https://sourceforge.net/apps/trac/pombase/wiki/CuratorTrainingPapers [wiki:OtherDirectAssay Papers needing ODA conversions] [[BR]] [wiki:WTemptyPapers Papers with WT info or no annotations] [[BR]] [wiki:AntoniasDoubleMutants] [[BR]] [wiki:AntoniasRNAmodsandmutants] [[BR]] https://sourceforge.net/apps/trac/pombase/wiki/CuratorTrainingPapers [[BR]] ||2900761||Antonia|| ||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-Mi||Phenotype: can conjugate but not undergo meiosis/sporulate||allele=Mifs15(del_nt43-129)|| ||mat1-Pi||Phenotype: can conjugate but not undergo meiosis/sporulate||allele=Piop7(del_nt19-357)|| ||mat1-Pc||Phenotype: can't conjugate||allele=Pcop5(del_nt17-480)|| ||mat1-Mc||Phenotype: can't conjugate||allele=Mcop7(del_nt19-546)|| ||mat1-Pc||severe reduction in spore formation||allele=deletion|| ||mat1-Pc||process: required for efficient meiosis||IMP, allele=deletion|| ||mat1-Mc||process: required for efficient meiosis||IMP, allele=deletion|| ||mat1-Pc||expression: constitutively expressed (low levels) (rich media)||IMP, allele=SP272(h+/h- meiotically competent diploid)|| ||mat1-Pc||expression: constitutively expressed (low levels) (rich media)||IMP, allele=SP720(fus1 deletion...capture as WT?)|| ||mat1-Mc||expression: constitutively expressed (low levels) (rich media)||IMP, allele=SP272(h+/h- meiotically competent diploid)|| ||mat1-Mc||expression: constitutively expressed (low levels) (rich media)||IMP, allele=SP720(fus1 deletion...capture as WT?)|| ||mat1-Pi||expression: not expressed (rich media)||IMP, allele=SP272(h+/h- meiotically competent diploid)|| ||mat1-Pi||expression: not expressed (rich media)||IMP, allele=SP720(fus1 deletion...capture as WT?)|| ||mat1-Mi||expression: not expressed (rich media)||IMP, allele=SP272(h+/h- meiotically competent diploid)|| ||mat1-Mi||expression: 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|| [[BR]] ||2328719||Antonia|| ||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))|| ||mat1-Pc||positive autoregulation of transcription in response to nitrogen starvation||allele=mat1-Pc-161()|| ||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))|| ||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))|| ||mat1-Pc||low constitutive expression in rich media||allele=H90(fus1 deletion)|| ||mat1-Pm||no constitutive expression in rich media||allele=H90(fus1 deletion)|| ||mat1-Pm||expression in response to nitrogen starvation is dependent on the presence of CL:0002674||annotation_extension=occurs_in(CL:0002675)|| ||mat1-Pc||upregulation in response to nitrogen starvation is '''not''' dependent on the presence of CL:0002674||annotation_extension=occurs_in(CL:0002675)|| ||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''' [[BR]] ||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?|| [[BR]] ||18077559|Antonia|| ||ams2 hip1||slow cell growth||allele=dbl mutant|| [[BR]] ||20230746||Antonia|| ||ams2|| remove NAS and TAS from artemis|||| ||ams2||protein is unstable during G2 and M phase, partially stable during G1 and stable during S|| ||ams2||protein stability: is stable during S phase, level increased|||| ||ams2||protein stability: is unstable during G2 phase, level decreased OR possibly only synthesised during S phase?|||| ||ams2||protein stability: is unstable during G1/M phase, level increased OR possibly only synthesised during S phase?|||| ||ams2||protein stability: is degraded by the SCF ubiquitin ligase pathway|||| [[BR]] ||20018864||Antonia|| ||ncs1||promoter region lies in -1-130 region caact esp important|||| ||ncs1||promoter for upregulation in response to calcium lies in -101-130 region|||| ||ncs1||promoter for basal expression lies in -1-130 region|||| ||prz1||binds caact in promoter region of ncs1|||| [[BR]] ||19606215||Antonia|| ||cnx1||some confusing data regarding apoptosis. Notes in hardcopy paper||allele=lumenal_cnx1p(aa_del488-560)|| ||cnx1||allele specifications may not be 100% correct|||| [[BR]] ||1563351||Antonia|| ||MatPi||expressed in response to nitrogen starvation and M factor in Pcells||IDA|| ||ste6||MatPi not expressed during N starvation and in presence of M factor in P cells||allele=deletion|| ||ras1||MatPi not expressed during N starvation and in presence of M factor in P cells||allele=deletion|| ||ras1||MatPi expressed during N starvation and in presence of