Annotation Conf. Call 2016-10-25: Difference between revisions

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| comment
| comment
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|''Molecular Function''
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|2a
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|gflB
|
|GO:0001965 G-protein alpha-subunit binding
|IPI
|gpaB (DDB_G0276267)
|
|1b
|-
|gflB
|
|GO:0005515 protein binding
|IPI
|rapA (DDB_G0291237)
|happens_during GO:0001965 G-protein alpha-subunit binding
|s2e + 2b
|-
|gflB
|
|NTR: activation of Rap1 GTPase activity
|IMP
|
|part_of GO:0071320 cellular response to cAMP
|
|-
|gflB
|
|GO:0001965 G-protein alpha-subunit binding
|IPI
|gpaB
|occurs_at SO:0100014 n_terminal_region
|SO term is defining where gflB binds to gpaB - need new relation?
|-
|gflB
|
|GO:0031267 small GTPase binding
|IPI
|RapA
|happens_during, has_direct_input activation of GTPase activity, gpaB
|maybe Rap GTPase binding should be added as child, all others are there
|-
|gflB
|
|GO:0017034 Rap guanyl-nucleotide exchange factor activity
|IDA
|
|has_input, happens_during, occurs_at rapA,activation of GTPase activity,  cell cortex
|
|-
|gflB
|
|GO:0005543 phospholipid binding
|IDA
|
|occurs_at SO:0100014 n_terminal_region
|Fig.5SA
|-
|gflB
|
|GO:0001965 G-protein alpha-subunit binding
|IPI
|gpaB
|activated by GppNHp (CHEBI:78408)
|or should this be GTP (CHEBI:15996); pg 460 left column
|-
|gflB
|
|GO:0017034 Rap guanyl-nucleotide exchange factor activity
|IDA
|
|has regulation target: rapA UniProt: P18613
|pg 461 left column
|-
|GflB
|
|GO:0005515 protein binding
|IPI
|GpaB
|
|
|-
|GflB
|
|GO:0005085 guanyl-nucleotide exchange factor activity
|IMP
|
|
|
|-
|GflB
|
|GO:0005085 guanyl-nucleotide exchange factor activity
|IDA
|
|has_input Rap1
|
|-
|GflB
|
|GO:0005515 protein binding
|IPI
|Rap1
|has_participant GpaB
|depends on Ga2 being bound to GPPnHp
|-
|GflB
|
|GO:0005515 protein binding
|IPI
|GpaB
|
|
|-
|GflB
|
|GO:0005515 protein binding
|IPI
|RACB, RACL
|
|
|-
|GflB
|
|GO:0005085 guanyl-nucleotide exchange factor activity
|IDA
|
|has_direct_input UniProtKB:P18613
|RAP1 is target
|-
|gpaB
|
|GO:0005515 protein binding
|IPI
|gflB (DDB_G0286773)
|
|1b
|-
|gpaB
|
|NTR: Ras guanyl-nucleotide exchange factor binding
|IC
|GO:0005515 protein binding
|
|1
|-
|gpaB
|
|GO:0032092 positive regulation of protein binding
|IDA
|
|has_regulation_target AND has_regulation_target gflB (DDB_G0286773) AND rapA (DDB_G0291237
|2b
|-
|gpaB
|
|GO:0005515 protein binding
|IPI
|GflB
|
|Possibly a new term for guanylyl-nucleotide exchange factor binding?  Also, see above.
|-
|gpaB
|
|GO:0005515 protein binding
|IPI
|gflB
|part_of GO:0007186 G-protein coupled receptor signaling pathway
|maybe new term 'nucleitide exchange factor binding? Cannot easily annotate that only activated (GTP bound) gpbA  binds to gflB
|-
|GpaB
|
|GO:0005515 protein binding
|IPI
|GflB
|
|
|-
|GskA
|
|GO:0004674 protein serine/threonine kinase activity
|IDA
|
|has_direct_input GflB
|
|-
|GskA
|
|GO:0004674 protein serine/threonine kinase activity
|IMP
|
|happens_during, part_of, has_regulation_target GO:0071320, GO:1905097, GflB
|full extension: happens_during GO:0071320, part_of GO:1905097, has_regulation_target GflB (GO:0071320 = cellular response to cAMP; GO:1905097 = regulation of guanyl-nucleotide exchange factor activity)
|-
|gskA
|
|GO:0004674 protein serine/threonine kinase activity
|IDA
|
|has_input gflB (DDB_G0286773)
|5d
|-
|GskA
|
|GO:0004674 protein serine/threonine kinase activity
|ISS
|human GSK3b
|has input GflB
|
|-
|GskA
|
|GO:0004674 protein serine/threonine kinase activity
|IDA
|
|has_direct_input UniProtKB:Q54L90
|
|-
|RACB
|
|GO:0005515 protein binding
|IPI
|GflB
|
|Fig. S1
|-
|RACL
|
|GO:0005515 protein binding
|IPI
|GflB
|
|Fig. S1
|-
|rapA
|
|GO:0005515 protein binding
|IPI
|gflB (DDB_G0286773)
|happens_during GO:0001965 G-protein alpha-subunit binding
|s2e + 2b
|-
|rapA
|
|GO:0005515 protein binding
|IPI
|GflB
|
|
|-
|rapA
|
|GO:0005515 protein binding
|IPI
|GflB
|happens_during activation of GTPase activity
|new term 'nucleitide exchange factor binding?
|-
|-
| ''Cellular Component''
|-  
|-  
|-
| gene
| gflB
|
| GO:0005737 cytoplasm
| IDA
|
|
| unstimulated cells
|-
| gflB
|
| GO:1904269 cell leading edge cell cortex
| IDA
|
|
| unstimulated cells
|-
| gflB
|
| GO:0005938 cell cortex
| IDA
|
| exists_during GO:0071320
| GO:0071320 = cellular response to cAMP; not sure how to capture cytoskeleton dependency, in conventional annotation extensions or LEGO; does the experiment with GflBP1 and LatA show plasma membrane GO:0005886?
|-
| gflB
|
| GO:0005737 cytoplasm
| IDA
|
|
| 5a
|-
| gflB
|
| GO:0005737 cytoplasm
| IDA
|
| exists_during asexual reproduction
|
|-
| gflB
|
| GO:0005938 cell cortex
| IDA
|
| exists_during response to cAMP
|
|-
| gflB
|
| GO:0031252 cell leading edge
| IDA
|
| exists_during chemotaxis to cAMP
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|-
| gflB
|
| GO:0005886 plasma membrane
| IDA
|
| exists_during chemotaxis to cAMP
|  annotated 'plasma membrane' because of latA + domain expression experiments, also Supp Fig. 5A shows Phospholipid binding (see MF)
|-
| GflB
|
| GO:0005938 cell cortex
| IDA
|
|
|
|-
| GflB
|
| GO:0031252 cell leading edge
| IDA
|
| exists_during chemotaxis (GO:0006935)
|
|-
| gflB
|
| GO:0005737 cytoplasm
| IDA
|
|
| pg 462 right column
|-
| gflB
|
| GO:0031252 cell leading edge
| IDA
|
| exists during: cell chemotaxis GO:0060326
| gradient treatment to induce chemotaxis; pg 462 right column
|-
| gflB
|
| GO:0005938 cell cortex
| IDA
|
| happens during: cellular response to cAMP GO:0071320
| uniform or global treatment with cAMP; pg 462 right column
|-
| gflB
|
| GO:0031256 leading edge membrane
| IDA
|
|
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|-
| gflB
|
| GO:0031252 cell leading edge
| IDA
|
|
|
|-
| gflB
|
| GO:1904269  cell leading edge cell cortex
| IDA
|
| localization_dependent_on ?Galpha2
| requires binding of active Galpha
|-
| Raf1
|
| GO:1904269 cell leading edge cell cortex
| IDA
|
|
|
|-
| Ral
|
| GO:1904269 cell leading edge cell cortex
| IDA
|
|
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|-
| Rap1
|
| GO:0009279 cell outer membrane
| IDA
|
|
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|-
| Rap1
|
| GO:0005886 plasma membrane
| IDA
|
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|-
| rapA
|
| GO:0005886 plasma membrane
| IDA
|
|
| 3a
|-
| rapA
|
| GO:0005886 plasma membrane
| IDA
|
|
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|-
| rasG
|
| GO:0005886 plasma membrane
| IDA
|
|
| 3a
|-
| RasG
|
| GO:0005886 plasma membrane
| IDA
|
|
|
|-
| RasG
|
| GO:0009279 cell outer membrane
| IDA
|
|
|
|-
| RasG
|
| GO:0005886 plasma membrane
| IDA
|
|
| GOID term
| evidence code
|
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| comment
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Revision as of 17:22, 19 October 2016

