wiki:AntoniasCuratedPapers

Version 23 (modified by antonialock, 10 years ago) (diff)

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https://sourceforge.net/apps/trac/pombase/wiki/CuratorTrainingPapers


21727087Antonia
gene term extension
dmr1 (ppr3)mitochondrial translation phenotype, less translation of mt proteinsallele=deletion
variousadd missing phenotype alleles


21745468Antonia
gene term extension
lkh1expressionupregulated during mitosis and cytokinesis (=mitotic cell cycle) (IDA)
lkh1, dsk1((phenotype)) severe growth defect (cell growth assay)allele=Δdsk1Δlkh1


17369611Antonia
gene term extension
rtt109Delta rtt109/Histone H3 K56R double-mutant phenotypeasynthetic sensitivity to DNA damage


9191268Antonia
gene term extension
mam1annotation_extension= does not ...
mam1how to capture transcription increased to nitrogen starvation?
mam1how to capture transcription increased in response to pheromone?


17248713Antonia
gene term extension
map1 expression suppressed in 2674. annotation_extension= doesnot occurs_in(CL:0002674 (but does occur in 2675)


2792737Antonia
gene term extension
mat1-Pcconstitutively expressed (how to capture expression pattern?)annotation_extension=occurs_in(CL:0002675)
mat1-PcUpregulated in response to nitrogen starvation (how to capture expression pattern?)annotation_extension=occurs_in(CL:0002675)
mat1-PiExpressed in response to nitrogen starvation (how to capture expression pattern?)annotation_extension=occurs_in(CL:0002675)
map1regulation of transcription, mating-type specificannotation_extension=occurs_in(CL:0002675)
map1transcription regulation phenotypeadd to annotation extension condition/during=nitrogen_starvation 2 annotations for this (2 targets, pi and pc)
map1transcription regulation phenotypeadd to annotation extension that transcription is downregulated (2 targets, pi and pc)
map1abnormal premeiotic DNA replication initiationallele=deletion


2900761Antonia
gene term extension
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
geneterm extension
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


10438147Antonia
genetermextension
gaf1experiments were performed in Sc. cerevisiae, but investigating pombe proteins
gaf1number of tas etc annotations for gene that can probably be removed once update is done
gaf1RNA polymerase II core promoter proximal region sequence-specific DNA bindinghas substrate GATA boxes (requested term from SO SO:0001840)
gaf1phenotype: has DNA binding activityallele=Gaf1N(AA1-120)
gaf1phenotype: abolished DNA binding activityallele=GAF1C(121-290)


17452352Antonia
genetermextension
ams2expression oscillates during cell cycle, peaks at S-phase (except hht2 which remain constant)
ams2delayed septationallele=deletion
ams2DNA replication appears normalallele=deletion
ams2RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcriptionadd extension: annotation_extension=acts_at(SO: GATA transcr factor - term is requested)
ams2 + hht2synthetic lethality, double mutantallele=deletion
sequence feature annotate AACCCT as a GATA transcription factor binding site, seq 5'-ATCA(C/A)AACCCTAACCCT-3'artemis?
ams2CC nuclear chromosomeacts at(SO:GATA transcr factor binding site


18077559|Antonia
genetermexpression
ams2 hip1slow cell growthallele=dbl mutant


20230746Antonia
genetermextension
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
ams2allele=overexpression(overexpression and allele=deletion(deletion)...correct way of writing this is?


18158900Antonia
sim3phenotype: abnormal chromatin silencing at centromere|abnormal at kinetochore(central core/cnt)allele=143(G81E),allele=205(E207K)
sim3phenotype: inviable at 18 degrees, inhibited growth at 25/32/36 degreesallele=deletion
double mutantsim3 mutants (allele=143(G81E),allele=205(E207K)) + overexpressed cnp1 = normal phenotype
double mutantsim3 mutants (allele=143(G81E),allele=205(E207K)) + overexpressed H4 = normal phenotype
double mutantsim3 mutants (allele=143(G81E),allele=205(E207K)) + overexpressed H3 = reduced viability (inviable ok)
sim3go biological process: protein localization to kinetochoreannotation_extension=does not happens_during G1


