wiki:MidoriCuratedPapers

Version 55 (modified by gomidori, 9 years ago) (diff)

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transferred from CuratorTrainingPapers

Additions that will require new curation sessions (longer-term)

21813639open new session to add these when supported
mcb1GO:0005737extension: throughout cell cycle (see nuclear pore/PMID:20970342 above)
mcb1GO:0005654extension: throughout cell cycle
mcb1GO:0000790extension: throughout cell cycle
mcb1-chk1 genetic interactionalleles OP-mcb1+chk1-deletion, mcb1-D2+chk1-deletion; mcb1-D22+chk1-deletionOP-mcb1+chk1-del phenotype small cells (FYPO:23), abnormal nuc morph (FYPO:62)
mcb1-rad3 genetic interactionalleles OP-mcb1+rad3-deletion, mcb1-D2+rad3-deletion; mcb1-D22+rad3-deletionOP-mcb1+rad3-del phenotype small cells (FYPO:23), abnormal nuc morph (FYPO:62)


20929775open new session to add these when supported
hht1,hht2,hht3all 3 T3A (triple mutant)phenotype decreased prot loc to cen (extension: Ark1); lagging chromosomes (qualifier=low expressivity)
hta1,hta2both S121A (triple mutant)phenotype decreased prot loc to cen (extension: Ark1); lagging chromosomes (qualifier=low expressivity)
hht1,hht2,hht3,sgo2delall 3 hht T3A + sgo2del (quadruple mutant)phenotypes abolished loc to cen (ext Ark1); lagging chromosomes (qualifier=high expressivity)
hht1,hht2,hht3, hta1,hta2all 3 H3 T3A, both H2 S121A (quintuple mutant)phenotypes abolished loc to cen (ext Ark1); lagging chromosomes (qualifier=high expressivity)
hht1,hht2,hht3all 3 T3A (triple mutant)genetic interaction synthetic lethal sgo2deletion
hht1,hht2,hht3, hta1,hta2all 3 H3 T3A, both H2 S121A (quintuple mutant)genetic interaction synthetic lethal
hht1,hht2,hht3, hta1,hta2all 3 H3 T3A, both H2 S121A (quintuple mutant) genetic interaction synthetic lethal
genetic interactionhrk1, swi6"asynthetic"; check for old same-pathway GO IGI
hht1,hht2,hht3all 3 T3A (triple mutant)genetic interaction "asynthetic" with hrk1deletion
Hrk1-Bir1physical interactionBIR domain of Bir1 (Pfam:PF00653)
hrk1 bub1 genetic interactionalleles hrk1 deletion; bub1-KD (kinase dead, K762R,D900N)phenotype slow growth
hrk1 sgo2 genetic interactionalleles both deletionphenotype slow growth
pds5 bub1 genetic interactionalleles pds5 deletion; bub1-KD (kinase dead, K762R,D900N)phenotype slow growth
pds5 sgo2 genetic interactionalleles both deletionphenotype slow growth
swi6 sgo2 genetic interactionalleles both deletionphenotype slow growth


21620704open new session to add these when supported
dip1 wsp1 genetic intalleles both deletionphenotypes: abnormal protein localization to actin cortical patch (crn1), abolished actin cortical patch internalization
how on earth to annotate anything based on figure 6?


PMID:21971174new session for these
cdt1 allele=noname(overexpression) mcm6-S1(E824G, D825N) normal ds break repair (FYPO:new)
cdc18 allele=noname(overexpression) mcm6-S1(E824G, D825N) normal ds break repair (FYPO:new)
cig2delta(deletion) sup) mcm6-S1(E824G, D825N) normal ds break repair (FYPO:new)


PMID:8895665new session
orc1 cdc30-4(unknown)update FYPO:217 evidence to PFGE when available
orc1/cdc30-4(unknown) + cdc18-K46(unknown) double mutantFYPO:173 ev:microscopy


PMID:1454522 new session
mcm4 cdc21noname(unknown)FYPO:786 change 'other' evidence to plasmid maintenance assay when in ECO


PMID:6887244 long-term note (new session)
additional note3 of 13 cold-sensitive mutants curated; if someone can figure out what genes the other 10 correspond to, we can annotate a few more phenotypes


