cam.ac.uk/pombe/curs/169dc6a662075c56/gene/1
frp1abolished ferric iron reductase activity, not req yetallele=G-100(W314->opal)
waiting reply from val on paper


7565608http://oliver0.sysbiol.cam.ac.uk/pombe/curs/07cc7abfbaa6d1b0
rds1cellular response to adenine starvation, term reqIMP - IEP is more appropriate perhaps..
ade genesfor FYPO:0000825 annotation add 'during cellular response to adenine starvation' term reqdon't add for cyr1
rds1 /controlled_curation="term=gene expression, mRNA level; annotation_extension=during(cellular response to adenine starvation); qualifier=increased; evidence=ECO:0000106; db_xref=7565608; date=20120504"


9135147http://oliver0.sysbiol.cam.ac.uk/pombe/curs/67ba83cbaba024a7
pck2 increased protein tyrosine phosphorylationallele=pck2delta(deletion),​​ annotation_extension=assayed_using(PomBase:SPBC119.08)
pmk1 | spk1sterileallele=pmk1delta(deletion), allele=spk1delta(deletion)
pmk1 | spk1abnormal morphologyallele=pmk1delta(deletion), allele=spk1delta(deletion), condition=PCO:0000014, condition=PCO:0000102
pmk1 | spk1normal response to salt stressallele=pmk1delta(deletion), allele=spk1delta(deletion), condition=PCO:0000014, condition=PCO:0000102
wis1 | pmk1 multiseptate microscopy, allele=wi1delta(deletion), allele=pmk1delta(deletion), condition=PCO:0000014, condition=PCO:0000102


1644306http://oliver0.sysbiol.cam.ac.uk/pombe/curs/1b8ed217ce984ab5
tnr1increased RNA level, northern evidence, need to find what this gene is...allele=tnr1-18(unknown), annotation_extension=assayed_using(SPBC26H8.01),​ condition=PCO:0000014,​ annotation_extension=happens_during(GO:0071301)
tnr1cellular response to vitamin b1 - which gene is this?? IMP
thi2gene expression: expressed in response to thiamine starvation. repressed in response to thiamine....
/controlled_curation="term=gene expression, mRNA level; annotation_extension=during(GO:0036225); qualifier=increased; evidence=ECO:0000106; db_xref=1644306; date=20120509"
/controlled_curation="term=gene expression, mRNA level; annotation_extension=during(GO:0071301); qualifier=absent; evidence=ECO:0000106; db_xref=1644306; date=20120509"
/controlled_curation="term=gene expression, mRNA level; annotation_extension=in_response_to(CHEBI:16892); qualifier=increased; evidence=ECO:0000106; db_xref=1644306; date=20120509"
/controlled_curation="term=gene expression, mRNA level; annotation_extension=in_response_to(CHEBI:17957); qualifier=decreased; evidence=ECO:0000106; db_xref=1644306; date=20120509"


7499352http://oliver0.sysbiol.cam.ac.uk/pombe/curs/5cbe479087353d2f
tnr3 increased thiamine level, chromatography evidence - requested form eco: http://code.google.com/p/evidenceontology/issues/detail?can=2&start=0&num=100&q=&colspec=ID%20Type%20Status%20Priority%20Owner%20Summary&groupby=&sort=&id=2allele=pho1-44delta(deletion), allele=tnr3-10(unknown)
tnr3 increased thiamine levelallele=pho1-44delta(deletion), allele=tnr3-5(unknown)
tnr3 increased thiamine levelallele=pho1-44delta(deletion), allele=tnr3-1(unknown)
pho4cellular response to thiamine starvationIMP


8675019http://oliver0.sysbiol.cam.ac.uk/pombe/curs/4b0970d0e5484486/
tnr1which gene is this? FYPO:0000825 northern evallele=tnr1-18(unknown), condition=PCO:0000014, annotation_extension=assayed_using(SPAC17A2.01)
bsu1cellular response to thiamine starvationIMP
thi3 | bsu1 slow aerobic cell growth allele=bsu1delta(deletion), allele=thi3-1(unknown), condition=PCO:0000014, condition=PCO:0000106
thi3 | bsu1 slow aerobic cell growth allele=bsu1delta(deletion), allele=thi3-1(unknown), condition=PCO:0000014, condition=PCO:0000107


