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

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Line 34: Line 34:
| protein binding
| protein binding
| GO:0005515
| GO:0005515
| 2/3
| 3/4
| IPI
| IPI
| bqt4
| bqt4
Line 44: Line 44:
| protein binding
| protein binding
| GO:0005515
| GO:0005515
| 2/3
| 3/4
| IPI
| IPI
| rap1
| rap1
Line 54: Line 54:
| protein binding
| protein binding
| GO:0005515
| GO:0005515
| 1/3
| 1/4
| IPI
| IPI
| bqt2, rap1
| bqt2, rap1
|  
|  
| Not sure if this is the correct representation, or if this should be a protein complex annotation.  This is the Y3H data.
| 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
| bqt2
Line 64: Line 74:
| protein binding
| protein binding
| GO:0005515
| GO:0005515
| 1/3
| 1/4
| IPI
| IPI
| bqt1, rap1
| bqt1, rap1
|  
|  
| Not sure if this is the correct representation, or if this should be a protein complex annotation.  This is the Y3H data.
| 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
| poz1
Line 74: Line 94:
| protein binding
| protein binding
| GO:0005515
| GO:0005515
| 1/3
| 1/4
| IPI
| IPI
| rap1
| rap1
Line 84: Line 104:
| protein binding
| protein binding
| GO:0005515
| GO:0005515
|  
| 2/4
| IPI
| IPI
| taz1
| taz1
Line 94: Line 114:
| protein binding
| protein binding
| GO:0005515
| GO:0005515
| 1/3
| 1/4
| IPI
| IPI
| bqt1, bqt2
| bqt1, bqt2
Line 104: Line 124:
| protein binding
| protein binding
| GO:0005515
| GO:0005515
| 1/3
| 1/4
| IPI
| IPI
| poz1
| poz1
|
|
|-
| rap1
|
| protein binding
| GO:0005515
| 1/4
| IPI
| bqt1
|
|
|-
| rap1
|
| protein binding
| GO:0005515
| 1/4
| IPI
| bqt2
|  
|  
|  
|  
Line 114: Line 154:
| protein binding
| protein binding
| GO:0005515
| GO:0005515
| 1/3
| 2/4
| IPI
| IPI
| rap1
| rap1
|
|
|-
| taz1
|
| telomeric DNA binding
| GO:0042162
| 1/4
| TAS
| happens_during mitotic G2 phase (GO:0000085)
|  
|  
|  
|  
Line 134: Line 184:
| mitotic telomere tethering at nuclear periphery
| mitotic telomere tethering at nuclear periphery
| GO:0044820
| GO:0044820
| 2/3
| 3/4
| IGI-1, IMP-1
| IGI-2, IMP-2 (one set of annotations notes both)
| bqt4
| bqt4
| during mitotic G2 phase (GO:0000085)
| during mitotic G2 phase (GO:0000085)
Line 144: Line 194:
| mitotic telomere tethering at nuclear periphery
| mitotic telomere tethering at nuclear periphery
| GO:0044820
| GO:0044820
| 3/3
| 4/4
| IGI-1, IMP-2
| IGI-1, IMP-3
| taz1
| taz1
| during mitotic G2 phase (GO:0000085) (2/3 included)
| during mitotic G2 phase (GO:0000085) (2/4 included)
|  
|  
|-
|-
Line 154: Line 204:
| mitotic telomere tethering at nuclear periphery
| mitotic telomere tethering at nuclear periphery
| GO:0044820
| GO:0044820
| 2/3
| 3/4
| IPI-1, IMP-2
| IPI-1, IMP-3
| bqt4
| bqt4
| during mitotic G2 phase (GO:0000085) (2/3 included)
| during mitotic G2 phase (GO:0000085) (2/4 included)
| one curator did both IMP and IGI
| 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
| cdc2
Line 164: Line 274:
| negative regulation of mitotic telomere tethering at nuclear periphery
| negative regulation of mitotic telomere tethering at nuclear periphery
| GO:1904537
| GO:1904537
| 1/3
| 1/4
| IGI
| IGI
| rap1
| rap1
Line 174: Line 284:
| negative regulation of protein binding
| negative regulation of protein binding
| GO:0032091
| GO:0032091
| 1/3
| 1/4
| IMP
| IMP
|  
|  
Line 184: Line 294:
| protein serine/threonine kinase activity
| protein serine/threonine kinase activity
| GO:0004674
| GO:0004674
| 2/3
| 2/4
| IDA
| IDA
|  
|  
Line 194: Line 304:
| ??