PMID:8298187new session? or not in tool?
noteadd mcm2 allele synonym nda1-376 = nda1-KM376; also nda1delta = mcm2delta, nda4delta = mcm5delta


PMID:1934126new session
cdc25-22(unknown) wee1-50(unknown) double mutantFYPO:681 same as cdc25-22(unknown) single mutant
cdc25-22(unknown) cdc2-1w(unknown) double mutantFYPO:681 same as cdc25-22(unknown) single mutant
cdc25-22(unknown) adh.nim1(overexpresssion) double mutantFYPO:681 same as cdc25-22(unknown) single mutant
cdc25-22(unknown) wee1-50(unknown) win1noname(unknown) triple mutantFYPO:681 same as cdc25-22(unknown) single mutant
cut1noname(unknown) cut2noname(unknown) double mutantFYPO:681 ev: microscopy


PMID:7865880 new session
allele=mis1-64(unknown),condition=PCO:0000005FYPO:786 change 'other' evidence to plasmid maintenance assay when in ECO
allele=mis1-223(unknown),condition=PCO:0000005FYPO:786 change 'other' evidence to plasmid maintenance assay when in ECO
allele=mis3-224(unknown),condition=PCO:0000005,condition=PCO:0000004FYPO:786 change 'other' evidence to plasmid maintenance assay when in ECO
allele=mis4-242(unknown),condition=PCO:0000005FYPO:786 change 'other' evidence to plasmid maintenance assay when in ECO
allele=mis5-268(unknown),condition=PCO:0000005FYPO:786 change 'other' evidence to plasmid maintenance assay when in ECO
allele=mis6-302(unknown),condition=PCO:0000005FYPO:786 change 'other' evidence to plasmid maintenance assay when in ECO
allele=mis10-421(unknown),condition=PCO:0000005FYPO:786 change 'other' evidence to plasmid maintenance assay when in ECO
prp2 allele=mis11-453(unknown),condition=PCO:0000005FYPO:786 change 'other' evidence to plasmid maintenance assay when in ECO
allele=mis12-537(unknown),condition=PCO:0000005,condition=PCO:0000004FYPO:786 change 'other' evidence to plasmid maintenance assay when in ECO
allele=mis5-268(unknown),condition=PCO:0000004FYPO:217 change 'other' evidence to PFGE when in ECO
mcm6 allele=mis5-268(unknown) + mcm4 cdc21noname(unknown)fypo:316 ev: cell growth
other stuffmis2, mis2 mis8, mis9 all apparently uncloned, so don't know which gene they correspond to
mis2 ?geneFYPO:786 ev: plasmid maint assay (or "other" if still waiting for ECO)allele=mis2-87(unknown),condition=PCO:0000005,condition=PCO:0000004 | allele=mis2-197(unknown),condition=PCO:0000004
mis7 ?geneFYPO:786 ev: plasmid maint assay (or "other" if still waiting for ECO)allele=mis7-322(unknown),condition=PCO:0000005
mis8 ?geneFYPO:786 ev: plasmid maint assay (or "other" if still waiting for ECO)allele=mis8-341(unknown),condition=PCO:0000005,condition=PCO:0000004
mis9 ?geneFYPO:786 ev: plasmid maint assay (or "other" if still waiting for ECO)allele=mis9-356(unknown),condition=PCO:0000005


PMID:8631307open new session to add these when supported
mcm4GO:0005634 extension: throughout cell cycle
cdc21-M68(unknown) cdc2-3w(unknown) double mutantFYPO:609 ev: microscopy
cdc21-M68(unknown) mcm4 C-terminus overexpression [note: overexp piece from BamHI site -- need position -- to endfypo:49
cdc21-M68(unknown) rad1noname(unknown) double mutantFYPO:23 FYPO:337 both ev: microscopy


PMID:19197239new session
top1delta tdp1deltaFYPO: sensitive to camptothecin ev. cell growth


PMID:8838655new session
mcm2GO:0005634extension: throughout cell cycle
mcm5GO:0005634extension: throughout cell cycle
mcm2FYPO:0000217upgrade evidence to PFGE when in ECO & canto
mcm2FYPO:0001133upgrade evidence to PFGE when in ECO & canto
mcm5FYPO:0000217upgrade evidence to PFGE when in ECO & canto
mcm5FYPO:0001133upgrade evidence to PFGE when in ECO & canto


