https://sourceforge.net/apps/trac/pombase/wiki/CuratorTrainingPapers
Papers needing ODA conversions
Papers with WT info or no annotations
AntoniasDoubleMutants
AntoniasRNAmodsandmutants
https://sourceforge.net/apps/trac/pombase/wiki/CuratorTrainingPapers
2900761 | Antonia
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mat2-P...or mat2-Pc/Pi? | Silenced (waiting for GeneDB to update cassette info so this can be annotated) | IMP mat1-
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mat3-M...or mat3-Mc/Mi? | Silenced (waiting for GeneDB to update cassette info so this can be annotated) | IMP mat1-
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mat1-Mi | Phenotype: can conjugate but not undergo meiosis/sporulate | allele=Mifs15(del_nt43-129)
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mat1-Pi | Phenotype: can conjugate but not undergo meiosis/sporulate | allele=Piop7(del_nt19-357)
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mat1-Pc | Phenotype: can't conjugate | allele=Pcop5(del_nt17-480)
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mat1-Mc | Phenotype: can't conjugate | allele=Mcop7(del_nt19-546)
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mat1-Pc | severe reduction in spore formation | allele=deletion
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mat1-Pc | process: required for efficient meiosis | IMP, allele=deletion
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mat1-Mc | process: required for efficient meiosis | IMP, allele=deletion
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mat1-Pc | expression: constitutively expressed (low levels) (rich media) | IMP, allele=SP272(h+/h- meiotically competent diploid)
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mat1-Pc | expression: constitutively expressed (low levels) (rich media) | IMP, allele=SP720(fus1 deletion...capture as WT?)
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mat1-Mc | expression: constitutively expressed (low levels) (rich media) | IMP, allele=SP272(h+/h- meiotically competent diploid)
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mat1-Mc | expression: constitutively expressed (low levels) (rich media) | IMP, allele=SP720(fus1 deletion...capture as WT?)
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mat1-Pi | expression: not expressed (rich media) | IMP, allele=SP272(h+/h- meiotically competent diploid)
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mat1-Pi | expression: not expressed (rich media) | IMP, allele=SP720(fus1 deletion...capture as WT?)
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mat1-Mi | expression: not expressed (rich media) | IMP, allele=SP272(h+/h- meiotically competent diploid)
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mat1-Mi | expression: not expressed (rich media) | IMP, allele=SP720(fus1 deletion...capture as WT?)
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All 4 are upregulated in response to nitrogen starvation. In diploid; downregulation at 6h compared to 4h, in haploid; no downregulation
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2328719 | Antonia
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map1 | transcription phenotype, target is not upregulated in response to nitrogen starvation | allele=deletion,annotation_extension=has_regulation_target(GeneDB_Spombe:mat1-PC,(strain is H90))
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mat1-Pc | positive autoregulation of transcription in response to nitrogen starvation | allele=mat1-Pc-161()
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map1 | transcription phenotype, target is not expressed in response to nitrogen starvation | allele=deletion,annotation_extension=has_regulation_target(GeneDB_Spombe:mat1-Pm,(strain is H90))
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mat1-Pc | transcription phenotype, target is not expressed in response to nitrogen starvation | allele=mat1-Pc-161(),annotation_extension=has_regulation_target(GeneDB_Spombe:mat1-Pm,(strain is H90))
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mat1-Pc | low constitutive expression in rich media | allele=H90(fus1 deletion)
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mat1-Pm | no constitutive expression in rich media | allele=H90(fus1 deletion)
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mat1-Pm | expression in response to nitrogen starvation is dependent on the presence of CL:0002674 | annotation_extension=occurs_in(CL:0002675)
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mat1-Pc | upregulation in response to nitrogen starvation is not dependent on the presence of CL:0002674 | annotation_extension=occurs_in(CL:0002675)
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ran1 | process: 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
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17452352
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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?