| ??
| ??
| ??
| 1/3
| 1/4
| ??
| ??
|  
|  
Line 204: Line 314:
| peptidyl-serine phosphorylation
| peptidyl-serine phosphorylation
| GO:0018105
| GO:0018105
| 2/3
| 2/4
| IGI-1, IMP-1
| IGI-1, IMP-1
| rap1
| rap1
Line 214: Line 324:
| peptidyl-threonine phosphorylation
| peptidyl-threonine phosphorylation
| GO:0018107
| GO:0018107
| 2/3
| 2/4
| IGI-1, IMP-1  
| IGI-1, IMP-1  
| rap1
| rap1
| during mitotic M phase (GO:0000087)
| 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)?
| 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
| cdc2
Line 224: Line 344:
| mitotic sister chromatid segregation
| mitotic sister chromatid segregation
| GO:0000070
| GO:0000070
| 1/3
| 1/4
| IC
| IC
| GO:1904537????????
| GO:1904537????????
Line 234: Line 354:
| protection from non-homologous end joining at telomere
| protection from non-homologous end joining at telomere
| GO:0031848
| GO:0031848
| 1/3
| 1/4
| IMP
| IMP
|  
|  
Line 244: Line 364:
| ??
| ??
| ??
| ??
| 1/3
| 1/4
| ??
| ??
|  
|  
Line 254: Line 374:
| ??
| ??
| ??
| ??
| 1/3
| 1/4
| ??
| ??
|  
|  
|  
|  
| Not sure if this observation [minichromosome loss] should lead to a 'regulation of mitotic sister chromatid segregation' type of annotation.
| 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
! Cellular Component Annotations
Line 274: Line 444:
| nuclear chromosome, telomeric region
| nuclear chromosome, telomeric region
| GO:0000784
| GO:0000784
| 2/3
| 3/4
| IDA
| IDA
|  
|  
|  
| exists_during mitotic G2 phase (GO:0000085) (1 included)
|  
| 1 included colocalizes_with
|-
|-
| ish1
| ish1
Line 284: Line 454:
| nuclear envelope
| nuclear envelope
| GO:0005635
| GO:0005635
| 2/3
| 3/4
| IDA
| IDA
|  
|  
|  
| exists_during mitotic G2 phase (GO:0000085)|exists_during mitotic M phase (GO:0000087) 1 included)
|  
| 1 included colocalizes_with
|-
|-
| atb2
| atb2
Line 294: Line 464:
| microtubule
| microtubule
| GO:0005874
| GO:0005874
| 2/3
| 3/4
| IDA
| IDA
|  
|  
| exists_during mitotic G2 phase (GO:0000085)|exists_during mitotic M phase (GO:0000087) 1 included)
| 1 included colocalizes_with (and used synonym tub1)
|-
| bqt4
|  
|  
| nuclear envelope
| GO:0005635
| 3/4
| IDA
|  
|  
| exists_during mitotic G2 phase (GO:0000085)|exists_during mitotic M phase (GO:0000087) 1 included)
| 1 included colocalizes_with
|-
|-
| bqt4
| bqt4
Line 304: Line 484:
| nuclear envelope
| nuclear envelope
| GO:0005635
| GO:0005635
| 1/3
| 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
| IDA
|  
|  
|  
|  
|  
| colocalizes_with
|-|}
|-|}

Revision as of 10:19, 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 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 3/4 IDA exists_during mitotic G2 phase (GO:0000085) (1 included) 1 included colocalizes_with
ish1 nuclear envelope GO:0005635 3/4 IDA exists_during mitotic M phase (GO:0000087) 1 included) 1 included colocalizes_with
atb2 microtubule GO:0005874 3/4 IDA exists_during mitotic M phase (GO:0000087) 1 included) 1 included colocalizes_with (and used synonym tub1)
bqt4 nuclear envelope GO:0005635 3/4 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