Construct composite modules on tracks with keynodes (analysis) - Revision history

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;Analysis title
:[[File:BSA-Construct-composite-modules-on-tracks-with-keynodes-icon.png]] Construct composite modules on tracks with keynodes
;Provider
:[[Biosoft]]
;Class
:{{Class|biouml.plugins.genomeenhancer.CMAOnTrackWithKeynode}}
;Plugin
:[[Biouml.plugins.genomeenhancer (plugin)|biouml.plugins.genomeenhancer (Genome Enhancer)]]

==== Description ====
Predicts composite module as "[[Construct composite modules on tracks (analysis)|Construct composite modules on tracks]]" analysis, but unlike it this one uses "[[Regulator search (analysis)|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 (<nowiki>'</nowiki>yes<nowiki>'</nowiki>) track
* '''Control track''' – Path to control (<nowiki>'</nowiki>no<nowiki>'</nowiki>) 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

[[Category:Analyses]]
[[Category:BSA (analyses group)]]
[[Category:Biosoft analyses]]
[[Category:Autogenerated pages]]

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 ;Analysis title
-:[[File:BSA-Construct-composite-modules-on-tracks-with-keynodes-icon.png]] Construct composite modules on tracks with keynodes
+:[[File:Composite-module-analyses-Construct-composite-modules-on-tracks-with-keynodes-icon.png]] Construct composite modules on tracks with keynodes
 ;Provider
 :[[Biosoft]]
@@ Line 56: / Line 56: @@
 [[Category:Analyses]]
-[[Category:BSA (analyses group)]]
+[[Category:Composite module analyses (analyses group)]]
 [[Category:Biosoft analyses]]
 [[Category:Autogenerated pages]]

@@ Line 15: / Line 15: @@
 * '''Experiment track''' – Path to experiment (<nowiki>'</nowiki>yes<nowiki>'</nowiki>) track
 * '''Control track''' – Path to control (<nowiki>'</nowiki>no<nowiki>'</nowiki>) track
 * '''Genetic algorithm parameters''' (expert) – Genetic algorithm parameters
 ** '''Number of iterations''' – Number of iterations
@@ Line 25: / Line 24: @@
 ** '''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
@@ Line 33: / Line 37: @@
 ** '''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