2249257http://oliver0.sysbiol.cam.ac.uk/pombe/curs/40213c281e540075

/controlled_curation="term=gene expression, mRNA level; annotation_extension=during(cellular response to thiamine starvation); qualifier=increased; evidence=ECO:0000106; db_xref=2249257; date=20120510"


2020549http://oliver0.sysbiol.cam.ac.uk/pombe/curs/1ff0297254ee616d


9560432http://oliver0.sysbiol.cam.ac.uk/pombe/curs/de924eb687e556b7
itr2 | itr1 normal cell growth allele=IM49(unknown),​​ allele=itr1-noname(overexpression), condition=PCO:0000005,​​ condition=PCO:0000014,​​ condition=PCO:0000102,​ condition=PCO:0000111


22245228http://curation.pombase.org/pombe/curs/7b18cacb1717e352
tpx1 | srx1 normal cellular response to hydrogen peroxideallele=srx1(overexpression), allele=tpx1(deletion)


10455235http://oliver0.sysbiol.cam.ac.uk/pombe/curs/32450f2b6ffd928f
gpx1 | ctt1 normal response to hydrogen peroxide ctt1=deleted, gpx1=overexpressed, 30 degrees
transcription factor deletionsreuest terms for during h202 and normal growthsee paper annotations


8549830http://curation.pombase.org/pombe/curs/78253143f2002b71
hxk1/hxk2slow growth on glucose carbon sourcedouble-deletion


2878925http://curation.pombase.org/pombe/curs/462720c354cd7b67/
pma mutantnormal ATPase activity unknown, in vitro
pma mutantnormal H+/hydrogen export/transport activity unknown, in vitro
pma mutantNormal enzyme in vitro response to Dio-9 unknown, in vitro
pma mutantNormal enzyme in vitro response to DCCD N,N'-dicyclohexylcarbodiimideunknown, in vitro
pma mutantNormal enzyme in vitro response to Miconazoleunknown, in vitro
pma mutantNormal enzyme in vitro response to DES diethylstilbestrolunknown, in vitro
pma mutantNormal enzyme in vitro response to Suloctidil unknown, in vitro
pma mutantNormal enzyme in vitro response to p-hydroxymercuribenzoate unknown, in vitro
pma mutantNormal enzyme in vitro response to protamine sulfate unknown, in vitro
pma mutantNormal enzyme in vitro response to decamethylene diguanidineunknown, in vitro
ade7-413|pma mutant slow growth adenine added, MM, liquid media
pma mutant decreased methionine transport into cell during nitrogen starvation
pma mutant decreased cellular pH CGAYE liquid


18556189http://curation.pombase.org/pombe/curs/a87bcb91d6476796/
varsee notes in session. May have to req new binding terms or define cofactor binding which influence activity elsewise. The cofactors are not strictly required_for, but rather catalyse/decrease activity
dextrin alpha-glucosidase activity qualifier=majorIDA
starch alpha-glucosidase activity qualifier=majorIDA


11136464http://curation.pombase.org/pombe/curs/0089b9465b71c321/
inv1|sut1slow growth on sucroseallele=deletion(both), sucrose MM
inv1|sut1slow growth on trehaloseallele=deletion(both), trehalose MM
inv1|sut1normal growth on maltoseallele=deletion(both), maltose MM


7898433http://curation.pombase.org/pombe/curs/5964257cca6cfa69
uvi15loss of viability in stationary phase upon nitrogen depletiondeletion, glucose min medium, normal temp


9560432http://curation.pombase.org/pombe/curs/de924eb687e556b7
itr2swap myo-inositol transport for myo-inositol transport into cell


17384198http://curation.pombase.org/pombe/curs/42b53662d27d7951
crm1integrate two BPs, have requested term from GO
other assaysRNA protection assay or transcript quantification assay