cnb1,ppb1dbl deletion mutant same phenotype as each single mutant (branched,elongated multi-septate cells + slow growth in presence of mgcl2worth annotating? i.e. shows may be linked perhaps? dbl mutant not more severe
cnb1,ppb1,pmp1dbl del + overexpressed = normal cell growth
cnb1,ppb1deletion,overexpr. slow growth in presence of mgcl2i.e. large amounts of catalytic domain is not functional without regulatory subunit. is this interesting to capture?
cnb1,ppb1∆C(L445->STOPdeletion,overexpressed. slow growth in presence of mgcl2constitutively active mutant is not active without regulatory subunit
cnb1,ppb1∆C(L445->STOPoverexpressed,overexpressed. phenotype growth arrest, round small bent pear-shaped cells. depolarized distr of cortical F-actin patchesnormal phenotype in presence of CHEBI:61049
cnb1,ppb1∆C(L445->STOP,prz1overexpressed,overexpressed, deleted. no growth arrest


16928959Antonia
∆yam8not involved in calcium response in presence of cacl2 or chlorpromazineIMP - phenotype decreased cellular signalling?
∆cch1not involved in calcium response in presence of cacl2 or chlorpromazineIMP


20018864Antonia
genetermextension
ncs1expression:upregulated in response to CHEBI:29108 NOT upregulated in response to CHEBI:6636, CHEBI:26710, CHEBI:32588, CHEBI:30911, CHEBI:32035, or CHEBI:61049IDA
deletion(prz1), overexpression(ncs1)slow growthcell growth assay
deletion(ncs1), overexpression(prz1)slow growthcell growth assay
deletion(prz1), overexpression(ncs1)inviable in_response_to(CHEBI:29108)IMP
deletion(ncs1), overexpression(prz1)inviable in_response_to(CHEBI:29108)IMP
deletion(ncs1),deletion(yam8)normal cell growth in_presence_of(CHEBI:33120cell growth assay
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


14722091Antonia
genetermextension
ncs1upregulated in response to CaCl2+


18362178Antonia
genetermextension
acr1phenotype:ringlike nuclear chromatinallele=acr1-936, requested term
nuc1phenotype:ringlike nuclear chromatinallele=nuc1-632, requested term
cut14phenotype=abnormal nucleolar rDNA separationallele=cut14-208,qualifier=at_high_temperature


21879336Antonia
rst2in a ∆pka1 mutant and sam5 and sam7 rst2 is phosphorylated under normal conditions (not in wt)
pka1normal protein localization
pka1normal protein localizationannotation_extension=exists_during:GO:0042149)


19606215Antonia
cnx1dbl mutant phenotype: abnormal cell wall morphologyallele=lumenal_cnx1p(aa_del488-560),allele=C-termTM_Cnx1p_cmyc(aa_del1-415)
cnx1some confusing data regarding apoptosis. Notes in hardcopy paperallele=lumenal_cnx1p(aa_del488-560)
cnx1allele specifications may not be 100% correct


18621924Antonia
cyr1,cgs1 dbl deletionnuclear export abolishedallele=deletion,annotation_extension=localizes(GeneDBSpombe:SPBC106.10)
cgschange annotation concerning localized to nucleus during GO:0009651 to nucleus excluding nucleoluswaiting to see if GO will give a term for this cellular component


12557273Antonia
pik3-/pik3-spore germination abolished, abnormal spore morphologyif a more specified term is added to CL then change CL:0000415 to homozygous diploid, if not then add allele=homozygous?
pik3-/pik3+FYPO:0000579 normal spore germinationadd this with either CL:0000415 + allele=heterozygous or more specific CL if given
pik3have requested 2 process terms from GO (+ve regulation of protein targeting to prospore/vacuolar membraneupdate if granted
pik3abnormal protein targeting to prospore membrane phenotypeallele=deletion,annotation_extension=localizes(PF:01363)


9191269Antonia
plc1qualifier in genedb for binding:"N-term", not clear if it binds N-term or if it binds via N-term"


9191271Antonia
matPimRNA levels increase in response to M-factoroccurs_in(CL:0002675


