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

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(Created page with "Category:Annotation Working Group =Agenda= ==Annotation consistency exercise== Pombe paper <br> http://www.ncbi.nlm.nih.gov/pubmed/22959349")
 
(add annotation summary)
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Pombe paper <br>
Pombe paper <br>
http://www.ncbi.nlm.nih.gov/pubmed/22959349
http://www.ncbi.nlm.nih.gov/pubmed/22959349
===Annotation Summary===
{| {{Prettytable}}
|-
! Gene
! Qualifier
! Term
! ID
! # of Annotations
! Evidence Code Summary
! 'With' field Summary
! Extension Summary
! Comments
|-
! Molecular Function Annotations
!
!
!
!
!
!
!
!
|-
| rap1
|
| protein binding
| GO:0005515
| 2/3
| IPI
| bqt4
|
|
|-
| bqt4
|
| protein binding
| GO:0005515
| 2/3
| IPI
| rap1
|
|
|-
| bqt1
|
| protein binding
| GO:0005515
| 1/3
| 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.
|-
| bqt2
|
| protein binding
| GO:0005515
| 1/3
| 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.
|-
| poz1
|
| protein binding
| GO:0005515
| 1/3
| IPI
| rap1
|
|
|-
| rap1
|
| protein binding
| GO:0005515
|
| IPI
| taz1
|
|
|-
| rap1
|
| protein binding
| GO:0005515
| 1/3
| 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
| 1/3
| IPI
| poz1
|
|
| taz1
|
| protein binding
| GO:0005515
| 1/3
| IPI
| rap1
|
|
|-
|-
! Biological Process Annotations
!
!
!
!
!
!
!
!
|-
| taz1
|
| mitotic telomere tethering at nuclear periphery
| GO:0044820
| 2/3
| IGI-1, IMP-1
| bqt4
| during mitotic G2 phase (GO:0000085)
|
|-
| bqt4
|
| mitotic telomere tethering at nuclear periphery
| GO:0044820
| 3/3
| IGI-1, IMP-2
| taz1
| during mitotic G2 phase (GO:0000085) (2/3 included)
|
|-
| rap1
|
| mitotic telomere tethering at nuclear periphery
| GO:0044820
| 2/3
| IPI-1, IMP-2
| bqt4
| during mitotic G2 phase (GO:0000085) (2/3 included)
| one curator did both IMP and IGI
|-
| cdc2
|
| negative regulation of mitotic telomere tethering at nuclear periphery
| GO:1904537
| 1/3
| IGI
| rap1
| during mitotic M phase (GO:0000087)
|
|-
| cdc2
|
| negative regulation of protein binding
| GO:0032091
| 1/3
| IMP
|
| during mitotic M phase (GO:0000087)|has_input-rap1|has_input-bqt4
|
|-
| cdc2
|
| protein serine/threonine kinase activity
| GO:0004674
| 2/3
| 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
|
| ??
| ??
| 1/3
| ??
|
|
| 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
| 2/3
| 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
| 2/3
| 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
|
| mitotic sister chromatid segregation
| GO:0000070
| 1/3
| IC
| GO:1904537????????
|
|
|-
| taz1
|
| protection from non-homologous end joining at telomere
| GO:0031848
| 1/3
| IMP
|
|
|
|-
| taz1
|
| ??
| ??
| 1/3
| ??
|
|
| Not sure if the overexpression constructs are suficient evidence to annotate taz1 to GO:0044820, mitotic telomere tethering at nuclear periphery
|-
| taz1
|
| ??
| ??
| 1/3
| ??
|
|
| Not sure if this observation [minichromosome loss] should lead to a 'regulation of mitotic sister chromatid segregation' type of annotation.
|-
! Cellular Component Annotations
!
!
!
!
!
!
!
!
|-
| taz1
|
| nuclear chromosome, telomeric region
| GO:0000784
| 2/3
| IDA
|
|
|
|-
| ish1
|
| nuclear envelope
| GO:0005635
| 2/3
| IDA
|
|
|
|-
| atb2
|
| microtubule
| GO:0005874
| 2/3
| IDA
|
|
|
|-
| bqt4
|
| nuclear envelope
| GO:0005635
| 1/3
| IDA
|
|
|
|-|}

Revision as of 09:03, 22 September 2015


Agenda

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 2/3 IPI bqt4
bqt4 protein binding GO:0005515 2/3 IPI rap1
bqt1 protein binding GO:0005515 1/3 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.
bqt2 protein binding GO:0005515 1/3 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.
poz1 protein binding GO:0005515 1/3 IPI rap1
rap1 protein binding GO:0005515 IPI taz1
rap1 protein binding GO:0005515 1/3 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 1/3 IPI poz1 taz1 protein binding GO:0005515 1/3 IPI rap1
Biological Process Annotations
taz1 mitotic telomere tethering at nuclear periphery GO:0044820 2/3 IGI-1, IMP-1 bqt4 during mitotic G2 phase (GO:0000085)
bqt4 mitotic telomere tethering at nuclear periphery GO:0044820 3/3 IGI-1, IMP-2 taz1 during mitotic G2 phase (GO:0000085) (2/3 included)
rap1 mitotic telomere tethering at nuclear periphery GO:0044820 2/3 IPI-1, IMP-2 bqt4 during mitotic G2 phase (GO:0000085) (2/3 included) one curator did both IMP and IGI
cdc2 negative regulation of mitotic telomere tethering at nuclear periphery GO:1904537 1/3 IGI rap1 during mitotic M phase (GO:0000087)
cdc2 negative regulation of protein binding GO:0032091 1/3 IMP has_input-rap1|has_input-bqt4
cdc2 protein serine/threonine kinase activity GO:0004674 2/3 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 ?? ?? 1/3 ?? 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 2/3 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 2/3 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 mitotic sister chromatid segregation GO:0000070 1/3 IC GO:1904537????????
taz1 protection from non-homologous end joining at telomere GO:0031848 1/3 IMP
taz1 ?? ?? 1/3 ?? Not sure if the overexpression constructs are suficient evidence to annotate taz1 to GO:0044820, mitotic telomere tethering at nuclear periphery
taz1 ?? ?? 1/3 ?? Not sure if this observation [minichromosome loss] should lead to a 'regulation of mitotic sister chromatid segregation' type of annotation.
Cellular Component Annotations
taz1 nuclear chromosome, telomeric region GO:0000784 2/3 IDA
ish1 nuclear envelope GO:0005635 2/3 IDA
atb2 microtubule GO:0005874 2/3 IDA
bqt4 nuclear envelope GO:0005635 1/3 IDA