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

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| comment
| comment
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| gflB
|''Cellular Component''
|
| GO:0030837 negative regulation of actin polymerization
| IMP
|
|
| part_of GO:0050920 regulation of chemotaxis?      presumably indirect, via effect on rapA activity; will be clearer in LEGO
|-
| gflB
|
| GO:new (cf. GO:0043520) positive regulation of myosin II filament assembly
| IMP
|
|
| part_of GO:0050920 regulation of chemotaxis?      presumably indirect, via effect on rapA activity; will be clearer in LEGO
|-
| gflB
|
| GO:0046580 negative regulation of Ras protein signal transduction
| IMP
|
| part_of GO:0071320 cellular response to cAMP
| 2e, 2f
|-
| gflB
|
| GO:0030010 establishment of cell polarity
| IMP
|
| part_of GO:0071320 cellular response to cAMP
| s3b, 3a, s4a
|-
| gflB
|
| NTR: negative regulation of Akt/PKB singalling
| IMP
|
|
| 3b, 3c, s4b
|-
| gflB
|
| NTR: negative regulation of actin polimerization
| IMP
|
| happens_during GO:0043327 chemotaxis to cAMP
| 4a-c
|-
| gflB
|
| NTR: positive regulation of myosin II polimerization
| IMP
|
| happens_during GO:0043327 chemotaxis to cAMP
| 4a-c
|-
| gflB
|
| GO:0043327 chemotaxis to cAMP
| IMP
|
|
| The observed developmental defects seem to be downstream of the cAMP signaling, so maybe in a LEGO diagram the process of chemotaxis to cAMP would have a positive causal relationship to the developmentl processes?  Also, 'chemotaxis to cAMP' does not seem to have a relationship to 'response to cAMP' in the ontology.  Should it?
|-
| gflB
|
| GO:0071320 cellular response to cAMP
| IMP
|
|
|
|-
| gflB
|
| GO:0043547 positive regulation of GTPase activity
| IMP
|
| has_regulation_target Rap1
|
|-
| gflB
|
| GO:0034260 negative regulation of GTPase activity
| IMP
|
| has_regulation_target RasG|RasB|RasC
| I'm not sure if it's okay to put all of these specific Ras targets when a pan-Ras antibody was used.
|-
| gflB
|
| GO:0007264 small GTPase mediated signal transduction
| IMP
|
|
|
|-
| gflB
|
| GO:0030836 negative regulation of actin filament polymerization
| IMP
|
|
| I'm not sure about making this annotation; if I'm understanding the model correctly, the regulation would be indirect.
|-
| gflB
|
| GO:new positive regulation of myosin II filament assembly
| IMP
|
|
|
|-
| gflB
|
| GO:0090630 activation of GTPase activity
| IMP
|
| has_regulation_target, happens_during, occurs_at rapA, response to cAMP, cell leading edge
| as rap is in ras superfamily, this is the most specific term
|-
| gflB
|
| GO:0046580 negative regulation of Ras protein signal transduction
| IMP
|
| has_regulation_target, happens_during, occurs_at | happens_during rasC, rasG, rasB , response to cAMP, cell leading edge | asexual reproduction
| alternative term: negative regulation of GTPase activity
|-
| gflB
|
| GO:0061118 regulation of positive chemotaxis to cAMP
| IMP
|
|
|
|-
| gflB
|
| GO:0030837 negative regulation of actin filament polymerization
| IMP
|
| happens_during(GO:0051591) response to cAMP ,occurs_at(GO:0005886) plasma membrane
|
|-
| gflB
|
| GO:0043520 regulation of myosin II filament assembly
| IMP
|
| happens_during(GO:0051591 response to cAMP ,occurs_at(GO:0005886) plasma membrane
|
|-
| gflB
|
| GO:0030010 establishment of cell polarity
| IMP
|
|
|
|-
| gflB
|
| GO:0071901 negative regulation of protein serine/threonine kinase activity
| IMP
|
| has_input gflB
|
|-
| gflB
|
| GO:0007264 small GTPase mediated signal transductions
| IMP
|
| has_regulation_target pkbA, pkgA
|
|-
| gflB
|
| GO:0030837 negative regulation of actin filament polymerisation
| IMP
|
|
|
|-
| gflB
|
| GO:0043520 regulation of myosin II filament assembly
| IMP
|
|
|
|-
| gflB
|
| GO:0006935 chemotaxis
| IMP
|
|
|
|-
| gflB
|
| GO:0046579 positive regulation of Ras protein signal transduction
| IMP
|
|
|
|-
| gflB
|
| GO:0061122 positive regulation of positive chemotaxis to cAMP
| IMP
|
|
| pg 460 right column
|-
| gflB
|
| GO:0032487 regulation of Rap protein signal transduction
| IMP
|
| happens during: cellular response to cAMP| has input: rapA GO:0071320|UniProt: P18613
| may need to request "positive regulation of Rap signal transduction; pg 461 right column
|-
| gflB
|
| GO:0046580 negative regulation of Ras protein signal transduction
| IMP
|
| happens during: cellular response to cAMP GO:0071320
| no input here as it could be RasG, RasB and or RasC; pg 461 right column
|-
| gflB
|
| GO:0030838 positive regulation of actin filament polymerisation
| IMP
|
| happens during: cellular response to cAMP| occurs at: cell leading GO:0071320|GO:0031252
| pg 462 right column
|-
| gflB
|
| GO:0043520 regulation of myosin II filament assembly
| IMP
|
| happens during: cellular response to cAMP| occurs at: cell leading GO:0071320|GO:0031252
| may need to request "positive regulation of myosin II filament assembly; pg 462 right column
|-
| gflB
|
| GO:0043327 chemotaxis to cAMP
| IMP
|
|
|-
| gflB
|
| GO:0046580 negative regulation of Ras protein signal transduction
| IMP
|
| regulates_o_has_participant RasG
|
|-
| gflB
|
| GO:0046579 positive regulation of Ras protein signal transduction
| IMP
|
| regulates_o_has_participant Rap1
|
|-
| gflB
|
| GO:0030837 negative regulation of actin filament polymerisation
| IMP
|
|
|
|-
| gflB
|
| GO:0043520 regulation of myosin II filament assembly
| IMP
|
|
| ask for positive regulation term
|-
| gflB
|
| GO:0061339 establishment or maintenance of monopolar cell polarity
|
|
|
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|-
| gflB
|
| GO:0060326 cell chemotaxis
| IMP
|
|
|
|-
| gflB
|
| GO:0046580 negative regulation of Ras protein signal transduction
|
|
| happens_during GO:0060326 cell chemotaxis
|
|-
| gflB
|
| GO:0032487 regulation of Rap protein signal transduction
| IMP
|
| happens_during GO:0060326 cell chemotaxis
|
|-
| gflB
|
| GO:0032487 regulation of Rap protein signal transduction
| IMP
|
| has_regulation_target UniProtKB:P18613
| RAP1 is target
|-
| gpaB
|
| GO:0043327 chemotaxis to cAMP
| IMP
|
|
| Table 1, Figure 1, Movies S1-S3.
|-
| gpaB
|
| GO:0048468 cell development
| IMP
|
|
| S1e
|-
| gpaB
|
| GO:0032092 positive regulation of protein binding
| IDA
|
| has_regulation_target GflB,rapA
| I'm not sure the exact meaning of this annotation is clear, i.e. that gpaB is regulating the binding of GflB to rapA.
|-
| gpaB
|
| GO:1905099 positive regulation of guanyl-nucleotide exchange factor activity
| IDA
|
| has_regulation_target, occurs_at gflB, GO:1904269 cell leading edge cell cortex
|
|-
| gpaB
|
| GO:1905099 positive regulation of guanyl-nucleotide exchange factor activity
| IDA
|
| has regul;ation target: gflB UniProt: Q54L90
|pg 461 left column
|-
| gpaB
|
| GO:1905099 positive regulation of guanyl-nucleotide exchange factor activity
| IDA
|
|
| request a PRO term for the active form?
 
