Difference between revisions of "Annotation Conf. Call 2015-09-22"

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(Agenda)
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=Agenda=
 
=Agenda=
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==Relations used in Col-16==
  
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Status on some questionable relations:
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* dependent_on
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* in_absence_of
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* in_presence_of
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* Already deprecated but annotations still exists;
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**independent_of
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** localization_dependent_on
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** requires_sequence_feature
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** requires_substance
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** not_exists_during
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** not_happens_during
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** During
 
==Annotation consistency exercise==
 
==Annotation consistency exercise==
 
Pombe paper <br>
 
Pombe paper <br>

Revision as of 06:55, 22 September 2015


Agenda

Relations used in Col-16

Status on some questionable relations:

  • dependent_on
  • in_absence_of
  • in_presence_of
  • Already deprecated but annotations still exists;
    • independent_of
    • localization_dependent_on
    • requires_sequence_feature
    • requires_substance
    • not_exists_during
    • not_happens_during
    • During

Annotation consistency exercise

Pombe paper
http://www.ncbi.nlm.nih.gov/pubmed/22959349

Annotation Summary

Gene Qualifier Term ID # of Annotations Evidence Code Summary 'With' field Summary Extension Summary Comments
Molecular Function Annotations
rap1 protein binding GO:0005515 3/4 IPI bqt4
bqt4 protein binding GO:0005515 3/4 IPI rap1
bqt1 protein binding GO:0005515 1/4 IPI bqt2, rap1 Not sure if this is the correct representation, or if this should be a protein complex annotation. This is the Y3H data.
bqt1 protein binding GO:0005515 1/4 IPI rap1
bqt2 protein binding GO:0005515 1/4 IPI bqt1, rap1 Not sure if this is the correct representation, or if this should be a protein complex annotation. This is the Y3H data.
bqt2 protein binding GO:0005515 1/4 IPI rap1
poz1 protein binding GO:0005515 1/4 IPI rap1
rap1 protein binding GO:0005515 2/4 IPI taz1
rap1 protein binding GO:0005515 1/4 IPI bqt1, bqt2 Not sure if this is the correct representation, or if this should be a protein complex annotation. This is the Y3H data.
rap1 protein binding GO:0005515 1/4 IPI poz1
rap1 protein binding GO:0005515 1/4 IPI bqt1
rap1 protein binding GO:0005515 1/4 IPI bqt2
taz1 protein binding GO:0005515 2/4 IPI rap1
taz1 telomeric DNA binding GO:0042162 1/4 TAS happens_during mitotic G2 phase (GO:0000085)
Biological Process Annotations
taz1 mitotic telomere tethering at nuclear periphery GO:0044820 3/4 IGI-2, IMP-2 (one set of annotations notes both) bqt4 during mitotic G2 phase (GO:0000085)
bqt4 mitotic telomere tethering at nuclear periphery GO:0044820 4/4 IGI-1, IMP-3 taz1 during mitotic G2 phase (GO:0000085) (2/4 included)
rap1 mitotic telomere tethering at nuclear periphery GO:0044820 3/4 IPI-1, IMP-3 bqt4 during mitotic G2 phase (GO:0000085) (2/4 included) one curator did both IMP and IGI
rap1 positive regulation of mitotic telomere tethering at nuclear periphery GO:new 1/4 IMP happens_during mitotic G2 phase (GO:0000085)
rap1 positive regulation of mitotic telomere tethering at nuclear periphery GO:new 1/4 IMP happens_during mitotic G2 phase (GO:0000085)
rap1 positive regulation of attachment of telomere to nuclear envelope GO:new 1/4 IMP happens_during mitotic G2 phase (GO:0000085)
