Cardiac conduction: Difference between revisions
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* New GO term(s) to describe 'plateau phase of the cardiac action potential', 'persistent or late inward current (INaL)', 'duration of the cardiac action potential'. | * New GO term(s) to describe 'plateau phase of the cardiac action potential', 'persistent or late inward current (INaL)', 'duration of the cardiac action potential'. | ||
* mutation in SCN5A leads to a prologation of Q-T interval, need some parent terms such as 'regulation of cardiomyocyte membrane depolarization', 'regulation of cardiomyocyte membrane repolarization' 'regulation of cardiomyocyte membrane potential' to capture information about changes in the ECG measurements. | * mutation in SCN5A leads to a prologation of Q-T interval, need some parent terms such as 'regulation of cardiomyocyte membrane depolarization', 'regulation of cardiomyocyte membrane repolarization' 'regulation of cardiomyocyte membrane potential' to capture information about changes in the ECG measurements. | ||
* At present the GO term 'blood circulation' is only linked to SNC5A via 'regulation' terms, should SNC5A be transitively associated with 'blood circulation', and if so how? | * At present the GO term GO:0008015 'blood circulation' is only linked to SNC5A via 'regulation' terms, should SNC5A be transitively associated with 'blood circulation', and if so how? | ||
'''Other''' | '''Other''' | ||
* what does 'density' in the phrase 'sodium channel current (INa) density' mean? | * what does 'density' in the phrase 'sodium channel current (INa) density' mean? |
Revision as of 09:16, 16 September 2011
GOC meeting link 2011_UCL_Meeting_Logistics
Venue and date
- South Wing Committee Room, University College London, Thursday 10th and Friday 11th (1/2 day) November 2011
Draft Programme
Thursday 10th November 2011 (room booked 9am-6pm)
9:15am | Coffee and breakfast pastries | |
9:30am | Welcome and introduction | Ruth |
9:35am | Introduction to GO | David |
9:55am | Check terms are applicable across Bilateria | Susan |
10:00am | Overview of current cardiac conduction description in GO, start to work on ontology | David |
11am | Coffee break | |
11:30am | ||
12:30pm | Lunch at Ask on Grafton Way. Menu | |
2pm | Continue with Ontology | |
2:45pm | ||
3:45pm | Coffee break | |
4pm | ||
5pm | Close |
Friday 11th November 2011 (room booked 9am to 1pm)
9:15am | Coffee and breakfast pastries | |
9:30am | Welcome back and questions | Ruth |
9:35am | Complete annotation documentation, decide how specific genes known to be involved in various cardiac conduction processes will be annotated using the new ontology | |
11am | Coffee break | |
11:30am | ||
1pm | Close |
Items to add to Programme
Please add any items to be added to the programme below
Working group
GO curators and editors: David, Ruth, Doug, Tanya, Becky, Paola, Stan, Susan
Expert scientists:
- Agreed to attend:
- Prof Peter Scambler p.scambler@ich.ucl.ac.uk (if needed)
- Prof Shoumo Bhattacharya shoumo@me.com
- Prof Paul Riley p.riley@ich.ucl.ac.uk
- Dr Ross A Breckenridge r.breckenridge@ucl.ac.uk (available on Thursday, probably not able to attend on Friday)
- Prof Andrew Tinker rmhaant@ucl.ac.uk
- Dr Pier Lambiase pier.lambiase@uclh.nhs.uk Consultant Cardiologist
- Bernard de Bono (virtual physiology)
Attendees
Name | Organization | Vegetarian (Y/N) |
---|---|---|
Ruth Lovering | BHF-UCL | N |
Varsha Khodiyar | BHF-UCL | N |
David Hill | The Jackson Laboratory | N |
Susan Tweedie | FlyBase, University of Cambridge | N |
Rebecca Foulger | GO editorial office, EBI | N |
Paola Roncaglia | GO editorial office, EBI | N |
Tanya Berardini | TAIR, Carnegie Institute for Science | N |
Doug Howe | Zfin | Remote attendance |
Stan Laulederkind | RGD | N |
Minutes GOC Satellite meeting 5:30 - 6:30 Thursday 19th May 2011 LA
- David, Ruth, Doug, Tanya, Becky, Paola, Stan
- Currently only 2 GO terms in this ontology:
- Cardiac conduction
- Atrioventricular node impulse conduction delay
- Missing links/terms
- regulation of cardiac muscle contraction
- regulation of heart rate
- strength of heart contraction
- blood pressure
- sensing
- systemic signaling
- hormone signaling (note forth coming development of this domain)
- action potential
- long synaptic potential
- synaptic plasticity
- regulation of membrane potential
- Ontology for development of the cardiac conduction system pretty much sorted, maybe a few additional cell types to add, but this shouldn't be the scope of this workshop.
- Workshop for ontology for neurological terms on 7th September 2011 - NOTE This has been delayed and might happen the week after the London GOC meeting/cardiac conduction workshop, but it's not sure yet.