|-
| gskA
|
| GO:0006468 protein phosphorylation
| IDA
|
| has_input AND negatively_regulates gflB (DDB_G0286773) AND GO:0072697 protein localization to cell cortex
| 5d, 5e
|-
| gskA
|
| GO:1904777 negative regulation of protein localization to cell cortex
| IMP
|
| has_regulation_target gflB (DDB_G0286773)
| 5e
|-
| gskA
|
| GO:0018105 peptidyl serine phosphorylation
| IMP
|
|
|
|-
| gskA
|
| GO:0018107 peptidyl threonine phosphorylation
| IMP
|
|
|
|-
| gskA
|
| GO:1904776 regulation of protein localization to cell cortex
| IMP
|
| has_regulation_target GflB
|
|-
| gskA
|
| GO:0006468 protein phosphorylation
| IDA
|
|has_input gflB
|
|-
| gskA
|
| GO:1904776 regulation of protein localization to cell cortex
| IMP
|
| has_regulation_target, occurs_at  gflB, leading edge
|
|-
| gskA
|
| GO:0018105 peptidyl-serine phosphorylation
| IMP
|
| has input: gflB UniProt: Q54L90
| pg 464 right column
|-
| gskA
|
| GO:0018107 peptidyl-threonine phosphorylation
| IMP
|
| has input: gflB UniProt: Q54L90
| pg 464 right column
|-
| gskA
|
| GO:1904777 negative regulation of protein localization to cell cortex
| IMP
|
| has regulation target: gflB|happens during: cellular response to cAMP UniProt: Q54L90|GO:0071320
|  pg 464 right column
|-
| gskA
|
| GO:0006468 protein phosphorylation
| IMP
|
| has_input GflB
|
|-
| gskA
|
| GO:1902463 protein localization to cell leading edge
|
|
| transports or maintains localization of GflB
|
|-
| rapA
|
| GO:0071320 cellular response to cAMP
| IEP
|
|
|
|-
| rasB
|
| GO:0071320 cellular response to cAMP
| IEP
|
|
| See above comment on pan-Ras antibody.
|-
| rasC
|
| GO:0071320 cellular response to cAMP
| IEP
|
|
| See above comment on pan-Ras antibody.
|-
| rasG
|
| GO:0071320 cellular response to cAMP
| IEP
|
|
| See above comment on pan-Ras antibody.
|-
|-
| ''Molecular Function''
|-  
|-  
| gflB
| gene
|
| GO:0017034 Rap guanyl-nucleotide exchange factor activity
| IDA
|
| has_regulation_target Rap1
|
|-
|gflB
|
|GO:0005515 protein binding
|IDA
|Ga2
|
|
|
|-
|gflB
|
|GO:0005515 protein binding
|IPI
|Rap1
|
|
|how to capture "requires presence of active Ga2" in conventional annotation? (I'm not even sure how to do it in LEGO)
| GOID term
|-
| evidence code
|gflB
|NOT
|NTR: Rho GTPase activator activity
|IDA
|
|
|
|
|S2b-d
| comment
|-
|-
|gflB
|
|GO:0005088 Ras guanyl-nucleotide exchange factor activity
|IMP
|
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|

Revision as of 17:20, 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
2a
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
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
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
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
Rap1 GO:0009279 cell outer membrane IDA
Rap1 GO:0005886 plasma membrane IDA
rapA GO:0005886 plasma membrane IDA 3a
rapA GO:0005886 plasma membrane IDA
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

Minutes

  • On call:
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