PMID:12136010new session
tsc1 leu1fypo:46; ev cell growth assay; cond. limiting leu
tsc1 ade2fypo:46; ev cell growth assay; cond. limiting ade
tsc2 leu1fypo:46; ev cell growth assay; cond. limiting leu
tsc2 ade2fypo:46; ev cell growth assay; cond. limiting ade
tsc1 tsc2fypo:46; ev cell growth assay; cond. limiting ade


PMID:9383050lots of mcm2 alleles done with one on chromosome, another on plasmid (cells otherwise haploid)
mcm2 allele on chromosome/allele on plasmidFYPO ID, high tempFYPO ID, normal temp (32, semi-restrictive)
cdc19-P1/mcm2+fypo:47 normal cell growthfypo:47
cdc19-P1/mcm2-M1fypo:49 inviablefypo:49, fypo:299 microcolony formation, fypo:5 abn. cell morph.
cdc19-P1/mcm2-M2fypo:49fypo:49, fypo:299, fypo:5
cdc19-P1/mcm2-M3fypo:49fypo:49, fypo:299, fypo:5
cdc19-P1/mcm2-M5fypo:49fypo:49, fypo:299, fypo:5
cdc19-P1/mcm2-M6fypo:49fypo:47
cdc19-P1/mcm2-M7fypo:47fypo:46 slow cell growth
cdc19-P1/mcm2-M8fypo:49fypo:46
cdc19-P1/mcm2-M9fypo:49fypo:49, fypo:299, fypo:5
cdc19-P1/mcm2-M10fypo:49fypo:49, fypo:299, fypo:5
cdc19-P1/cdc19-P1fypo:49n/a
cdc19-P1/nda1-KM376fypo:47n/a
cdc19-P1/mcm2-D1fypo:47fypo:47
cdc19-P1/mcm2-D2fypo:47fypo:47
cdc19-P1/mcm2-D3fypo:47fypo:47
cdc19-P1/mcm2-D4fypo:49fypo:49, fypo:299, fypo:5
cdc19-P1/mcm2-D6fypo:49fypo:46
cdc19-P1/mcm2-D7fypo:49fypo:49, fypo:299, fypo:5
cdc19-P1/mcm2-D8fypo:49fypo:46
cdc19-P1/mcm2-D9fypo:49fypo:47
cdc19-P1/mcm2-D10fypo:49fypo:46
wt or deletion setviable at 32dg? (with mcm2 allele of interest overexpressed)
chromosome/plasmidfypo ID, normal temp
mcm2+/mcm2-M1fypo:47
mcm2+/mcm2-M2fypo:47
mcm2+/mcm2-M3fypo:47
mcm2+/mcm2-M5fypo:47
mcm2+/mcm2-M6fypo:47
mcm2+/mcm2-M7fypo:47
mcm2+/mcm2-M8fypo:47
mcm2+/mcm2-M9fypo:47
mcm2+/mcm2-M10fypo:47
mcm2+/mcm2-D1fypo:47
mcm2+/mcm2-D2fypo:47
mcm2+/mcm2-D3fypo:47
mcm2+/mcm2-D4fypo:47
mcm2+/mcm2-D6fypo:47
mcm2+/mcm2-D7fypo:47
mcm2+/mcm2-D8fypo:47
mcm2+/mcm2-D9fypo:47
mcm2+/mcm2-D10fypo:47
mcm2delta/mcm2+fypo:47
mcm2delta/mcm2-M6fypo:49
mcm2delta/mcm2-M7fypo:47
mcm2delta/mcm2-M8fypo:49
mcm2delta/cdc19-P1fypo:47
mcm2delta/mcm2-D1fypo:47
mcm2delta/mcm2-D2fypo:47
mcm2delta/mcm2-D3fypo:47
gene expression complexities
mcm2-M7, D1, D2, D3 and wt alleleslevel of expression from plasmid with nmt promoter much higher with cdc19-P1 on chromosome than with mcm2+ on chr
Mcm2 protein nearly same throughout cell cycle; modest decrease in G2could use artemis gene exp syntax, but don't have a"throughout cell cycle" GO term or extension
ordinary double mutant phenotypes
mcm2 cdc19-P1, mcm4+ overexpslow growth; fypo:150; fypo:614 facsnormal temp
mcm2 cdc19-P1, mcm5+ overexpslow growth; fypo:150; fypo:614 facsnormal temp
mcm2 cdc19-P1, mcm6+ overexpslow growth; fypo:150; fypo:614 facsnormal temp
mcm2 cdc19-P1, cdc6 poldelta-ts1slow cell growth, elong cells, curved cells; normal temp 25 or 29; at 32 dg branched cells, t-shaped cells, inviable high temp (tho 32 is top of PCO "normal" range)
mcm2 cdc19-P1, cdc1-7slow cell growth, elong cells, curved cells; normal temp 25 or 29; at 32 dg branched cells, t-shaped cells, inviable high temp (tho 32 is top of PCO "normal" range)
mcm2 cdc19-P1, cdc18-K46inviable high temp (done at 32, top of PCO "normal" range)


