Pleiotropic effects of SCZ-associated genes (Mäki-Marttunen et al. 2017)

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Accession:187615
Python and MATLAB scripts for studying the dual effects of SCZ-related genes on layer 5 pyramidal cell firing and sinoatrial node cell pacemaking properties. The study is based on two L5PC models (Hay et al. 2011, Almog & Korngreen 2014) and SANC models (Kharche et al. 2011, Severi et al. 2012).
Reference:
1 . Mäki-Marttunen T, Lines GT, Edwards AG, Tveito A, Dale AM, Einevoll GT, Andreassen OA (2017) Pleiotropic effects of schizophrenia-associated genetic variants in neuron firing and cardiac pacemaking revealed by computational modeling. Transl Psychiatry 7:5 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism:
Cell Type(s): Neocortex L5/6 pyramidal GLU cell; Cardiac atrial cell;
Channel(s): I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I h; I K,Ca; I Sodium; I Calcium; I Potassium; I A, slow; Na/Ca exchanger; I_SERCA; Na/K pump; Kir;
Gap Junctions:
Receptor(s):
Gene(s): Nav1.1 SCN1A; Cav3.3 CACNA1I; Cav1.3 CACNA1D; Cav1.2 CACNA1C;
Transmitter(s):
Simulation Environment: NEURON; MATLAB; Python;
Model Concept(s): Schizophrenia;
Implementer(s): Maki-Marttunen, Tuomo [tuomo.maki-marttunen at tut.fi];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I h; I K,Ca; I Sodium; I Calcium; I Potassium; I A, slow; Na/Ca exchanger; I_SERCA; Na/K pump; Kir;
function str=MTentrystr(entry,myallmutval,coeff)

if nargin < 2
    myallmutval = 1;
end
if nargin < 3
    coeff = {'',''};
end

nVals = cellfun(@(x)length(x{2}),entry);
cumprodnVals = cumprod(nVals);
thesemutvars = [];
for imutvar=1:length(entry)
  if ~iscell(entry{imutvar}{1})
    entry{imutvar}{1} = {entry{imutvar}{1}};
  end
  if ~iscell(entry{imutvar}{2})
    entry{imutvar}{2} = {entry{imutvar}{2}};
  end
  thesemutvars = [thesemutvars {entry{imutvar}{1}}];
end

allmutvars = repmat({thesemutvars},cumprodnVals(end),1);
allmutvals = [];
for iallmutval = 1:cumprodnVals(end)
  allmutvals = [allmutvals, {zeros(length(thesemutvars),1)}];
end
for iallmutval = 1:cumprodnVals(end)
  for imutvar = 1:length(entry)
    if imutvar==1
      allmutvals{iallmutval}(imutvar) = entry{imutvar}{2}{1}(mod(iallmutval-1,nVals(imutvar))+1);
    else
      allmutvals{iallmutval}(imutvar) = entry{imutvar}{2}{1}(mod(floor((iallmutval-1)/cumprodnVals(imutvar-1)),nVals(imutvar))+1);          
    end
  end
end


str='';
for ivar=1:length(entry)
  underscoreind = strfind(entry{ivar}{1}{1},'_');
  if ~isempty(underscoreind)
    entry{ivar}{1}{1} = entry{ivar}{1}{1}(1:underscoreind-1);
  end
  if ~isempty(strfind(entry{ivar}{1}{1},'offm')) || ~isempty(strfind(entry{ivar}{1}{1},'offh')) || ~isempty(strfind(entry{ivar}{1}{1},'ehcn'))
    str = [str entry{ivar}{1}{1} ': ' repmat('+',allmutvals{myallmutval}(ivar)>=0,1) num2str(allmutvals{myallmutval}(ivar)) ' mV' coeff{1}];
  else
    str = [str entry{ivar}{1}{1} ': *' num2str(allmutvals{myallmutval}(ivar)) coeff{2}];
  end
  if ivar < length(entry)
    str = [str char(10)];
  end
end