wiki:AntoniasCuratedPapers

Version 973 (modified by antonialock, 7 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
AntoniasDoubleMutants
AntoniasRNAmodsandmutants
https://sourceforge.net/apps/trac/pombase/wiki/CuratorTrainingPapers


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


20018864Antonia
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
cnx1some confusing data regarding apoptosis. Notes in hardcopy paperallele=lumenal_cnx1p(aa_del488-560)
cnx1allele specifications may not be 100% correct


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


7975894Antonia
promoter elementfig6&7


8314086Antonia
sxa2expressed in presence of p-factor
map2expressed in H- cells


18059475Antonia
ste11annotate promoter proximal element FLEX1 and FLEXL1 to ste11, artemis


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


1448087
pyp2552 bp 5' UTR


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


1448066
-asked for a term to describe HMW complex. Link to it - GO:0090424


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


19285552
gpa1can probably migrate some terms to abnormal decrease in transcription/increase, see what midori says


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


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
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"


1644306http://oliver0.sysbiol.cam.ac.uk/pombe/curs/1b8ed217ce984ab5
tnr3/thi1change FYPO terms so that extension is in term
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"


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)


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"


2878925http://curation.pombase.org/pombe/curs/462720c354cd7b67/
pma mutantnormal ATPase 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
pma mutant decreased cellular pH CGA - should this be decreased medium pH?YE liquid


7898433http://curation.pombase.org/pombe/curs/5964257cca6cfa69
uvi15gene expression, change in response to L-canavanine to during the above once the term is inartemis


10867006ste11 promoter


8227198
cyr1decreased cellular cAMP level following glucose stimulussubstrate quantification, glucose/glycerol + glucose added allele=git2-7
cyr1decreased cellular cAMP level following glucose stimulussubstrate quantification, glucose/glycerol + glucose added, allele=git2-61
cgs2increased cellular cAMP level following glucose stimulussubstrate quantification, glucose/glycerol + glucose added, allele=cgs2-2
cyr1normal cellular cAMP level during glucose starvationsubstrate quantification, allele=git2-7
cyr1normal cellular cAMP level during glucose starvationsubstrate quantification, allele=git2-61
gpa2decreased cellular cAMP level during glucose starvationsubstrate quantification, allele=git8-60
gpa2decreased cellular cAMP level following glucose stimulussubstrate quantification, glucose/glycerol + glucose added, allele=git8-60
hsp90decreased cellular cAMP level following glucose stimulussubstrate quantification, glucose/glycerol + glucose added, allele=git10-201
git1decreased cellular cAMP level following glucose stimulussubstrate quantification, glucose/glycerol + glucose added, allele=git1-1
git3decreased cellular cAMP level following glucose stimulussubstrate quantification, glucose/glycerol + glucose added, allele=git3-200
git5decreased cellular cAMP level following glucose stimulussubstrate quantification, glucose/glycerol + glucose added, allele=git5-75
git7decreased cellular cAMP level following glucose stimulussubstrate quantification, glucose/glycerol + glucose added, allele=git7-235
git5increased cellular cAMP level during glucose starvationsubstrate quantification, glucose/glycerol, allele=git5-75
pka1increased cellular cAMP level during glucose starvationsubstrate quantification, glucose/glycerol, allele=git6-261


8736869http://curation.pombase.org/pombe/curs/14f96251db4cbe9b
krp1decreased or abolished for R102A, same substrate for both annotations? otherwise add in a xenobiotic condition


9418887http://oliver0.sysbiol.cam.ac.uk/pombe/curs/b6bfec3d1b81e412
krp1normal protein processingcan I add a assayed_using?


