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

Revision as of 15:04, 7 August 2013

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 weight matrices
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

@@ Line 19: / Line 19: @@
 * '''To''' – To position (relative to gene start)
 * '''Profile''' – Predefined set of weight matrices
-* '''Optimize cutoffs''' (expert) – Matrix cutoffs from profile will be tuned to maximize p-value
+* '''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)