9388669Antonia
krp1abolished enzymatic activityallele=R82A, qualifier=in_vitro


10792724Antonia
sxa2Normal carboxypeptidase activityK309A
sxa2Normal carboxypeptidase activityK309A,R310K
sxa2No carboxypeptidase activityK309A,R310A
sxa2No carboxypeptidase activityS460*(delS460-Y507)
sxa2No carboxypeptidase activity563(W247->amber
sxa1remove the artemis annotation to BP conjugation with cellular fusion


map3/mam2diploid strain (CL:0000415) cannot sporulate if both receptors expressed at the same time


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
pat1/ras1mat1-Pm transcribedallele=pat1-114/deletion, at high temp
pat1/ste6mat1-Pm transcribedallele=pat1-114/deletion, at high temp
8196631Antonia
mfm1/mfm2FYPO:0000584 decreased sporulationallele=deletion (both)
mfm1/mfm3FYPO:0000584 decreased sporulationallele=deletion (both)
mfm2/mfm3FYPO:0000584 decreased sporulationallele=deletion (both)
mfm1/mfm2/mfm3FYPO:0000583 sporulation abolishedallele=deletion (all 3)
mfm1/mfm2/mfm3FYPO:0000583 sporulation abolishedallele=deletion (all 3),annotation_extension=in_presence_of(M-factor - externally added),annotation_extension=occurs_in:CL0002674
mfm1/mfm2/mfm3FYPO:0000590 normal sporulationallele=deletion (all 3),annotation_extension=occurs_in:CL0002674
mfm1expressed in CL:0002674happens during(GO:0006995) - cellular response to nitrogen starvation
mfm2expressed in CL:0002674happens_during(GO:0000278) - mitotic cell cycle
mfm2expression increased in CL:0002674happens during(GO:0006995) - cellular response to nitrogen starvation
mfm3expressed in CL:0002674happens during(GO:0006995) - cellular response to nitrogen starvation
mfm1not expressed in CL:0002675
mfm2not expressed in CL:0002675
mfm3not expressed in CL:0002675
mfm1expression increasedannotation_extension=occurs_in:CL:0002674,annotation_extension=in_presence_of(GeneDBSpombe:SPCC1795.06 - map2),happens during(GO:0006995) - cellular response to nitrogen starvation
mfm2expression increasedannotation_extension=occurs_in:CL:0002674,annotation_extension=in_presence_of(GeneDBSpombe:SPCC1795.06 - map2),happens during(GO:0006995) - cellular response to nitrogen starvation
mfm3expression increasedannotation_extension=occurs_in:CL:0002674,annotation_extension=in_presence_of(GeneDBSpombe:SPCC1795.06 - map2),happens during(GO:0006995) - cellular response to nitrogen starvation


154790Antonia
mfm1/2/3Add on gene page that the final peptide gene product is 9 amino acids long and consists of YTPKVPYM


7975894Antonia
gpa1phenotype: increased expression of MatPi? during nitrogen starvation; constitutively active. Pheromone doesn't influence transcriptionQ244L
ras1phenotype: increased expression of Matpi during nitrogen starvation in the presence of pheromoneG17V
mat1Pm/pipromoter element mapped in paper -61- -41 (ccctctttctttgttccttat


7813430Antonia
krp1expressed in mitotically growing cells
krp1expressed in response to nitrogen starvation
krp1dibasic endopeptidase activity - have one for serine peptidase activity, use that one?need to request term


8314086Antonia
sxa2expressed in presence of p-factor
map2expressed in H- cells
cyr1/sxa2phenotype G1 arrest in presence of P-factor in rich mediaallele=deletion
cyr1/sxa2abnormal/increased shmoo formation in presence of P-factor in rich mediaallele=deletion


18059475Antonia
fkh2reduced zygote formationallele=deletion
fhl1reduced zygote formationallele=deletion
mei4reduced zygote formationallele=deletion
fkh2/fhl1reduced zygote formationallele=deletion
fkh2/mei4reduced zygote formationallele=deletion
fkh2/fhl1/mei4reduced zygote formationallele=deletion
ste11annotate promoter proximal element FLEX1 and FLEXL1 to ste11, artemis
fkh2reduced zygote formationallele=T314E
fkh2reduced zygote formationallele=S462E
fkh2normal zygote formationallele=S481E
fkh2reduced zygote formationallele=T314E,S462E,S481E
fkh2normal zygote formationallele=T314A,S462A,S481A
fkh2normal cell morphologyallele=T314E
fkh2normal cell morphologyallele=S462E
cig2increased rate of zygote formationallele=deletion,happens_during(GO:0006995 - cellular response to nitrogen starvation)
cig2/fkh2increased zygote formationallele=deletion,happens_during(GO:0006995 - cellular response to nitrogen starvation)
cig2/fkh2/fhl1reduced zygote formationallele=deletion,happens_during(GO:0006995 - cellular response to nitrogen starvation)
cig2/fkh2/mei4reduced zygote formationallele=deletion,happens_during(GO:0006995 - cellular response to nitrogen starvation)
cig2/fkh2/fhl1/mei4reduced zygote formationallele=deletion,happens_during(GO:0006995 - cellular response to nitrogen starvation)


7651414Antonia
mat1have annotated M specific genes to the genes closest to the centromere (around 2120000). eg mat3m, matmc_2 NOT mat1-m or matmc_1. I think this is correct but dbl-check once artemis files are updated on genedb
mat1-mm)expressed in response to P-factor and nitrogen starvationIDA
mat1-pmexpressed in response to nitrogen starvationIDA


10867006Antonia
ste11Unable to bind DNA region outside of the consensus motifste91


9418887Antonia
krp1abolished serine endopeptidase activityallele=S371A ODA, qualifier=in_vitro
krp1abolished serine endopeptidase activityallele=K81I,R82A,R102K,S371A ODA, qualifier=in_vitro
krp1abolished serine endopeptidase activityallele=R82A ODA, qualifier=in_vitro
krp1abolished serine endopeptidase activityallele=K81I,R82A ODA, qualifier=in_vitro
krp1normal serine endopeptidase activityallele=R102K ODA, qualifier=in_vitro
krp1abolished serine endopeptidase activityallele=R82A,R102K ODA, qualifier=in_vitro
krp1abolished serine endopeptidase activityallele=I81I,R82AR102K ODA, qualifier=in_vitro
krp1reduced serine endopeptidase activityallele=R102A ODA, qualifier=in_vitro
krp1reduced serine endopeptidase activityallele=R82A,R102A ODA, qualifier=in_vitro
krp1reduced serine endopeptidase activityallele=K81I,R82A,R102A ODA, qualifier=in_vitro
krp1abolished serine endopeptidase activityallele=aa_del579-709 ODA, qualifier=in_vitro
krp1abolished serine endopeptidase activityallele=aa_del591-709 ODA, qualifier=in_vitro
krp1normal serine endopeptidase activityallele=aa_del612-709 ODA, qualifier=in_vitro


10931354Antonia
krp1no enzymatic activity (abolished serine endopeptidase activity)allele=S271A ODA
krp1normal enzymatic activity (normal serine endopeptidase activity)allele=R102K ODA
krp1normal enzymatic activity (normal serine endopeptidase activity)allele=R82A ODA
krp1no enzymatic activity (abolished serine endopeptidase activity)allele=R82A,R102K ODA
krp1normal enzymatic activity (normal serine endopeptidase activity)allele=R82A,R102K,qualifier=overexpression ODA
krp1no enzymatic activity (abolished serine endopeptidase activity)allele=R102A ODA
krp1normal enzymatic activity (normal serine endopeptidase activity)allele=R102A,qualifier=overexpression ODA
krp1no enzymatic activity (abolished serine endopeptidase activity)allele=R82A,R102A ODA
krp1normal enzymatic activity (normal serine endopeptidase activity)allele=R82A,R102A,qualifier=overexpression ODA
krp1no enzymatic activity (abolished serine endopeptidase activity)allele=aa_del579-709 ODA
krp1no enzymatic activity (abolished serine endopeptidase activity)allele=aa_del591-709 ODA


15580593Antonia
mam2negative regulation of pheromone INDEPENDENT signal transduction. If I can't get this term from GO then use negative regulation of signal transduction involved in conjugation with cellular fusion + add the extension "in absence of P-factor" (occurs in M-cells)
Mam2 mutantsphenotype: constitutively active (if term goes inM cells


