Annotation Conf. Call 2016-06-28: Difference between revisions
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==Annotation Consistency Exercise== | ==Annotation Consistency Exercise== | ||
*[http://www.ncbi.nlm.nih.gov/pubmed/27146270 Drosophila SLC22A Transporter Is a Memory Suppressor Gene that Influences Cholinergic Neurotransmission to the Mushroom Bodies.] | *[http://www.ncbi.nlm.nih.gov/pubmed/27146270 Drosophila SLC22A Transporter Is a Memory Suppressor Gene that Influences Cholinergic Neurotransmission to the Mushroom Bodies.] | ||
*'''How to capture biological process aspects of memory?''' | *'''How to capture biological process aspects of memory?''' | ||
**The paper identifies a ‘memory suppressor gene’ (Solute Carrier 22A of Drosophila (DmSLC22A) (FlyBase:CG7442; FBgn0037140). How to capture the biology described - memory, learning, conditioning? What new terms are needed to capture the process? Alternatively, is it better to capture these experiments only as phenotypes? | **The paper identifies a ‘memory suppressor gene’ (Solute Carrier 22A of Drosophila (DmSLC22A) (FlyBase:CG7442; FBgn0037140). How to capture the biology described - memory, learning, conditioning? What new terms are needed to capture the process? Alternatively, is it better to capture these experiments only as phenotypes? |
Revision as of 05:37, 27 June 2016
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Agenda
Annotation Consistency Exercise
- Drosophila SLC22A Transporter Is a Memory Suppressor Gene that Influences Cholinergic Neurotransmission to the Mushroom Bodies.
- How to capture biological process aspects of memory?
- The paper identifies a ‘memory suppressor gene’ (Solute Carrier 22A of Drosophila (DmSLC22A) (FlyBase:CG7442; FBgn0037140). How to capture the biology described - memory, learning, conditioning? What new terms are needed to capture the process? Alternatively, is it better to capture these experiments only as phenotypes?
- Leave the expression/mechanistic sections and have a look at these four sections of this paper:
- Drosophila CG7442 Is a Memory Suppressor Gene Functioning in MBn and DAn
- Drosophila CG7442 Overexpression Impairs Memory
- DmSLC22A Regulates Both Memory Acquisition and Retention
- DmSLC22A Modulates Memory Strength by Regulating Cholinergic Neurotransmission in the MB Calyx
Protein Binding Annotations
- Review Protein Binding Annotation Guidelines
- Use of With/From vs Annotation Extensions
- Annotation of Direct vs Indirect Binding
- Types of Experiments Used to Inform Physical Interactions
- Yeast two hybrid
- CoIP followed by Western blot
- CoIP followed by mass spec
- GST pull down using recombinant proteins
- GST pull down using lysate
- Types of Experiments Used to Inform Physical Interactions
- Use Cases
- GO:0030674 protein binding, bridging - The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way. Source: GOC:mah, GOC:vw, GOC:bf
- Evidence codes: IDA, IPI
- IPI has With/From, AE, or both With/From and AE
- AE uses has_input or has_direct_input for relation
- GO:0043495 protein anchor - Interacting selectively and non-covalently with both a protein or protein complex and a membrane, in order to maintain the localization of the protein at a specific location on the membrane. Source: GOC:go_curators
- Evidence codes: IDA, IGI, IMP, IPI
- IPI only uses With/From
- GO:0030674 protein binding, bridging - The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way. Source: GOC:mah, GOC:vw, GOC:bf