wiki:AntoniasCuratedPapers

Version 709 (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
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


17384198http://curation.pombase.org/pombe/curs/42b53662d27d7951
other assaysRNA protection assay or transcript quantification assay


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


22017871http://curation.pombase.org/pombe/curs/4d5512a5dc8ea4bc

Phenotypes:

ubr1increased protein level during cellular response to hypoxiaallele=deletion,assayed_using(sre1 precursor)
ubr1increased protein level during cellular response to hypoxiaallele=deletion,assayed_using(PR:000028992)
ubr1increased protein level during cellular response to oxygenallele=deletion,assayed_using(PR:000028992)
rhp6increased protein level during cellular response to hypoxiaallele=deletion,assayed_using(PR:000028992)
rhp6normal protein level during cellular response to hypoxiaallele=deletion,assayed_using(sre1 precursor)
rhp6increased protein level during cellular response to oxygenallele=deletion,assayed_using(PR:000028992)
sre1 | ubr11 normal protein level during cellular response to hypoxiaallele=sre1-N(recheck, cellpress down atm), allele=ubr11-delta,assayed_using(PR:000028992)
sre1 | ubr11 normal protein level during cellular response to oxygenallele=sre1-N(recheck, cellpress down atm), allele=ubr11-delta,assayed_using(PR:000028992)
sre1 normal protein level during cellular response to hypoxiaallele=sre1-N(recheck, cellpress down atm),assayed_using(PR:000028992)
sre1 | ofd1increased protein level during cellular response to oxygenallele=ofd1delta, allele=sre1-N, assayed_using(PR:000028992)
sre1 | ofd1increased protein level during cellular response to hypoxiaallele=ofd1delta, allele=sre1-N, assayed_using(PR:000028992)
ubr1 | ofd1increased protein level during cellular response to oxygenallele=ofd1delta, allele=ubr1delta, assayed_using(PR:000028992)
ubr1 | ofd1increased protein level during cellular response to hypoxiaallele=ofd1delta, allele=ubr1delta, assayed_using(PR:000028992)
ubr1 | nro1increased protein level during cellular response to oxygenallele=nro1delta, allele=ubr1delta, assayed_using(PR:000028992)
ubr1 | nro1increased protein level during cellular response to hypoxiaallele=nro1delta, allele=ubr1delta, assayed_using(PR:000028992)
ofd1increased protein level during cellular response to oxygenallele=ofd1delta, assayed_using(PomBase:SPAC222.11), NORTHERN
nro1decreased RNA level during cellular response to hypoxiaallele=deleteion, assayed using(PomBase:SPAC222.11), northern
nro1normal RNA level during cellular response to hypoxiaallele=deleteion, assayed using(PomBase:SPBC19C2.09), northern
ofd1decreased protein binding during cellular response to hypoxiaallele=H142A, assayed_using(PomBase:SPCC4B3.07)
ofd1overexpressed ofd1 C terminal domain -> decreased binding of sre1 to hem13 (chip assay)

Processes:

general:have requested cellular response to oxygen use TG after I get this
ofd1negative regulation of sterol regulatory element DNA bindingannotation_extension=requires_sequence_feature(Pfam:13640) | annotation_extension=happens_during(cellular response to oxygen
nro1+ve reg of cellular response to hypoxiaIDA


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?


10792724http://curation.pombase.org/pombe/curs/a525406360ac556a
sxa2change abnormal protein modification to protein processingassayed using itself
sxa2put in inactivated pfactor in the extension


22840777http://curation.pombase.org/pombe/curs/f94801dfb551d839
pap1normal RNA level during cellular response to Purvalanol A allele=deletion, annotation_extension=assayed_using(PomBase:SPCC663.03), RT-PCR
SPBC530.05normal RNA level during cellular response to purvalanol Adeletion, quant pCr, assayed using pmd1
SPBC530.08 normal cell growth on Purvalanol Adeletion, yes, standard temp, agar plates
SPBC16G5.16 normal cell growth on Purvalanol Adeletion, yes, standard temp, agar plates
SPBC1773.16C normal cell growth on Purvalanol Adeletion, yes, standard temp, agar plates
SPBC1773.12 normal cell growth on Purvalanol Adeletion, yes, standard temp, agar plates
SPAPB24D3.01 normal cell growth on Purvalanol Adeletion, yes, standard temp, agar plates
SPAC17C9.16cnormal cellular response to Purvalanol Adeletion, yes, normal temp, agar
SPBC36.03cnormal cellular response to Purvalanol Adeletion, yes, normal temp, agar


