| Version 1151 (modified by , 6 years ago) (diff) |
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HTPpapersgeneexpression
Papers needing ODA conversions
AntoniasDoubleMutants
AntoniasRNAmodsandmutants
AntoniasWeirdPhenotypes
https://sourceforge.net/apps/trac/pombase/wiki/CuratorTrainingPapers
| PMID:1783290 | Antonia | |
| K region (interval between mat2 and mat3) | deletion of this region increases meiotic recombination (between mat1 and his2) | K region deletion |
| 2900761 | Antonia |
| characterization of the genomic features in the mating type region |
| PMID:21357609 | Antonia |
| mutations in mitochondrial promoters affect transcription |
| 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 |
| 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 |
| 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 hip1 | slow cell growth | allele=dbl mutant |
| 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 |
| 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 |
| 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 |
| 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 |
| 7975894 | Antonia | |
| promoter element | fig6&7 |
| 8314086 | Antonia | |
| sxa2 | expressed in presence of p-factor | |
| map2 | expressed in H- cells |
| 18059475 | Antonia | |
| ste11 | annotate promoter proximal element FLEX1 and FLEXL1 to ste11, artemis |
| 21960007 | ||
| mag1 | structure PDB ID 3S61 | according to authors, does not appear to match however |
| 1448087 | ||
| pyp2 | 552 bp 5' UTR |
| 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:
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 | ||
| SPAC3H1.10 | MOD requested: cadmium containing modified residue | residue=C173| |
| 19285552 | ||
| gpa1 | can probably migrate some terms to abnormal decrease in transcription/increase, see what midori says |
| 9191271 | ||
| mfm1 | dbl check annotations, allele descr for phenotype annotation | has_regulation_target(PomBase:SPMTR.02)) |
| 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 | ||
| 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" |
| 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" |
| 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) |
| 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"
| 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 |
| 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 |
| 10867006 | ste11 promoter |
| 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 |
| 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 |
| 9418887 | http://oliver0.sysbiol.cam.ac.uk/pombe/curs/b6bfec3d1b81e412 | |
| krp1 | normal protein processing | can I add a assayed_using? |
| 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
| 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"=
| http://curation.pombase.org/pombe/curs/42b53662d27d7951 | |
| cuf1 | change nuclear protein accumulation to nuclear protein accumulation in response to copper |
| 8065367 | http://curation.pombase.org/pombe/curs/0b84151023ead28b | |
| cut8 | viable vegetative cell population should go to "small" colonies | wt op |
| http://curation.pombase.org/pombe/curs/08562810fce65760# |
| SO terms |
| http://curation.pombase.org/pombe/curs/1d6c5bf0855bd48b |
| waiting for GO term then need to curate paper |
| http://curation.pombase.org/pombe/curs/6faee029dd2c988c | |
| pap1 | have asked GO what enzyme term to use |
| missing annotations |
| http://oliver0.sysbiol.cam.ac.uk/pombe/curs/219e86a87274fe5f/ro/ |
| http://curation.pombase.org/pombe/curs/4f633d62f95cab65 |
| uncurated community curation session, pending fypo |
| TAS to mmi1 complex from this paper Pla1, Pab2, Rrp6 (or ref in paper) |
| http://curation.pombase.org/pombe/curs/5c6727a02c994591 |
| GO annotation issue #1152 and NTR alpha glucan synthase activity. Might want to move up all 1,3 and 1,4 glucan synthase activity terms to less specific term |