PMID:9658174
gene expression - Mcm2, Mcm4, Mcm5, Mcm6protein levels constant throughout cell cycle (ev: western)
annotated physical interactionsno change throughout cell cycle
negative resultno physical interaction between Mcms and Cdc18


PMID:9705504
gene expression - Mcm3protein level constant throughout cell cycle (ev: western)
GO mcm3 nucleus 5634 IDAextension: throughout cell cycle
mcm3-mcm5 phys int "tight"what to do about interaction strength/affinity?


PMID:9914167
mcm2 cdc19-P1FYPO:848 change 'other' evidence to PFGE when in ECO
mcm2 cdc19-P1FYPO:1386 change 'other' evidence to staining when in ECO
mcm*delta::his3+ (* = 2, 4, 5, or 6)deletion phenotype is that of haploid spore derived from mcm*delta::his3+/mcm*+ diploid; detected protein presumed to be residual from diploid
mcm2delta::his3+/mcm2(cdc19-P1) diploidcouldn't construct; hypothesize that ts mcm2 haploinsufficient
mcm4delta::his3+/mcm4(cdc21-M68) constructed & sporulated at 36dgmcm4delta::his3+ spores: DNA synthesis abolished (didn't enter S phase); 75% abnormal nuclear or cell division


PMID:10388806
many, many double and triple mutant phenotypes
rum1+ overexp, cdc18-K46fypo:1427 facs
rum1+ overexp, cdc23-M36fypo:1427 facs
rum1+ overexp, cdc6(pold-1)fypo:1427 facs
rum1+ overexp, orc1(orp1-4)fypo:1427 facs
rum1+ overexp, cdc17-K42fypo:1426 facs
rum1+ overexp, cdc24-g1fypo:1426 facs
rum1+ overexp, cdc20-M10fypo:1426 facs
rum1+ overexp, rad4-116fypo:1426 facs
rum1+ overexp, cdc1-7fypo:1428 facs
rum1+ overexp, cdc10-V50fypo:1428 facs
rum1+ overexp, pol1-1fypo:1428 facs
rum1+ overexp, mcm2(cdc19-P1)fypo:1428 facs
rum1+ overexp, mcm4(cdc21-M68)fypo:1428 facs
rum1+ overexp, cig1delta::ura4+fypo:1425 facs, enlarged nuc fypo:344 ev: micr, elong fypo:839 ev: micr
rum1+ overexp, cig2delta::ura4+fypo:1425 facs, enlarged nuc fypo:344 ev: micr, elong fypo:839 ev: micr
rum1+ overexp, cig1delta::ura4+, cig2delta::ura4+fypo:1428 facs
cdc13delta::ura4+, cdc10-V50fypo:1428 facs; elong fypo:839 ev: micr, cond high temp
cdc13delta::ura4+, mcm2(cdc19-P1)fypo:1428 facs; elong fypo:839 ev: micr, cond high temp
cdc13delta::ura4+, mcm4(cdc21-M68)fypo:1428 facs; elong fypo:839 ev: micr, cond high temp
cdc13delta::ura4+, cdc6(pold-1)fypo:1428 facs; elong fypo:839 ev: micr, cond high temp
cdc13delta::ura4+, cdc18-K46fypo:1428 facs; elong fypo:839 ev: micr, cond high temp
cdc13delta::ura4+, cdc18delta::p[nmt*.cdc18+-LEU2]fypo:1428 ev facs, fypo:1430 ev:facs
cdc13delta::ura4+, mcm2delta::his3+fypo:1428 ev facs, abn chr morph fypo:848 ev: 'other' (for PFGE)
cdc13delta::ura4+, mcm4delta::his3+fypo:1428 ev facs, abn chr morph fypo:848 ev: 'other' (for PFGE)


