Site search result optimization (analysis)

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Analysis title
TF-binding-site-search-Site-search-result-optimization-icon.png Site search result optimization
Provider
Institute of Systems Biology
Class
OptimizeSiteSearchAnalysis
Plugin
ru.biosoft.bsa (Bio-sequences analyses plugin)

Description

Tune matrix weights to minimize p-values.

Parameters:

  • Input yes track – Site search result for genes expressed in experiment
  • Input no track – Site search result for background genes
  • P-value cutoff – Matrix will be removed from result if p-value cannot be optimized to values lower than specified cutoff
  • Optimization type – Whether to optimize only matrix cutoffs, promoter windows or both
  • Output yes track – Filtered site search result for expressed genes
  • Output no track – Filtered site search result for background genes
  • Overrepresented matrices in summary – Remove underrepresented matrices from the output (not applicable if no-set is not specified)
  • Output name – Output name
  • Output profile – Output profile
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