Difference between revisions of "Construct composite modules (analysis)"

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Predict composite module using site search on genes result
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;Analysis title
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:[[File:Composite-module-analyses-Construct-composite-modules-icon.png]] Construct composite modules
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;Provider
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:[[geneXplain GmbH]]
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;Class
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:{{Class|biouml.plugins.cma.CMAAnalysis}}
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;Plugin
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:[[Biouml.plugins.cma (plugin)|biouml.plugins.cma (Composite module analyst)]]
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==== Description ====
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Predicts composite module using the result of the "[[Site search on gene set (analysis)|Site search on gene set]]" analysis. Composite modules - combinations of binding sites common for promoters of functionally related genes and responsible for the major component of the gene expression pattern of these genes. For more information see <nowiki>[</nowiki>1<nowiki>]</nowiki>.
  
 
==== Parameters: ====
 
==== Parameters: ====
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** '''Elite size''' – Number of elite organisms (i.e. best organisms to survive unconditionally)
 
** '''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)
 
** '''Mutation rate''' – This controls how often mutation occurs and how significant they are (0..1)
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* '''Score calculation parameters''' (expert) – Parameters which control score calculation
 
** '''Penalty rate''' – Which penalty value will be assigned
 
** '''Penalty rate''' – Which penalty value will be assigned
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** '''Site models in focus''' – At least one of these models must present in the resulting composite model to have non-zero score
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** '''Site models in focus table''' (expert) – The table of site models in focus
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** '''All modules contain site model in focus''' – If checked, then each module must contain at least one site model from the focus
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** '''Focused sequences percent''' – Minimal percent of sequences in yes-set which actually contains sites of site models in focus
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** '''Sequence column''' – Column to take sequences from
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** '''Sequences in focus''' – Selected sequences should be in the result top
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** '''Top sequences size (percent)''' – Size of sequences (in percent) that will be considered as top
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** '''Sequences in focus in top (percent)''' – Minimal percent of sequences in focus in the top
 
* '''Model parameters''' – Model parameters
 
* '''Model parameters''' – Model parameters
 
** '''Min modules''' – Minimal number of modules
 
** '''Min modules''' – Minimal number of modules
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*** '''Min module width''' – Minimal width (sigma) of the module
 
*** '''Min module width''' – Minimal width (sigma) of the module
 
*** '''Max module width''' – Maximal width (sigma) of the module
 
*** '''Max module width''' – Maximal width (sigma) of the module
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*** '''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
 
* '''Output path''' – Path to store result
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'''References:'''
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# Alexander Kel, Tatiana Konovalova, Tagir Valeev, Evgeny Cheremushkin, Olga Kel-Margoulis, Edgar Wingender. ''Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations.'' Bioinformatics. 2006 May 15; 22(10):1190-7. Epub 2006 Feb 10. doi: [https://dx.doi.org/10.1093/bioinformatics/btl041 10.1093/bioinformatics/btl041]
  
 
[[Category:Analyses]]
 
[[Category:Analyses]]
[[Category:BSA (analyses group)]]
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[[Category:Composite module analyses (analyses group)]]
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[[Category:GeneXplain analyses]]
 
[[Category:Autogenerated pages]]
 
[[Category:Autogenerated pages]]

Latest revision as of 18:14, 9 December 2020

Analysis title
Composite-module-analyses-Construct-composite-modules-icon.png Construct composite modules
Provider
geneXplain GmbH
Class
CMAAnalysis
Plugin
biouml.plugins.cma (Composite module analyst)

[edit] Description

Predicts composite module using the result of the "Site search on gene set" analysis. Composite modules - combinations of binding sites common for promoters of functionally related genes and responsible for the major component of the gene expression pattern of these genes. For more information see [1].

[edit] Parameters:

  • Site search result – Result of previous site search run with background track
  • 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
    • Site models in focus table (expert) – The table of site models in focus
    • 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
    • Sequence column – Column to take sequences from
    • Sequences in focus – Selected sequences should be in the result top
    • Top sequences size (percent) – Size of sequences (in percent) that will be considered as top
    • Sequences in focus in top (percent) – Minimal percent of sequences in focus in the top
  • Model parameters – 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

References:

  1. Alexander Kel, Tatiana Konovalova, Tagir Valeev, Evgeny Cheremushkin, Olga Kel-Margoulis, Edgar Wingender. Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations. Bioinformatics. 2006 May 15; 22(10):1190-7. Epub 2006 Feb 10. doi: 10.1093/bioinformatics/btl041
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