Difference between revisions of "Site search on gene set (analysis)"

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;Analysis title
 
;Analysis title
:[[File:BSA-Site-search-on-gene-set-icon.png]] Site search on gene set
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:[[File:TF-binding-site-search-Site-search-on-gene-set-icon.png]] Site search on gene set
 
;Provider
 
;Provider
 
:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
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;Class
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:{{Class|ru.biosoft.bsa.analysis.GeneSetSiteSearch}}
 
;Plugin
 
;Plugin
:ru.biosoft.bsa (Bio-sequences analyses plugin)
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:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]
  
 
==== Description ====
 
==== Description ====
Compound analysis to search sites on gene set and generate summary
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Compound analysis to search sites on gene set and generate summary.
  
 
==== Parameters: ====
 
==== Parameters: ====
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* '''From''' – From position (relative to gene start)
 
* '''From''' – From position (relative to gene start)
 
* '''To''' – To position (relative to gene start)
 
* '''To''' – To position (relative to gene start)
* '''Profile''' – Predefined set of weight matrices
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* '''Profile''' – Predefined set of site models
* '''Optimize cutoffs''' (expert) – Matrix cutoffs from profile will be tuned to maximize p-value
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* '''Optimize cutoffs''' – Matrix cutoffs from profile will be tuned to maximize p-value
 
* '''Optimize window''' (expert) – From/to positions will be optimized for each matrix to maximize p-value
 
* '''Optimize window''' (expert) – From/to positions will be optimized for each matrix to maximize p-value
 
* '''P-value cutoff''' (expert) – Matrix will be removed from result if p-value cannot be optimized to values lower than specified cutoff (parameters ignored if both cutoff and window optimizations are switched off)
 
* '''P-value cutoff''' (expert) – Matrix will be removed from result if p-value cannot be optimized to values lower than specified cutoff (parameters ignored if both cutoff and window optimizations are switched off)
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[[Category:Analyses]]
 
[[Category:Analyses]]
[[Category:BSA (analyses group)]]
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[[Category:TF binding site search (analyses group)]]
 
[[Category:ISB analyses]]
 
[[Category:ISB analyses]]
 
[[Category:Autogenerated pages]]
 
[[Category:Autogenerated pages]]

Latest revision as of 18:15, 9 December 2020

Analysis title
TF-binding-site-search-Site-search-on-gene-set-icon.png Site search on gene set
Provider
Institute of Systems Biology
Class
GeneSetSiteSearch
Plugin
ru.biosoft.bsa (Bio-sequences analyses plugin)

[edit] Description

Compound analysis to search sites on gene set and generate summary.

[edit] Parameters:

  • Yes set – Set of genes expressed in experiment (test set)
  • No set – Set of background genes (control set)
  • Species – Taxonomical species
  • From – From position (relative to gene start)
  • To – To position (relative to gene start)
  • Profile – Predefined set of site models
  • Optimize cutoffs – Matrix cutoffs from profile will be tuned to maximize p-value
  • Optimize window (expert) – From/to positions will be optimized for each matrix to maximize p-value
  • P-value cutoff (expert) – Matrix will be removed from result if p-value cannot be optimized to values lower than specified cutoff (parameters ignored if both cutoff and window optimizations are switched off)
  • Remove non-optimized sites (expert) – Delete preliminary site search result to save drive space
  • Overrepresented matrices in summary (expert) – Remove underrepresented matrices from the output (not applicable if no-set is not specified)
  • Output path – Output path
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