- Ideally Paola to attend this meeting (note Paola has a neurobiology background)
Action items
- All:
- Work towards identifying scope of workshop, set by mid July
- Set up table for annotation guide - what genes to annotate to these new GO terms, perhaps capture experimental information here. Eg how to interpret changes in P or QRS intervals associated with specific genes.
- Add figures to wiki to illustrate cardiac conduction processes
- Add useful reviews/papers to wiki
- Ruth:
- Contact experts above (max 5 experts)
- Book rooms
- Ask experts to review blood pressure ontology
- Ask Varsha for her draft ontology
- Doug:
- Look at differences and similarities between zebrafish and mammalian cardiac conduction processes
- My notes on comparative anatomy and functioning of card. cond.
- David and Tanya
- Set up overview of ontology
- Stan
- Review hormone literature/ontology
- Aspects of cardiac conduction affected by hormones
- Paola
- Pacemaker
- Susan
- Look at differences and similarities between Drosophila and mammalian cardiac conduction processes
- Becky
- Look at key signaling pathways that regulate heart rate & cardiac conduction.
Useful papers
The emerging genetic landscape underlying cardiac conduction system function PMID: 21538814 [1]
Wnt11 patterns a myocardial electrical gradient through regulation of the L-type Ca(2+) channel (zebrafish) PMID: 20657579 [2]
The cardiac conduction system. PMID: 21357845 [3]
The Anatomy and Physiology of the Sinoatrial Node—A Contemporary Review PMID: 20946278 [4]
Genetic and physiologic dissection of the vertebrate cardiac conduction system. PLoS Biol. 2008 May 13;6(5):e109. PubMed PMID: 18479184; PubMed Central PMCID: PMC2430899. [5]
Induction and patterning of the cardiac conduction system. Int J Dev Biol. 2002 Sep;46(6):765-75. Review. PubMed PMID: 12382942. [6]
Development of the cardiac conduction system. Semin Cell Dev Biol. 2007 Feb;18(1):90-100. Epub 2007 Jan 4. Review. PubMed PMID: 17289407. [7]
Neuregulin-1 promotes formation of the murine cardiac conduction system. Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10464-9. Epub 2002 Jul 29. PubMed PMID: 12149465; PubMed Central PMCID: PMC124940. [8]
The heart and heart conducting system in the kingdom of animals: A comparative approach to its evolution. Exp Clin Cardiol. 2007 Fall;12(3):113-8. PubMed PMID: 18650991; PubMed Central PMCID: PMC2323757. [9] GREAT COVERAGE OF COMPARATIVE ANATOMY AND FUNCTION OF CARDIAC CONDUCTION SYSTEMS
Useful figures
Relevant Source Forge Requests
Cardiac conduction [[10]]
Regulation of skeletal muscle contraction via regulation of the release of sequestered calcium ion [[11]]
Cardiac muscle contraction [[12]]
Regulation of ventricular cardiac muscle repolarization [[13]]
Relaxation of cardiac muscle [[14]]
Heart contraction terms [[15]]
Ontology discussion documents
Varsha's original ontology suggestions File:HeartConductionDraftOntology2009.pdf
Varsha's notes on discussion of ontology with Andy Tinker File:HeartConductionOntologyDiscussion.pdf
Ontology queries
SCN5A encodes for the major cardiac voltage-gated Na+ channel (PMID:14500339[1]) which is associated with human arrhythmic syndromes (PMID:21895525[2]). Which of the following process terms should it be annotated to
- cardiac muscle contraction (regulation term better)
- positive regulation of cardiac muscle contraction
- positive regulation of heart rate, or just regulation of heart rate?
- New term: sodium ion import is a child to sodium ion transmembrane transport
- cardiac conduction
- regulation of atrial cardiomyocyte membrane repolarization (or new parent atrial cardiomyocyte membrane repolarization)
- regulation of ventricular cardiomyocyte membrane repolarization (or new parent term: ventricular cardiomyocyte membrane repolarization)
- positive regulation of action potential or new term initiation of action potential, or is 'action potential' covered by membrane depolarization
- in line with regulation of skeletal muscle contraction via membrane action potential new term regulation of cardiomyocyte contraction via membrane action potential
- membrane depolarization
- regulation of ventricular cardiomyocyte membrane depolarization
- regulation of atrial cardiomyocyte membrane depolarization
- New GO term cardiomyocyte/heart refractory period
- New GO term propagation of the action potential, or is this covered by membrane depolarization
- New GO term(s) to describe 'plateau phase of the cardiac action potential', 'persistent or late inward current (INaL)', 'duration of the cardiac action potential'.
- mutation in SCN5A leads to a prologation of Q-T interval, need some parent terms such as 'regulation of cardiomyocyte membrane depolarization', 'regulation of cardiomyocyte membrane repolarization' 'regulation of cardiomyocyte membrane potential' to capture information about changes in the ECG measurements.
- At present the GO term GO:0008015 'blood circulation' is only linked to SNC5A via 'regulation' terms, should SNC5A be transitively associated with 'blood circulation', and if so how?
Other
- what does 'density' in the phrase 'sodium channel current (INa) density' mean?