rap1 negative regulation of mitotic telomere tethering at nuclear periphery GO:new 1/4 IMP happens_during mitotic G2 phase (GO:0000085)
rap1 negative regulation of attachment of telomere to nuclear envelope GO:new 1/4 IMP happens_during mitotic G2 phase (GO:0000085)
rap1 positive regulation of chromosome segregation GO:0051984 1/4 IC 1. negative regulation of mitotic telomere tethering at nuclear periphery 2. negative regulation of attachment of telomere to nuclear envelope happens_during mitotic M phase (GO:0000087)
cdc2 negative regulation of mitotic telomere tethering at nuclear periphery GO:1904537 1/4 IGI rap1 during mitotic M phase (GO:0000087)
cdc2 negative regulation of protein binding GO:0032091 1/4 IMP has_input-rap1|has_input-bqt4
cdc2 protein serine/threonine kinase activity GO:0004674 2/4 IDA has_input-rap1 There is no direct evidence to show that phosphorylation of rap1 by cdc2 is what causes dissociation of the tethering. But the authors are suggesting that.
nda3  ??  ?? 1/4  ?? I wasn't sure if there was any GO annotation here wrt regulation of phosphorylation, or if the nda3 mutation was just being used to block the cell cycle at a particular point.
cdc2 peptidyl-serine phosphorylation GO:0018105 2/4 IGI-1, IMP-1 rap1 during mitotic M phase (GO:0000087) would love to be able to specify the residues; I'm not always certain if this type of evidence also supports an annotation to the corresponding MF term. Also, I don't know if/what the appropriate way to capture an annotation extension would be for this, has_input(Rap1p)?
cdc2 peptidyl-threonine phosphorylation GO:0018107 2/4 IGI-1, IMP-1 rap1 during mitotic M phase (GO:0000087) would love to be able to specify the residues; I'm not always certain if this type of evidence also supports an annotation to the corresponding MF term. Also, I don't know if/what the appropriate way to capture an annotation extension would be for this, has_input(Rap1p)?
cdc2 postive regulation of peptidyl-serine phosphorylation GO:0033138 1/4 IMP has_regulation_target rap1:Q96TL7; part_of negative regulation of mitotic telomere tethering at nuclear periphery; happens_during GO:0000087 mitotic M phase
cdc2 mitotic sister chromatid segregation GO:0000070 1/4 IC GO:1904537????????
taz1 protection from non-homologous end joining at telomere GO:0031848 1/4 IMP
taz1  ??  ?? 1/4  ?? Not sure if the overexpression constructs are suficient evidence to annotate taz1 to GO:0044820, mitotic telomere tethering at nuclear periphery
taz1  ??  ?? 1/4  ?? Not sure if this observation [minichromosome loss] should lead to a 'regulation of mitotic sister chromatid segregation' type of annotation.
taz1 attachment of telomere to nuclear envelope GO:0070197 1/4 IMP (or IGI) bqt4 (for IGI) during mitotic G2 phase (GO:0000085)
bqt4 attachment of telomere to nuclear envelope GO:0070197 1/4 IMP during mitotic G2 phase (GO:0000085)
rap1 attachment of telomere to nuclear envelope GO:0070197 1/4 IMP during mitotic G2 phase (GO:0000085)
taz1 chromosome segregation GO:0007059 1/4 IMP during mitotic M phase (GO:0000087)
bqt4 chromosome segregation GO:0007059 1/4 IMP during mitotic M phase (GO:0000087)
Cellular Component Annotations
taz1 nuclear chromosome, telomeric region GO:0000784 2/4 IDA exists_during mitotic G2 phase (GO:0000085) (1 included) 1 included colocalizes_with
ish1 nuclear envelope GO:0005635 2/4 IDA exists_during mitotic M phase (GO:0000087) 1 included) 1 included colocalizes_with
atb2 microtubule GO:0005874 2/4 IDA exists_during mitotic M phase (GO:0000087) 1 included) 1 included colocalizes_with (and used synonym tub1)
bqt4 nuclear envelope GO:0005635 2/4 IDA exists_during mitotic M phase (GO:0000087) 1 included) 1 included colocalizes_with
bqt4 nuclear envelope GO:0005635 1/4 IMP colocalizes_with; author states: 'Strong punctate signals of Taz1-GFP-Bqt4DN were observed at the NE throughout the cell cycle'
taz1 nuclear envelope GO:0005635 1/4 IDA colocalizes_with