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18077559|Antonia
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ams2 hip1 | slow cell growth | allele=dbl mutant
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20230746 | Antonia
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ams2 | remove NAS and TAS from artemis |
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ams2 | protein is unstable during G2 and M phase, partially stable during G1 and stable during S
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ams2 | protein stability: is stable during S phase, level increased |
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ams2 | protein stability: is unstable during G2 phase, level decreased OR possibly only synthesised during S phase? |
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ams2 | protein stability: is unstable during G1/M phase, level increased OR possibly only synthesised during S phase? |
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ams2 | protein stability: is degraded by the SCF ubiquitin ligase pathway |
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20018864 | Antonia
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ncs1 | promoter region lies in -1-130 region caact esp important |
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ncs1 | promoter for upregulation in response to calcium lies in -101-130 region |
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ncs1 | promoter for basal expression lies in -1-130 region |
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prz1 | binds caact in promoter region of ncs1 |
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19606215 | Antonia
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cnx1 | some confusing data regarding apoptosis. Notes in hardcopy paper | allele=lumenal_cnx1p(aa_del488-560)
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cnx1 | allele specifications may not be 100% correct |
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1563351 | Antonia
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MatPi? | expressed in response to nitrogen starvation and M factor in Pcells | IDA
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ste6 | MatPi? not expressed during N starvation and in presence of M factor in P cells | allele=deletion
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ras1 | MatPi? not expressed during N starvation and in presence of M factor in P cells | allele=deletion
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ras1 | MatPi? expressed during N starvation and in presence of M factor in P cells, not constitutively expressed | allele=ras1val17
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7975894 | Antonia
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promoter element | fig6&7 |
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8314086 | Antonia
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sxa2 | expressed in presence of p-factor |
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map2 | expressed in H- cells |
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18059475 | Antonia
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ste11 | annotate promoter proximal element FLEX1 and FLEXL1 to ste11, artemis |
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21960007
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mag1 | structure PDB ID 3S61 | according to authors, does not appear to match however
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1448087
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pyp2 | 552 bp 5' UTR |
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11470243
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fas2 | increased accumulation of see below | allele=H201(I1276T),annotation_extension=condition(at_high_temperature)
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fas2 | increased accumulation of see below | allele=H265(Q4Y),annotation_extension=condition(at_high_temperature)
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fas2 | increased accumulation of see below | allele=H518(I600N),annotation_extension=condition(at_high_temperature)
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fas2 | decreased accumulation of see below | allele=H201(I1276T),annotation_extension=condition(at_high_temperature)
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fas2 | decreased accumulation of see below | allele=H265(Q4Y),annotation_extension=condition(at_high_temperature)
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fas2 | decreased accumulation of see below | allele=H518(I600N),annotation_extension=condition(at_high_temperature)
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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
1448066
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- | asked for a term to describe HMW complex. Link to it - GO:0090424 |
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12905027
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SPAC3H1.10 | MOD requested: cadmium containing modified residue | residue=C173|
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19285552
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gpa1 | can probably migrate some terms to abnormal decrease in transcription/increase, see what midori says |
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9191271
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mfm1 | dbl check annotations, allele descr for phenotype annotation | has_regulation_target(PomBase:SPMTR.02))
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1644306 | http://oliver0.sysbiol.cam.ac.uk/pombe/curs/1b8ed217ce984ab5
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tnr3/thi1 | change FYPO terms so that extension is in term |
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tnr1 | increased 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)
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tnr1 | cellular response to vitamin b1 - which gene is this?? | IMP
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thi2 | gene expression: expressed in response to thiamine starvation. repressed in response to thiamine.... |
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/controlled_curation="term=gene expression, mRNA level; annotation_extension=during(GO:0036225); qualifier=increased; evidence=ECO:0000106; db_xref=1644306; date=20120509"
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/controlled_curation="term=gene expression, mRNA level; annotation_extension=during(GO:0071301); qualifier=absent; evidence=ECO:0000106; db_xref=1644306; date=20120509"
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/controlled_curation="term=gene expression, mRNA level; annotation_extension=in_response_to(CHEBI:16892); qualifier=increased; evidence=ECO:0000106; db_xref=1644306; date=20120509"
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/controlled_curation="term=gene expression, mRNA level; annotation_extension=in_response_to(CHEBI:17957); qualifier=decreased; evidence=ECO:0000106; db_xref=1644306; date=20120509"
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/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"
2878925 | http://curation.pombase.org/pombe/curs/462720c354cd7b67/
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pma mutant | normal ATPase activity | unknown, in vitro
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pma mutant | Normal enzyme in vitro response to Dio-9 | unknown, in vitro
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pma mutant | Normal enzyme in vitro response to DCCD N,N'-dicyclohexylcarbodiimide | unknown, in vitro
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pma mutant | Normal enzyme in vitro response to Miconazole | unknown, in vitro
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pma mutant | Normal enzyme in vitro response to DES diethylstilbestrol | unknown, in vitro
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pma mutant | Normal enzyme in vitro response to Suloctidil | unknown, in vitro
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pma mutant | Normal enzyme in vitro response to p-hydroxymercuribenzoate | unknown, in vitro
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pma mutant | Normal enzyme in vitro response to protamine sulfate | unknown, in vitro
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pma mutant | Normal enzyme in vitro response to decamethylene diguanidine | unknown, in vitro
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pma mutant | decreased cellular pH CGA - should this be decreased medium pH? | YE liquid
