Cardiac conduction: Difference between revisions

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= SCN5A =  
=== SCN5A ===  
encodes for the major cardiac voltage-gated Na+ channel (PMID:14500339<ref>PMID:14500339</ref>) which is associated with human arrhythmic syndromes (PMID:21895525<ref>PMID:21895525</ref>).
encodes for the major cardiac voltage-gated Na+ channel (PMID:14500339<ref>PMID:14500339</ref>) which is associated with human arrhythmic syndromes (PMID:21895525<ref>PMID:21895525</ref>).
Which of the following process terms should it be annotated to  
Which of the following process terms should it be annotated to  

Revision as of 12:14, 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
  1. 2011 Cardiac conduction workshop Logistics


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
  • David and Tanya
    • Set up overview of ontology
  • 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

PMID: 21538814


cardiac action potential cartoon

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


= SCN1B = Sodium channel β1- and β2-subunits (SCN1B, SCN2B) also associated with cardiac conduction associated diseases (PMID:19808477[3])

Other

  • what does 'density' in the phrase 'sodium channel current (INa) density' mean?

mutations in multiple ion channel genes including KCNQ1, KCNE2, KCNJ2, KCNA5, SUR2A, and SCN5A as well as the gap junction gene GJA5 and the nuclear protein NUP155 have been associated with AF.

  1. PMID:14500339
  2. PMID:21895525
  3. PMID:19808477