21324894http://curation.pombase.org/pombe/curs/0d6e46fca4be8cc5
san1BP GO:1901044 Label: protein polyubiquitination involved in nucleus-associated proteasomal ubiquitin-dependent protein catabolic processIMP
11298744 http://oliver0.sysbiol.cam.ac.uk/pombe/curs/9829ae1d7c3785b1
agl1soluble starch alpha-glucosidase activityIDA
agl1maltase activityenzyme assay data alleles are: normal activity: D287N, E484D, D676N, and E714Q | decreased: D218N, D355N/E, and D877N abolished: D481N/E/A, E484Q/A, and D647N/E/A


9813085http://curation.pombase.org/pombe/curs/b91556d0478e3dea
gpt1oligosaccharide glucosylation, child of macromolecule glycosylationIMP
alg6decreased glc1man9GlcNAc levelDNJ added, chromatography, deletion
alg6absent glc2man9GlcNAcDNJ added, chromatography, deletion
alg6absent glc3man9GlcNAcDNJ added, chromatography, deletion
alg6increased man9GlcNAcDNJ added, chromatography, deletion
alg6increased man8GlcNAcDNJ added, chromatography, deletion
alg6decreased glc1man9GlcNAc levelchromatography, deletion
alg6|gpt1decreased glc1man9GlcNAc levelDNJ added, chromatography, deletion of both
alg6|gpt1increased man9GlcNAc levelDNJ addedchromatography, deletion of both
alg6|gpt1absent glc2man9GlcNAcDNJ added, chromatography, deletion of both
alg6|gpt1absent glc3man9GlcNAcDNJ added, chromatography, deletion of both
alg6|gpt1decreased glc1man9GlcNAc levelchromatography, deletion of both
alg6|gpt1decreased man9GlcNAc levelchromatography, deletion of both
alg6|gpt1absent glc2man9GlcNAcchromatography, deletion of both
alg6|gpt1absent glc3man9GlcNAcchromatography, deletion of both
gls2|alg6absent glc2man9GlcNAcchromatography, deletion of both
gls2|alg6absent glc3man9GlcNAcchromatography, deletion of both
gls2|alg6increased glc1man9GlcNAcchromatography, deletion of both
gls2|alg6increased man9GlcNAcchromatography, deletion of both
gls2|alg6increased man8GlcNAcchromatography, deletion of both
gpt1|alg6increased RNA levelnorthern, annotation_extension=assayed_using(PomBase:SPAC22A12.15c)
gpt1|alg6increased RNA levelnorthern, annotation_extension=assayed_using(PomBase:SPAC22A12.15c)
alg6lower cell density in stationary phasedeletion, glucose minimal medium, liquid, normal temp
gpt1 | alg6lower cell density in stationary phasedeletion, glucose minimal medium, liquid, normal temp
gpt1 | alg6slower cell growth ratedeletion, glucose minimal medium, liquid, normal temp
gpt1 | alg6flocculating cells, microscopydeletion, glucose minimal medium, normal temp
gpt1 | alg6round/swollen cells (they are not small), microscopydeletion, glucose minimal medium, normal temp
gpt1 | alg6slow growth at high temperaturedeletion, glucose minimal medium, normal temp
gls2 | alg6slow aerobic cell growth on glucose carbon sourcenormal glucose MM, high temp, agar plates
gls2 | alg6normal aerobic cell growth on glucose carbon sourcenormal glucose MM, normal temp
gpt1 | alg6slow aerobic cell growth on glucose carbon sourcenormal glucose MM, normal temp, agar plates
gpt1 | alg6slow aerobic cell growth on glucose carbon sourcenormal glucose MM, high temp, agar plates
deletion alg6 | overexpressed gpt1normal cell growthplate, normal glucose MM, normal temp
deletion alg6 | overexpressed gpt1normal cell growthplate, normal glucose MM, high temp
gpt1|alg6normal morphologydeletion, sorbitol added, normal glucose MM, liquid
gpt1|alg6normal cell growth on gluocose carbon sourcedeletion, sorbitol added, normal glucose MM
deletion alg6 | overexpressed gpt1normal morphologynormal glucose MM, high temp
deletion alg6| deletion gpt1|overexpression gpt1(Y1312A,D1352A)round/swollen cellsnormal temp, glucose MM
deletion alg6| deletion gpt1|overexpression gpt1(Y1312A,D1352A)slow growth at high temphigh temp, glucose MM
gls2 | alg6normal morphologynormal glucose MM, normal temp