19171118http://curation.pombase.org/pombe/curs/881f48fa75b1371a
sod2normal cellular response to lithiumstandard temp, liquid, LiCl? added, MMP163A, P183A, D298N, D389N, E390Q, E392Q, E397Q
sod2normal cellular response to lithiumstandard temp, agar, LiCl? added, MMT142S, P146S, P146D, P146K, P163A, D298N, D389N, E390Q, E392Q, E397Q


16502473http://curation.pombase.org/pombe/curs/dad3b136d74916c1/
sib1normal cell growth during iron starvationdeletion


19734666http://curation.pombase.org/pombe/curs/35b5b191ed2039f2, cucl2 added
vma1decreased cellular glutamine levelallele=deletion, yes, cucl2 added
vma1decreased cellular valine levelallele=deletion, yes, cucl2 added
vma1decreased cellular lysine levelallele=deletion, yes, cucl2 added
vma1decreased cellular histidine levelallele=deletion, yes, cucl2 added
vma1decreased cellular arginine levelallele=deletion, yes, cucl2 added
vma1normal vacuolar cysteine levelallele=deletion, yes, cucl2 added
vma1increased vacuolar glutamate levelallele=deletion, yes, cucl2 added
vma1decreased vacuolar glutamine levelallele=deletion, yes, cucl2 added


15075270http://curation.pombase.org/pombe/curs/9a4ed1603d089abe
liz1pantothenate import into cellIGI to cerevisiae like the MF terms
liz1decreased pantothenate import into cellallele=deletion
liz1increased pantothenate import into cellwt overexpressed
liz1pantothenate import into cellIMP


12557275http://curation.pombase.org/pombe/curs/9569cc1253e3417a
vht1change IGI annotations to transmembrane transport and transport into cell
vht1dethiobiotin bindingIGI to cerevisiae
vht1absent biotin importallele=deletion
vht1increased biotin importwt overexpressed
vht1biotin transmembrane transportIMP, annotation_extension=inhibited_by(CHEBI:3259)
vht1dethiobiotin transmembrane transportIMP,
vht1NEED TO REQUEST dethiobiotin import into cellIMP
vht1biotin import into cellIMP
vht1inviableallele=deletion, biotin absent, mm, standard temp, agar
vht1inviableallele=deletion, limited biotin aded, mm, standard temp, agar
vht1decreased growthallele=deletion, biotin added, mm, standard temp, agar
vht1inviableallele=deletion, limited desthiobiotin added, mm, standard temp, agar
vht1normal growthallele=deletion, desthiobiotin added, mm, standard temp, agar
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"


12557275http://curation.pombase.org/pombe/curs/947219ec962a1b36
nic1high affinity nickel cation transmembrane transporter activityannotation_extension=inhibited_by(CHEBI:48828)IMP


22869600http://curation.pombase.org/pombe/curs/086fa578860a41d0
seg1even distribution of proteins normally concentrated at the cell tip throughout the cortex/plasma membrane (child of abnormal protein localization to cell cortex)allele= glutamine rich domain and polybasic C-terminus 1-296
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

11071923http://curation.pombase.org/pombe/curs/6a65148752d79293
int6elongated in response to caffeinedeletion, caffeine added, yes, microscopy
int6multiseptate in response to caffeinedeletion, caffeine added, yes, microscopy
int6lysed cells in response to caffeinedeletion, yes, agar, caffeine added, microscopy


9852154http://curation.pombase.org/pombe/curs/67631dafe77debd1
plo1regulation of spindle assembly involved in mitosischange in session, need to term request


14008http://curation.pombase.org/pombe/curs/cc0a2203f689cfc8
hpt1normal adenine importpur1, substance quant
hpt1decreased guanine importpur1, substance quant
apt1decreased adenine importdap1, substance quant
apt1normal guanine importdap1, substance quant
apt1increased level of 5-Phosphoribosyl diphosphate CHEBI:17111dap1, substance quant
hpt1increased level of 5-Phosphoribosyl diphosphate CHEBI:17111pur1, substance quant


20306http://curation.pombase.org/pombe/curs/641e9af49e65dc1e/
apt1requested from chebi tetrasodium pyrophosphatereplace ID in extension


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


1293882http://curation.pombase.org/pombe/curs/514dd7a2a9dcca89
mae1succinate:hydrogen symporter activity requested from GO


2076550http://curation.pombase.org/pombe/curs/77cbd4768ce15b4e
swi4-1 increased amount of hetrothallic H+ cells electrophoresis
swi4-1 mating cassette duplicationselectrophoresis


1317550http://curation.pombase.org/pombe/curs/722b74f950617459
swi4-1 increased amount of hetrothallic H+ cells electrophoresis
swi4-1 mating cassette duplicationselectrophoresis


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/