12557275http://curation.pombase.org/pombe/curs/9569cc1253e3417a
vht1change IGI annotations to transmembrane transport and transport into cell
vht1dethiobiotin bindingIGI to cerevisiae
vht1dethiobiotin import into cellIMP
vht1biotin import into cellIMP
spac1b3.15cbiotin transmembrane transportNOT, IGI to cerevisiae
spac1b3.15cdethiobiotin transmembrane transportNOT, IGI to cerevisiae
REQUEST CELLULAR RESPONSE TO BIOTIN STARVATION

/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"

mpr1e6d7e22d7df32487

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


8346915http://curation.pombase.org/pombe/curs/8699a16a5d40e84b
ade2search inbox for no need to add substrates if they are implicit in the reaction


10735857http://curation.pombase.org/pombe/curs/495144e748000da3
ght3gluconate import (change existing term)IMP

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"=


9135083http://curation.pombase.org/pombe/curs/6ff4c9edff12167b


http://curation.pombase.org/pombe/curs/42b53662d27d7951
cuf1change nuclear protein accumulation to nuclear protein accumulation in response to copper


11729194http://curation.pombase.org/pombe/curs/0e75134c69a78468
pnk1nucleotide dephosphorylation involved in DNA repairIMP


12056900http://curation.pombase.org/pombe/curs/d23920dd53aeb0c5
pnk1nucleotide dephosphorylation involved in DNA repairIDA


11349150http://curation.pombase.org/pombe/curs/0afc32dc747285ae
pot1viable vegetative cells with circular(ized) chromosomesdeletion, gel
pot1G-rich strand telomeric DNA binding IDA


22978652http://curation.pombase.org/pombe/curs/0afc32dc747285ae
pot1G-rich strand telomeric DNA bindingIDA, inhibited_by(CHEBI:34653)


8065367http://curation.pombase.org/pombe/curs/0b84151023ead28b
cut8viable vegetative cell population should go to "small" colonieswt op


http://curation.pombase.org/pombe/curs/eef07d879f4207d2 have asked about extensions

http://curation.pombase.org/pombe/curs/e64102699ced97dc
need to talk to Val
http://curation.pombase.org/pombe/curs/8a0da77ab1315722/
txl1normal level of protein-ubiquitin conjugatesdeletion, gel elec
txc1normal level of protein-ubiquitin conjugatesdeletion, gel elec
http://curation.pombase.org/pombe/curs/08562810fce65760#
rad3decreased level of phosphorylated H2A during S-phasedeletion, chip
swi1H2A phosphorylation absent at mating type locus during S phasedeletion, chip
swi3H2A phosphorylation absent at mating type locus during S phasedeletion, chip
swi1increased level of phosphorylated h2a at rDNA during G2deletion, chip
swi1increased level of phosphorylated h2a at rDNA during S phasedeletion, chip
swi1increased level of phosphorylated h2a at tDNA during S phasedeletion, chip
cds1increased level of phosphorylated h2a during cellular response to HUdeletion, chip
clr4decreased level of phosphorylated H2A at centromere otrdeletion, chip
swi6normal level of phosphorylated H2A at centromere otrdeletion, chip
clr4normal level of phosphorylated H2A at mating type locusdeletion, chip
swi6normal level of phosphorylated H2A at mating type locusdeletion, chip
clr4decreased level of phosphorylated H2A at subtelomere during S phasedeletion, chip
swi6decreased level of phosphorylated H2A at subtelomere during S-phasedeletion, chip
taz1normal level of phosphorylated H2A at subtelomeredeletion, chip
clr4decreased punctate nuclear localizationdeletion, micro, assayed_using(PomBase:brc1)
clr4normal protein localization to rDNAdeletion, chip, assayed_using(PomBase:brc1)
rqh1increased level of phosphorylated h2a at rDNAdeletion, chip
http://curation.pombase.org/pombe/curs/4bd674ce652a4adc
terms in session
http://curation.pombase.org/pombe/curs/eef07d879f4207d2
terms in session
http://curation.pombase.org/pombe/curs/78331c9ee6d7b27a
terms in session
http://curation.pombase.org/pombe/curs/4ac217676e2be734
terms in session - NOTE BP needs glycosylation of glycoproteins general term (not known what step or what sugar)
http://curation.pombase.org/pombe/curs/74e71f74b286b84c
increased trehalose 6-p level, decreased trehalose level, or MF activity term? all during heat response
http://curation.pombase.org/pombe/curs/b6cb6d3911a0b608
terms in session
http://curation.pombase.org/pombe/curs/90f7e4d9459a5548
terms in session and send to author
http://curation.pombase.org/pombe/curs/f48d48d052e6ec31
terms in session and send to author
ttp://curation.pombase.org/pombe/curs/86a759e366cff322/
terms in session and send to author


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


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