11016847http://curation.pombase.org/pombe/curs/373f4c6a1e37adf9
yam8decreased conjugation frequencyallele=yam8delta, mating medium, calcium excluded, normal temp
yam8decreased conjugation frequencyallele=ehs1-1, mating medium, calcium excluded, normal temp
yam8normal conjugation frequencyallele=yam8delta, mating medium, calcium added, normal temp
yam8decreased conjugation frequencyallele=ehs1-1, mating medium, calcium added, normal temp
yam8 | pck2normal growth at high tempallele=ehs1-1, allele=pck2(overexpressed),high temp, YES
yam8 | pck2slow growth at high tempallele=yam8delta, allele=pck2(overexpressed),high temp, YES
yam8 | pck2normal conjugation freqallele=ehs1-1, allele=pck2(overexpressed)
yam8 | pck2decreased conjugation freqallele=yam8delta, allele=pck2(overexpressed)
yam8 | pck2normal growth on cilofunginallele=ehs1-1, allele=pck2(overexpressed),normal temp, YES
yam8 | pck2sensitive to cilofunginallele=yam8delta, allele=pck2(overexpressed),normal temp, YES
yam8 | pck2normal growth on calcofluor whiteallele=ehs1-1, allele=pck2(overexpressed),normal temp, YES
yam8 | pck2sensitive to calcofluor whiteallele=yam8delta, allele=pck2(overexpressed),normal temp, YES
yam8 | pck1sensitive to calcofluor whiteallele=ehs1-1, allele=pck2(overexpressed),normal temp, YES
yam8 | pck1sensitive to cilofunginallele=ehs1-1, allele=pck1(overexpressed),normal temp, YES
yam8 | pck1slow growth at high tempallele=ehs1-1, allele=pck1(overexpressed),high temp, YES
|pck2 | yam8
pck2increased level of calcium in cellallele=overexpression, normal temp, glucose MM
pck2| yam8normal level of calcium in cellallele=ehs1-1, allele=pck2(overexpression), normal temp, glucose MM
pck2normal cell growth on glucose carbon sourceallele=overexpression, solid agar plates, Ca ions excluded, standard glucose minimal medium, standard temperature
pck2 | yam8slow growthallele=pck2(overexpression),allele=ehs1-1, solid agar plates, glucose minimal medium, standard temperature
pck2 | yam8normal cell growthallele=pck2(overexpression),allele=ehs1-1, calcium excluded, solid agar plates, glucose minimal medium, standard temperature
pck2 | yam8 normal growthallele=pck2(overexpression),allele=yam8delta, solid agar plates, glucose minimal medium, standard temperature
normal growthallele=pck2(overexpression),allele=yam8delta, calcium excluded, solid agar plates, glucose minimal medium, standard temperature
yam8 | pck2inviableallele=ehs1-1, allele=pck2delta
yam8 | pck2viableallele=yam8delta, allele=pck2delta
yam8|pck2normal morphologyallele=pck2(overexpression),allele=yam8delta, glucose MM, standard temp microscopy
yam8|pck2lysed cellsallele=pck2(overexpression),allele=ehs1-1, glucose MM, standard temp microscopy


missing annotations
http://oliver0.sysbiol.cam.ac.uk/pombe/curs/219e86a87274fe5f/ro/


HTP gene expression data
15004206for future ref
19366728table 3 + gene expression omnibus GEOhashGSE14319for future ref


misc to add
positive reg of protein targeting to vacuolar membrane