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

Latest revision as of 18:15, 9 December 2020

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

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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 ;Analysis title
-:[[File:BSA-Site-search-on-gene-set-icon.png]] Site search on gene set
+:[[File:TF-binding-site-search-Site-search-on-gene-set-icon.png]] Site search on gene set
 ;Provider
 :[[Institute of Systems Biology]]
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 ==== Description ====
-Compound analysis to search sites on gene set and generate summary
+Compound analysis to search sites on gene set and generate summary.
 ==== Parameters: ====
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 [[Category:Analyses]]
-[[Category:BSA (analyses group)]]
+[[Category:TF binding site search (analyses group)]]
 [[Category:ISB analyses]]
 [[Category:Autogenerated pages]]