Construct composite modules on tracks with keynodes (analysis)

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Analysis title
BSA-Construct-composite-modules-on-tracks-with-keynodes-icon.png Construct composite modules on tracks with keynodes
Provider
Biosoft
Class
CMAOnTrackWithKeynode
Plugin
biouml.plugins.genomeenhancer (Genome Enhancer)

Description

Predicts composite module as "Construct composite modules on tracks" analysis, but unlike it this one uses "Regulator search" analysis during calculating score of the composite module (score is used to select the best module). Regulator search finds master-regulators which affects transcription factors included in the modules.

Parameters:

  • Experiment track – Path to experiment ('yes') track
  • Control track – Path to control ('no') track
  • Max proteins (expert) – Maximal number of proteins on site
  • Genetic algorithm parameters (expert) – Genetic algorithm parameters
    • Number of iterations – Number of iterations
    • Population size – Population size
    • Non-change limit – Number of iterations to stop after if best score is not improved
    • Elite size – Number of elite organisms (i.e. best organisms to survive unconditionally)
    • Mutation rate – This controls how often mutation occurs and how significant they are (0..1)
  • Score calculation parameters (expert) – Parameters which control score calculation
    • Penalty rate – Which penalty value will be assigned
    • Site models in focus – At least one of these models must present in the resulting composite model to have non-zero score
    • All modules contain site model in focus – If checked, then each module must contain at least one site model from the focus
    • Focused sequences percent – Minimal percent of sequences in yes-set which actually contains sites of site models in focus
  • Model parameters – Model parameters
    • Max radius – Maximal search radius
    • Max keynodes (expert) – Maximal number of keynodes to use during score calculation
    • Score cutoff (expert) – Molecules with Score lower than specified will be excluded from the result
    • Penalty (expert) – Penalty value for false positives
    • Search collection – Collection containing reactions
    • Species – Species to which analysis should be confined
    • Multi Gauss model parameters (expert) – Multi Gauss model parameters
      • Min modules – Minimal number of modules
      • Max modules – Maximal number of modules
      • Gaussian model (expert) – Gaussian model
        • Min models – Minimal number of site models in module
        • Max models – Maximal number of site models in module
        • Min sites to account – Minimal number of sites to account
        • Max sites to account – Maximal number of sites to account
        • Min module width – Minimal width (sigma) of the module
        • Max module width – Maximal width (sigma) of the module
        • Pairs mode – Whether the sites of at least two different site models satisfying the cut-off condition must be present on the sequence
  • Output path – Path to store result
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