15659165Antonia
mam2negative regulation of pheromone INDEPENDENT signal transduction. Sequesters G alpha. If I can't get this term from GO then use negative regulation of signal transduction involved in conjugation with cellular fusion + add the extension "in absence of P-factor" (occurs in M-cells)
Mam2P261Lphenotype: constitutively active (if term goes inM cells
mam2cellular component, homodimeric complex; will come under GO:0043235IDA
mam2/gpa1interaction evidence is wrong, but it's the best fit....should I not curate this? I think the evidence is pretty strong


19285552Antonia
rgs1phenotype: increased sensitivity to pheromoneallele=deletion, in M cells


21118960
srw1another phenotype: decreased cell cycle arrest in response to pheromoneallele=mutPste9(A->C and G-> T and vice versa throughout 27 bp reb1 binding region -198 - -172
srw1decreased sporulationmutPste9
srw1 ectopically expressed | reb1 deletionnormal cell cycle arrest in response to pheromonephenotype
reb1|wee1phenotype: slow growth at high temperatureallele=deletion(reb1)/wee1-50
reb1|wee1phenotype: multiseptate (0000118)allele=deletion(reb1)/wee1-50
reb1|wee1phenotype: weeallele=deletion(reb1)/wee1-50
reb1|wee1phenotype: spheroid cellsallele=deletion(reb1)/wee1-50
reb1|wee1phenotype: DNA content increasedallele=deletion(reb1)/wee1-50
reb1|wee1phenotype: normal cell growth at high temperaturein_presence_of:CHEBI:44423, allele=deletion(reb1)/wee1-50
reb1|cdc10phenotype: slow growth at high temperatureallele=deletion(reb1)/cdc10-129
reb1|cdc10phenotype: abnormal? cell cycle arrestqualifier=at_high_temperature,allele=deletion(reb1)/cdc10-129
reb1 change cell cycle arrest in mitotic G1 phase to "increased rate of"allele=overexpression


21680738
ins1negative regulation of the mevalonate pathway, negative regulation of HMG-CoA reductase activityIMP, regulates phosphorylation of hmg1, annotation_extension=in_absence_of(CHEBI:16646) (sugar)
sds23negative regulation of the mevalonate pathway, negative regulation of HMG-CoA reductase activityIMP, regulates phosphorylation of hmg1, annotation_extension=in_absence_of(CHEBI:16646) (sugar)
ppe1positive regulation of the mevalonate pathway, positivr regulation of HMG-CoA reductase activityIMP, regulates dephosphorylation of hmg1, annotation_extension=in presence of sugar / during cell growth


9427748
pmp1abolished enzymatic activityallele=C158S
pmp1abolished enzymatic activityannotation_extension=in_presence_of(CHEBI:35607) a tyrosine phosphatase inhibitor
deletion ppb1|overexpression pmp1suppresses salt stress sensitivity
deletion pmp1|expression of const. active ppb1deltaC (C-term truncated)suppresses salt stress sensitivity
deletion pmp1|expression of const. active ppb1deltaC (C-term truncated)suppresses FK506 sensitivity
deletion pmp1|expression of ppb1 overexpressedsensitive to salt stress and FK506
deletion pmp1|deletion ppb1|deletion pmk1normal cell growth
deletion ppb1|deletionpmk1filamentous and multiseptateallele=deletion
deletion ppb1|overexpression pmp1normal morphology


8227198
pka1there is an existing annotation to negative regulation of transcription by glucose...is this git6?


18279662
-MF misfolded glycoprotein bindingIDA
-ph normal enzymatic activity (normal GO:0000224 activity)allele=ΔH1(del_aa1-15)
-ph abolished enzymatic activity. (abolished GO:0000224 activity)allele=ΔH1ΔH2(del_aa1-38)
-ph abolished protein bindingallele=ΔH1(del_aa1-15)


21949882
ofd2abolished enzyme activity (abolished GO:0016706)allele=H132


11937031
drc1normal protein bindinghas_substrate(cdc2),allele=CD5A(T154A,T99A,T74A,T60A,S87A)
drc1abolished protein binding/interaction with Cut5allele=CD5A(T154A,T99A,T74A,T60A,S87A)


21858190
cbf11binds GTGGGAACSL response element, term requested from SO


11461899
stm1upregulated mRNA during nitrogen starvationIDA