Bluejeans URL: https://bluejeans.com/993661940

Agenda

Meetings

Next GOC Meeting - USC, Los Angeles, CA, November 4-6, 2016

  • Link to a registration form is now available for the USC Meeting on the Meeting Logistics Page.
  • Register for meeting and dinner, just dinner, just meeting.
  • No registration fee for the Noctua workshop.

Discussion of Outstanding github Tickets

Annotation Consistency Exercise

Abstract AIM:To elucidate the sequential transfer of iron amongst ferritin, transferrin and transferrin receptor under various iron status conditions. METHODS:Incorporation of 59Fe into mucosal and luminal proteins was carried out in control WKY rats. The sequential transfer of iron amongst ferritin, transferrin and transferrin receptor was carried out in iron deficient, control and iron overloaded rats. The duodenal proteins were subjected to immunoprecipitation and quantitation by specific ELISA and in situ localization by microautoradiography and immunohistochemistry in tandem duodenal sections. Human duodenal biopsy (n = 36) collected from subjects with differing iron status were also stained for these proteins. RESULTS:Ferritin was identified as the major protein that incorporated iron in a time-dependent manner in the duodenal mucosa. The concentration of mucosal ferritin was significantly higher in the iron excess group compared to control, iron deficient groups (731.5 +/- 191.96 vs 308.3 +/- 123.36, 731.5 +/- 191.96 vs 256.0 +/- 1.19, P < 0.005), while that of luminal transferrin which was significantly higher than the mucosal did not differ among the groups (10.9 +/- 7.6 vs 0.87 +/- 0.79, 11.1 +/- 10.3 vs 0.80 +/- 1.20, 6.8 +/- 4.7 vs 0.61 +/- 0.63, P < 0.001). In situ grading of proteins and iron, and their superimposition, suggested the occurrence of a sequential transfer of iron. This was demonstrated to occur through the initial binding of iron to luminal transferrin then to absorptive cell surface transferrin receptors. The staining intensity of these proteins varied according to the iron nutrition in humans, with intense staining of transferrin receptor observed in iron deficient subjects. CONCLUSION:It is concluded that the intestine takes up iron through a sequential transfer involving interaction of luminal transferrin, transferrin-transferrin receptor and ferritin.

Annotations

Gene/Marker Name Qualifier GO ID/term Evidence Code With/From Annotation Extension Comment
Biological Process
gene GOID term evidence code comment
Cellular Component
gene GOID term evidence code comment
Molecular Function
gene GOID term evidence code comment

Minutes

  • On call: