Category talk:CACAO Fall 2015

GO Term (GitHub) Requests

Ask us for help if this is your first Term Request. You'll need to read through this NTR Guide as well. Making an entry here only reminds us you have made a term request on the proper page, this table is not where the GO Consortium will address your requests- you must do that on GitHub.

If you do not yet have a GitHub ticket for your request, you should not edit this table.

User	Type	GO ID	term name	GitHub Link	GONUTS Link	Status	Notes
[[User:yourusername]]	Please select one	Leave this blank UNTIL a GO is assigned- then please fill it in!		Link to the GitHub ticket where the request was made	Link to the annotation. Format as [[Special:Cacao/annotation/10937]]: Special:Cacao/annotation/10937	Please select one	Provide your suggested GO term name, etc.
User:Mxb5379	New term request	GO:0098865	modification by symbiont of host bicellular tight junctions	https://github.com/geneontology/go-ontology/issues/12083	Special:Cacao/annotation/10974	accepted by GOC	modification by symbiont of host occluding cell-cell junction/bicellular tight junction Child of http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0044067#term=info Still waiting for IDs
User:Kaylamichbrown	New term request			https://github.com/geneontology/go-ontology/issues/12126		requested	histone H3-K4 monomethylation PMID:26320581^[1]
User:Mxb5379	New term request	GO:0098864	modification by symbiont of host occluding cell-cell junction	https://github.com/geneontology/go-ontology/issues/12083	Special:Cacao/annotation/10974	accepted by GOC	modification by symbiont of host occluding cell-cell junction/bicellular tight junction Child of http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0044067#term=info Still waiting for IDs
User:Madstidham1	New term request	GO:0098867	intramembranous bone growth	https://github.com/geneontology/go-ontology/issues/12111	Special:Cacao/annotation/10991	accepted by GOC	NTR: Intramembranous bone growth
User:Madstidham1	New term request	GO:1904770	intramembranous bone morphogenesis	https://github.com/geneontology/go-ontology/issues/12111		accepted by GOC	NTR: Intramembranous bone morphogenesis
edit table

Homework, Due by class 15 Sep

TAMU Homework:

1) Fill in the FOUR notes fields designated for your team in the FOLLOWING table ("Annotation Practice- Notes field").

If you don't yet know how to edit the table:

Login
Edit the table
Edit the row you want to change
Add your info to the Notes Field
Save the row to the table
Save the table to the page

Make sure you SAVE TWICE!!

Ask us for help editing if you can't get it to work. You can email the answers to us if you absolutely need to, but remember to consult with your teammates to make sure all the rows assigned to your team get done- they might also be able to help you edit the table. You'll have to learn how to work with these tables by next week to make your annotations though.

2) See if you can find some papers that look promising for annotations (Try for about 3-4)

You don't have to spend hours trying to read through the papers you think might work. We don't expect anyone other than returning students to have UniProt IDs or GO Terms yet. Remember to find papers on proteins (no papers that are reviews, clinical trials, only RNA, or about the handgrip strength of Lithuanian athletes), and try to be able to answer the following if we ask:

What organism is this on?
What specific protein(s) are you thinking of annotating?
What specific figure(s)/table(s) might work for an annotation?
Remember, it must be an experiment the authours did- no cartoons, schematics, general overview/graphical summary figures
What potential GO term would you try to look up? Look in your figure(s) for a
- chemical activity OR
- biological process OR
- location in the cell
What kind of experiment did they do in this figure (a general idea is OK, we don't expect you to know specific details)? Did they use a mutant strain/organism, or did they do a chemical assay (or both)?? Did they manually compare sequences or use some type of microscopy, etc.?

Concentrate on the Title/Abstract, figure captions, and Conclusion sections- these will give you the most information. Skim over the rest to be able to answer the above items.

Annotation Practice- Notes field

CACAO is unique in that we use the Notes field to identify the specific figures or tables that the annotation is based on.

Below are some examples of annotations done by other databases. The paper, protein, and GO term are already determined; you need to supply appropriate notes.