PMID:19286980
psd1delta,psd2deltaviable rich med, std temp; viable minimal med, std temp
psd1delta,psd3deltaviable rich med, std temp; viable minimal med, std temp
psd2delta,psd3deltaviable rich med, std temp; viable minimal med, std temp
psd1delta,psd2deltanormal cell morph rich med, std temp, limited eth pco:169|
psd1delta,psd3deltanormal cell morph rich med, std temp, limited eth pco:169
psd2delta,psd3deltanormal cell morph rich med, std temp, limited eth pco:169
psd1delta,psd2delta,psd3deltaviable rich med, std temp; inviable minimal med, std temp
psd1delta,psd2delta,psd3deltafypo:38, minimal med, std temp; rich med, std temp
psd1delta,psd2delta,psd3deltadecr PE fypo:1285 rich med, minimal, minimal + ethanolamine; all std temp
psd1delta,psd2delta,psd3deltaincr PS fypo:1505 rich med, minimal, minimal + ethanolamine; all std temp
psd1delta,psd2delta,psd3deltanormal PC fypo:1506 rich med, minimal, minimal + ethanolamine; all std temp
psd1delta,psd2delta,psd3deltanormal PI fypo:1507 rich med, minimal, minimal + ethanolamine; all std temp
psd1delta,psd2delta,psd3deltafypo:1496 minimal pco:169 std temp
psd1delta,psd2delta,psd3deltafypo:339 minimal pco:169 std temp
psd1delta,psd2delta,psd3deltafypo:20 minimal pco:169 std temp
psd1delta,psd2delta,psd3deltafypo:21 minimal pco:169 std temp
psd1delta,psd2delta,psd3deltafypo:1390 minimal pco:169 std temp
psd1delta,psd2delta,psd3deltafypo:672 rich pco:154 std temp
psd1delta,psd2delta,psd3deltafypo:673 rich pco:154 std temp
psd1delta,psd2delta,psd3deltafypo:5 ext has_penetrance(FYPO_EXT:0000003) minimal pco:154 std temp
psd1delta,psd2delta,psd3deltafypo:5 ext has_penetrance(FYPO_EXT:0000001) minimal pco:169 std temp
psd1delta,psd2delta,psd3deltafypo:161 rich pco:169 std temp
psd1delta,psd2delta,psd3deltafypo:182 rich pco:169 std temp
all evidence cell growth or microscopy as appropriate


PMID:19168988
note: SPAPB2B4.04c has pmc1 as synonym (used in the paper), so document allele synonyms
SPAPB2B4.04cdelta,cta5deltafypo:1419 rich med std temp
SPAPB2B4.04cdelta,SPCC1672.11cdeltafypo:1487 fypo:636 rich med std temp
pmr1delta,cta5deltafypo:1487 fypo:636 rich med std temp
pmr1delta,SPCC1672.11cdeltafypo:1487 fypo:636 rich med std temp
cta5delta,SPCC1672.11cdeltafypo:1487 fypo:636 rich med std temp
SPAPB2B4.04cdelta,cta5deltafypo:98 ext has_expressivity(FYPO_EXT:0000001) rich std temp
SPAPB2B4.04cdelta,cta5deltafypo:92 ext has_expressivity(FYPO_EXT:0000001) rich std temp
SPAPB2B4.04cdelta,SPCC1672.11cdeltafypo:98 ext has_expressivity(FYPO_EXT:0000001) rich std temp
SPAPB2B4.04cdelta,cta5deltafypo:286 minimal std temp
SPAPB2B4.04cdelta,SPCC1672.11cdeltafypo:286 minimal std temp
SPAPB2B4.04cdelta,cta5delta, overexp pmr1+fypo:1020 minimal std temp
SPAPB2B4.04cdelta,cta5deltafypo:1020 pco:114 minimal std temp
multi-way genetic interactionoverexp pmr1+ sup (SPAPB2B4.04cdelta,cta5delta fypo:98)
gene expressionpmr1+ > SPAPB2B4.04c+ > cta5+ during veg growth GO:0072690, but nothing else shown (e.g. change upon stimulus/during GO BP); one measurement