M factor in P cells, not constitutively expressed||allele=ras1val17|| [[BR]] ||7975894||Antonia|| ||promoter element||fig6&7|||| [[BR]] ||8314086||Antonia|| ||sxa2||expressed in presence of p-factor|||| ||map2||expressed in H- cells|||| [[BR]] ||18059475||Antonia|| ||ste11||annotate promoter proximal element FLEX1 and FLEXL1 to ste11, artemis|||| [[BR]] ||21960007|| ||mag1||structure PDB ID 3S61||according to authors, does not appear to match however|| [[BR]] ||1448087|| ||pyp2||552 bp 5' UTR|||| [[BR]] ||11470243|| ||fas2||increased accumulation of see below||allele=H201(I1276T),annotation_extension=condition(at_high_temperature)|| ||fas2||increased accumulation of see below||allele=H265(Q4Y),annotation_extension=condition(at_high_temperature)|| ||fas2||increased accumulation of see below||allele=H518(I600N),annotation_extension=condition(at_high_temperature)|| ||fas2||decreased accumulation of see below||allele=H201(I1276T),annotation_extension=condition(at_high_temperature)|| ||fas2||decreased accumulation of see below||allele=H265(Q4Y),annotation_extension=condition(at_high_temperature)|| ||fas2||decreased accumulation of see below||allele=H518(I600N),annotation_extension=condition(at_high_temperature)|| For the 3 mutants above: [[BR]] 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 [[BR]] 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 [[BR]] ||1448066|| ||-||asked for a term to describe HMW complex. Link to it - GO:0090424|||| [[BR]] ||12905027|| ||SPAC3H1.10||MOD requested: cadmium containing modified residue||residue=C173| [[BR]] ||19285552|| ||gpa1||can probably migrate some terms to abnormal decrease in transcription/increase, see what midori says|||| [[BR]] ||9191271|| ||mfm1||dbl check annotations, allele descr for phenotype annotation||has_regulation_target(PomBase:SPMTR.02))|| [[BR]] ||8321236||http://oliver0.sysbiol.cam.ac.uk/pombe/curs/169dc6a662075c56/gene/1|| ||frp1||abolished ferric iron reductase activity, not req yet||allele=G-100(W314->opal)|| ||||waiting reply from val on paper|||| [[BR]] ||7565608||http://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" [[BR]] ||1644306||http://oliver0.sysbiol.cam.ac.uk/pombe/curs/1b8ed217ce984ab5|| ||tnr3/thi1||change FYPO terms so that extension is in term|||| ||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)|| ||tnr1||cellular response to vitamin b1 - which gene is this?? || IMP|| ||thi2||gene 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" || [[BR]] ||8675019||http://oliver0.sysbiol.cam.ac.uk/pombe/curs/4b0970d0e5484486/|| ||tnr1||which gene is this? FYPO:0000825 northern ev||allele=tnr1-18(unknown), condition=PCO:0000014, annotation_extension=assayed_using(SPAC17A2.01) || [[BR]] ||2249257||http://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" [[BR]] ||2878925||http://curation.pombase.org/pombe/curs/462720c354cd7b67/|| ||pma mutant||normal ATPase activity ||unknown, in vitro|| ||pma mutant||Normal enzyme in vitro response to Dio-9 || unknown, in vitro || ||pma mutant||Normal enzyme in vitro response to DCCD N,N'-dicyclohexylcarbodiimide||unknown, in vitro || ||pma mutant||Normal enzyme in vitro response to Miconazole||unknown, in vitro || ||pma mutant||Normal enzyme in vitro response to DES diethylstilbestrol||unknown, in vitro || ||pma mutant||Normal enzyme in vitro response to Suloctidil ||unknown, in vitro || ||pma mutant||Normal enzyme in vitro response to p-hydroxymercuribenzoate ||unknown, in vitro || ||pma mutant||Normal enzyme in vitro response to protamine sulfate ||unknown, in vitro || ||pma mutant||Normal enzyme in vitro response to decamethylene diguanidine||unknown, in vitro || ||pma mutant ||decreased cellular pH CGA - should this be decreased medium pH?