Page	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
ECOLI:DNAK	GO:0005737	cytoplasm	PMID:16858726^[2]	IDA: Inferred from Direct Assay		C	Figure 1 and Table 2	complete
ARATH:PPR16	GO:0042170	plastid membrane	PMID:21908688^[3]	IDA: Inferred from Direct Assay		C	Figure 5	complete
HUMAN:GRDN	GO:0032956	regulation of actin cytoskeleton organization	PMID:16139227^[4]	IMP: Inferred from Mutant Phenotype		P	Figure 4	complete
MOUSE:GREM1	GO:1900086	positive regulation of peptidyl-tyrosine autophosphorylation	PMID:20660291^[5]	IDA: Inferred from Direct Assay		P	Team Team You cannot B. cereus, Figure 2!	complete
MYCTU:3BHS	GO:0003854	3-beta-hydroxy-delta5-steroid dehydrogenase activity	PMID:17630785^[6]	IDA: Inferred from Direct Assay		F	Team Team You cannot B. cereus, Figure 2!	complete
DICDI:IFKA	GO:0004694	eukaryotic translation initiation factor 2alpha kinase activity	PMID:12697064^[7]	IMP: Inferred from Mutant Phenotype		F	Team G-nomes notes written	complete
ARATH:PPR16	GO:0042170	plastid membrane	PMID:21908688^[3]	IDA: Inferred from Direct Assay		C	Figure 5B, line 48, AT1G06270 Pentatricopeptide repeat (PPR) Plastid/ER (M)	complete
HUMAN:GRDN	GO:0032956	regulation of actin cytoskeleton organization	PMID:16139227^[4]	IMP: Inferred from Mutant Phenotype		P	Figure 5C. Consistent with the immunofluorescence analysis, the density of the cortical actin filaments visible in electron micrographs of the cytoplasmic surface under the plasma membrane of Girdin-depleted Vero cells is lower than that in the control cells, where more tightly organized actin fibers predominate	complete
MOUSE:GREM1	GO:1900086	positive regulation of peptidyl-tyrosine autophosphorylation	PMID:20660291^[5]	IDA: Inferred from Direct Assay		P	(Figure 2A-B). VEGFR2 activation is also abrogated by the VEGFR2 tyrosine kinase inhibitor SU54168 both in gremlin and VEGF-A–activated ECs (Figure 2C). Accordingly, VEGFR2 phosphorylation, abrogated by SU5416, was observed in fetal bovine aortic VEGFR2-GM7373 ECs stimulated by gremlin	complete
MYCTU:3BHS	GO:0003854	3-beta-hydroxy-delta5-steroid dehydrogenase activity	PMID:17630785^[6]	IDA: Inferred from Direct Assay		F	Team G-nomes notes written	complete
DICDI:IFKA	GO:0004694	eukaryotic translation initiation factor 2alpha kinase activity	PMID:12697064^[7]	ISS: Inferred from Sequence or Structural Similarity	SGD:S000002691 UniProtKB:P15442	F	Team Hardy Weinburgers, write your notes here! Please note: The UPKB and SGD refer to the same protein. We only allow you to use UniProt identifiers in this column.	complete
DICDI:IFKA	GO:0004694	eukaryotic translation initiation factor 2alpha kinase activity	PMID:12697064^[7]	ISS: Inferred from Sequence or Structural Similarity	SGD:S000002691 UniProtKB:P15442	F	Team Bob Ross, write your notes here! Please note: The UPKB and SGD refer to the same protein. We only allow you to use UniProt identifiers in this column.	complete
DICDI:IFKA	GO:0004694	eukaryotic translation initiation factor 2alpha kinase activity	PMID:12697064^[7]	ISS: Inferred from Sequence or Structural Similarity	SGD:S000002691 UniProtKB:P15442	F	Team You cannot B. cereus, Figure 1! Please note: The UPKB and SGD refer to the same protein. We only allow you to use UniProt identifiers in this column.	complete
DICDI:IFKA	GO:0004694	eukaryotic translation initiation factor 2alpha kinase activity	PMID:12697064^[7]	ISS: Inferred from Sequence or Structural Similarity	SGD:S000002691 UniProtKB:P15442	F	Team G-nomes notes written Please note: The UPKB and SGD refer to the same protein. We only allow you to use UniProt identifiers in this column.	complete
MOUSE:GREM1	GO:1900086	positive regulation of peptidyl-tyrosine autophosphorylation	PMID:20660291^[5]	IDA: Inferred from Direct Assay		P	Figure 2A,B,C. VEGFR2 activation mediates the proangiogenic activity of gremlin in vitro and in vivo.	complete
HUMAN:GRDN	GO:0032956	regulation of actin cytoskeleton organization	PMID:16139227^[4]	IMP: Inferred from Mutant Phenotype		P	Team You cannot B. cereus, Figure 5.	complete
edit table

Suggested Papers

I've run across these papers, and they either possibly have annotations or they seem to lead in to possible annotations.