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8227198
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cyr1 | decreased cellular cAMP level following glucose stimulus | substrate quantification, glucose/glycerol + glucose added allele=git2-7
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cyr1 | decreased cellular cAMP level following glucose stimulus | substrate quantification, glucose/glycerol + glucose added, allele=git2-61
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cgs2 | increased cellular cAMP level following glucose stimulus | substrate quantification, glucose/glycerol + glucose added, allele=cgs2-2
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cyr1 | normal cellular cAMP level during glucose starvation | substrate quantification, allele=git2-7
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cyr1 | normal cellular cAMP level during glucose starvation | substrate quantification, allele=git2-61
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gpa2 | decreased cellular cAMP level during glucose starvation | substrate quantification, allele=git8-60
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gpa2 | decreased cellular cAMP level following glucose stimulus | substrate quantification, glucose/glycerol + glucose added, allele=git8-60
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hsp90 | decreased cellular cAMP level following glucose stimulus | substrate quantification, glucose/glycerol + glucose added, allele=git10-201
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git1 | decreased cellular cAMP level following glucose stimulus | substrate quantification, glucose/glycerol + glucose added, allele=git1-1
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git3 | decreased cellular cAMP level following glucose stimulus | substrate quantification, glucose/glycerol + glucose added, allele=git3-200
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git5 | decreased cellular cAMP level following glucose stimulus | substrate quantification, glucose/glycerol + glucose added, allele=git5-75
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git7 | decreased cellular cAMP level following glucose stimulus | substrate quantification, glucose/glycerol + glucose added, allele=git7-235
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git5 | increased cellular cAMP level during glucose starvation | substrate quantification, glucose/glycerol, allele=git5-75
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pka1 | increased cellular cAMP level during glucose starvation | substrate quantification, glucose/glycerol, allele=git6-261
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vht1 | dethiobiotin import into cell | IMP
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vht1 | biotin import into cell | IMP
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spac1b3.15c | biotin transmembrane transport | NOT, IGI to cerevisiae
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spac1b3.15c | dethiobiotin transmembrane transport | NOT, IGI to cerevisiae
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REQUEST CELLULAR RESPONSE TO BIOTIN STARVATION
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/controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to biotin starvation); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:12557275; date=20121107"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0072690); qualifier=present; evidence=ECO:0000106; db_xref=PMID:12557275; date=20121107"
from M - nothing wrong in this one, but I think if GO makes the name/synonym changes in SF 3584253, the MF annotations could change to GO:0000155 (now 'two-component sensor activity'; I suggested 'phosphorelay sensor kinase activity')
https://sourceforge.net/tracker/?func=detail&aid=3584253&group_id=36855&atid=440764
GHT6
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071333); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0009267); qualifier=decreased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071328); qualifier=decreased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to D-gluconate); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to glycerol); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
GHT5
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071333); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0009267); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071328); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to D-gluconate); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to glycerol); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
GHT2
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071333); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0009267); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071328); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to D-gluconate); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to glycerol); qualifier=decreased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
GHT1
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071333); qualifier=absent; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0009267); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071328); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to D-gluconate); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to glycerol); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
GHT3
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071333); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0009267); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071328); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to D-gluconate); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to glycerol); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
GHT4
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071333); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0009267); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071328); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to D-gluconate); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"
/controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to glycerol); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"=
http://curation.pombase.org/pombe/curs/eef07d879f4207d2
have asked about extensions
http://curation.pombase.org/pombe/curs/08562810fce65760#
|
rad3 | decreased level of phosphorylated H2A during S-phase | deletion, chip
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swi1 | H2A phosphorylation absent at mating type locus during S phase | deletion, chip
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swi3 | H2A phosphorylation absent at mating type locus during S phase | deletion, chip
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swi1 | increased level of phosphorylated h2a at rDNA during G2 | deletion, chip
|
swi1 | increased level of phosphorylated h2a at rDNA during S phase | deletion, chip
|
swi1 | increased level of phosphorylated h2a at tDNA during S phase | deletion, chip
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cds1 | increased level of phosphorylated h2a during cellular response to HU | deletion, chip
|
clr4 | decreased level of phosphorylated H2A at centromere otr | deletion, chip
|
swi6 | normal level of phosphorylated H2A at centromere otr | deletion, chip
|
clr4 | normal level of phosphorylated H2A at mating type locus | deletion, chip
|
swi6 | normal level of phosphorylated H2A at mating type locus | deletion, chip
|
clr4 | decreased level of phosphorylated H2A at subtelomere during S phase | deletion, chip
|
swi6 | decreased level of phosphorylated H2A at subtelomere during S-phase | deletion, chip
|
taz1 | normal level of phosphorylated H2A at subtelomere | deletion, chip
|
clr4 | decreased punctate nuclear localization | deletion, micro, assayed_using(PomBase:brc1)
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clr4 | normal protein localization to rDNA | deletion, chip, assayed_using(PomBase:brc1)
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rqh1 | increased level of phosphorylated h2a at rDNA | deletion, chip
|
ttp://curation.pombase.org/pombe/curs/86a759e366cff322/
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terms in session and send to author
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HTP gene expression data
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15004206 | for future ref
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19366728 | table 3 + gene expression omnibus GEOhashGSE14319 | for future ref
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