||YE liquid|| [[BR]] ||7898433||http://curation.pombase.org/pombe/curs/5964257cca6cfa69|| ||uvi15||gene expression, change in response to L-canavanine to during the above once the term is in||artemis|| [[BR]] ||10867006||ste11 promoter|| [[BR]] ||8227198|| ||cyr1||decreased cellular cAMP level following glucose stimulus||substrate quantification, glucose/glycerol + glucose added allele=git2-7|| ||cyr1||decreased cellular cAMP level following glucose stimulus||substrate quantification, glucose/glycerol + glucose added, allele=git2-61|| ||cgs2||increased cellular cAMP level following glucose stimulus||substrate quantification, glucose/glycerol + glucose added, allele=cgs2-2|| ||cyr1||normal cellular cAMP level during glucose starvation||substrate quantification, allele=git2-7|| ||cyr1||normal cellular cAMP level during glucose starvation||substrate quantification, allele=git2-61|| ||gpa2||decreased cellular cAMP level during glucose starvation||substrate quantification, allele=git8-60|| ||gpa2||decreased cellular cAMP level following glucose stimulus||substrate quantification, glucose/glycerol + glucose added, allele=git8-60|| ||hsp90||decreased cellular cAMP level following glucose stimulus||substrate quantification, glucose/glycerol + glucose added, allele=git10-201|| ||git1||decreased cellular cAMP level following glucose stimulus||substrate quantification, glucose/glycerol + glucose added, allele=git1-1|| ||git3||decreased cellular cAMP level following glucose stimulus||substrate quantification, glucose/glycerol + glucose added, allele=git3-200|| ||git5||decreased cellular cAMP level following glucose stimulus||substrate quantification, glucose/glycerol + glucose added, allele=git5-75|| ||git7||decreased cellular cAMP level following glucose stimulus||substrate quantification, glucose/glycerol + glucose added, allele=git7-235|| ||git5||increased cellular cAMP level during glucose starvation||substrate quantification, glucose/glycerol, allele=git5-75|| ||pka1||increased cellular cAMP level during glucose starvation||substrate quantification, glucose/glycerol, allele=git6-261|| [[BR]] ||8736869||http://curation.pombase.org/pombe/curs/14f96251db4cbe9b|| ||krp1||decreased or abolished for R102A, same substrate for both annotations? otherwise add in a xenobiotic condition|| [[BR]] ||9418887||http://oliver0.sysbiol.cam.ac.uk/pombe/curs/b6bfec3d1b81e412|| ||krp1||normal protein processing||can I add a assayed_using?|| [[BR]] ||12557275||http://curation.pombase.org/pombe/curs/9569cc1253e3417a|| ||vht1||change IGI annotations to transmembrane transport and transport into cell|||| ||vht1||dethiobiotin binding||IGI to cerevisiae|| ||vht1||dethiobiotin import into cell||IMP|| ||vht1||biotin import into cell||IMP|| ||spac1b3.15c||biotin transmembrane transport||NOT, IGI to cerevisiae|| ||spac1b3.15c||dethiobiotin transmembrane transport||NOT, 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" ||mpr1||e6d7e22d7df32487|| 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 [[BR]] ||8346915||http://curation.pombase.org/pombe/curs/8699a16a5d40e84b|| ||ade2||search inbox for no need to add substrates if they are implicit in the reaction|| 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"= [[BR]] ||9135083||http://curation.pombase.org/pombe/curs/6ff4c9edff12167b|| [[BR]] ||http://curation.pombase.org/pombe/curs/42b53662d27d7951|| ||cuf1||change nuclear protein accumulation to nuclear protein accumulation in response to copper|| [[BR]] ||8065367||http://curation.pombase.org/pombe/curs/0b84151023ead28b|| ||cut8||viable vegetative cell population should go to "small" colonies||wt op|| [[BR]] http://curation.pombase.org/pombe/curs/eef07d879f4207d2 have asked about extensions ||http://curation.pombase.org/pombe/curs/08562810fce65760#|| ||SO terms|| ||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/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/f48d48d052e6ec31|| ||terms in session and send to author|| ||http://curation.pombase.org/pombe/curs/548cabd71c9a6463/|| ||cki1||replace chebi text with termID|||| [[BR]] ||http://curation.pombase.org/pombe/curs/ce75498c19ea15fb|| ||cys11||decreased cysteine synthase activity ||deletion, enzyme assay|| ||cys2||decreased cysteine synthase activity ||cys2-1(G411D), enzyme assay|| ||leu1||increased cysteine synthase activity ||leu1-, enzyme assay|| ||http://curation.pombase.org/pombe/curs/545c8d5d5cd1fec0|| ||terms in session|| ||http://curation.pombase.org/pombe/curs/fa30fa9e2e0880e6|| ||gea1||normal vacuolar fusion duringhypotonic stress ||diploid, microscopy|| ||gea1||decreased protin localization to cell septum ||diploid, microscopy, asayed using eng1|| [[BR]] ||HTP gene expression data|| ||15004206||||for future ref|| ||19366728||table 3 + gene expression omnibus GEOhashGSE14319||for future ref|| [[BR]] ||missing annotations|| ||http://oliver0.sysbiol.cam.ac.uk/pombe/curs/219e86a87274fe5f/ro/||