Annotation Conf. Call 2015-09-22
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 | |||
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. | ||
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 | |||
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 |