Site search on gene set (analysis)
From BioUML platform
Revision as of 11:14, 31 May 2013 by BioUML wiki Bot (Talk | contribs)
- Analysis title
Site search on gene set
- Provider
- Institute of Systems Biology
- Class
GeneSetSiteSearch- Plugin
- ru.biosoft.bsa (Bio-sequences analyses plugin)
Description
Compound analysis to search sites on gene set and generate summary
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 weight matrices
- Optimize cutoffs (expert) – 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