PMID:9164876

References

↑ Zhang, Y et al. (2015) Evolving Catalytic Properties of the MLL Family SET Domain. Structure 23 1921-33 PubMed GONUTS page
↑ Lasserre, JP et al. (2006) A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis. Electrophoresis 27 3306-21 PubMed GONUTS page
↑ ^3.0 ^3.1 Narsai, R et al. (2011) In-depth temporal transcriptome profiling reveals a crucial developmental switch with roles for RNA processing and organelle metabolism that are essential for germination in Arabidopsis. Plant Physiol. 157 1342-62 PubMed GONUTS page
↑ ^4.0 ^4.1 ^4.2 Enomoto, A et al. (2005) Akt/PKB regulates actin organization and cell motility via Girdin/APE. Dev. Cell 9 389-402 PubMed GONUTS page
↑ ^5.0 ^5.1 ^5.2 Mitola, S et al. (2010) Gremlin is a novel agonist of the major proangiogenic receptor VEGFR2. Blood 116 3677-80 PubMed GONUTS page
↑ ^6.0 ^6.1 Yang, X et al. (2007) Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase. Biochemistry 46 9058-67 PubMed GONUTS page
↑ ^7.0 ^7.1 ^7.2 ^7.3 ^7.4 Fang, R et al. (2003) IfkA, a presumptive eIF2 alpha kinase of Dictyostelium, is required for proper timing of aggregation and regulation of mound size. BMC Dev. Biol. 3 3 PubMed GONUTS page

CACAO II assignments, week of 6 October

Emma:

Lorna:

If they're already assessed, go ahead and do it again, as the assessment may not be right. Try not to read the other assessments until you've done yours. Don't tick the radios yet, at least until Friday or Saturday.

Andy:

User:Jkane94

User:Njd5204 I can't remember if I sent them any, actually...

[PMID:26320581-1] Zhang, Y et al. (2015) Evolving Catalytic Properties of the MLL Family SET Domain. Structure 23 1921-33 PubMed GONUTS page

[PMID:16858726-2] Lasserre, JP et al. (2006) A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis. Electrophoresis 27 3306-21 PubMed GONUTS page

[PMID:21908688-3] 3.0 ^3.1 Narsai, R et al. (2011) In-depth temporal transcriptome profiling reveals a crucial developmental switch with roles for RNA processing and organelle metabolism that are essential for germination in Arabidopsis. Plant Physiol. 157 1342-62 PubMed GONUTS page

[PMID:16139227-4] 4.0 ^4.1 ^4.2 Enomoto, A et al. (2005) Akt/PKB regulates actin organization and cell motility via Girdin/APE. Dev. Cell 9 389-402 PubMed GONUTS page

[PMID:20660291-5] 5.0 ^5.1 ^5.2 Mitola, S et al. (2010) Gremlin is a novel agonist of the major proangiogenic receptor VEGFR2. Blood 116 3677-80 PubMed GONUTS page

[PMID:17630785-6] 6.0 ^6.1 Yang, X et al. (2007) Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase. Biochemistry 46 9058-67 PubMed GONUTS page

[PMID:12697064-7] 7.0 ^7.1 ^7.2 ^7.3 ^7.4 Fang, R et al. (2003) IfkA, a presumptive eIF2 alpha kinase of Dictyostelium, is required for proper timing of aggregation and regulation of mound size. BMC Dev. Biol. 3 3 PubMed GONUTS page

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Category talk:CACAO Fall 2015

Contents

GO Term (GitHub) Requests

Homework, Due by class 15 Sep

Annotation Practice- Notes field

Suggested Papers

References

CACAO II assignments, week of 6 October

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