PMID:10409743
hsk1 gene expboth mRNA and protein "relatively constant throughout cell cycle"
dfp1 C-term del, exact residues not specifiedinviable; no further data
dfp1 him1-3A, chk1delta::ura4+cut annotation_extension=has_penetrance(FYPO_EXT:0000002), micr, HU added
cds1delta::ura4+,chk1delta::ura4+cut annotation_extension=has_penetrance(FYPO_EXT:0000001), micr, HU added
Dfp1 "hyperphosphorylated" in presence of HU


PMID:10411894
Dfp1 "hyperphosphorylated" in presence of HUrequires Cds1 kinase


PMID:10490657
orc1 GO:790throughout cell cycle
mcm6 go:5634throughout cell cycle
lots of Mcm2 & Mcm6 in unspecified "soluble" fractionthroughout cell cycle
cdc10-129, overexp cdc18+normal prot loc to chromatin fypo:1509; annotation_extension=assayed_using(PomBase:SPBC211.04c)


PMID:10588642
mcm6 nucleus go:5634throughout cell cycle
mcm2/cdc19-P1, crm1-11Rfypo:838 prot loc; high temp; annotation_extension=assayed_using(PomBase:SPBC211.04c)
mcm4/cdc21-M68, crm1-11Rfypo:838 prot loc; high temp; annotation_extension=assayed_using(PomBase:SPBC211.04c)
mcm2/cdc19-P1, mcm3-HAfypo:783 prot loc; high temp; annotation_extension=assayed_using(PomBase:SPBC4.04c)|assayed_using(PomBase:SPCC16A11.17)|assayed_using(PomBase:SPBC211.04c)
mcm2/cdc19-P1, mcm3-HAfypo:1424 prot loc; high temp; annotation_extension=assayed_using(PomBase:SPBC4.04c)|assayed_using(PomBase:SPCC16A11.17)
mcm4/cdc21-M68, mcm3-HAfypo:783, fypo:1424 all prot loc; high temp; annotation_extension=assayed_using(PomBase:SPBC4.04c)|assayed_using(PomBase:SPCC16A11.17)|assayed_using(PomBase:SPBC211.04c)
crm1-809, mcm3-HAfypo:838 prot loc; low temp; annotation_extension=assayed_using(PomBase:SPBC4.04c)|assayed_using(PomBase:SPCC16A11.17)|assayed_using(PomBase:SPBC211.04c)
GFP-beta-galactosidase + SV40 NLSnucleus
GFP-beta-galactosidase + mcm2-M9 residues 5-10 (mutated NLS1)cytoplasm
GFP-beta-galactosidase + Mcm2 residues 114-118 (NLS2)cytoplasm
mcm2/cdc19, mcm2-M9 overexpinviable
mcm2/cdc19, mcm2-M9 overexp, mcm3-HAinviable; fypo:783, fypo:1424 all prot loc; std temp; annotation_extension=assayed_using(PomBase:SPCC1682.02c)|assayed_using(PomBase:SPCC16A11.17)|assayed_using(PomBase:SPBC211.04c)
crm1-809, mcm2+ overexpfypo:783; prot loc; low temp; annotation_extension=assayed_using(PomBase:SPBC4.04c)
crm1-809, mcm2-M2fypo:783; prot loc; low temp; annotation_extension=assayed_using(PomBase:SPBC4.04c)
crm1-809, mcm2-M9fypo:783; prot loc; low temp; annotation_extension=assayed_using(PomBase:SPBC4.04c)
crm1-809, mcm2-M10fypo:783; prot loc; low temp; annotation_extension=assayed_using(PomBase:SPBC4.04c)
crm1-809, mcm2-D6fypo:783; prot loc; low temp; annotation_extension=assayed_using(PomBase:SPBC4.04c)
crm1-809, mcm2-D7fypo:783; prot loc; low temp; annotation_extension=assayed_using(PomBase:SPBC4.04c)


PMID:11606526
Mcm7 expressionprotein present throughout cell cycle
Cdc23"insoluble"


Additions to existing sessions (short wait for whatever's needed)