Difference between revisions of "Site search on gene set (analysis)"
From BioUML platform
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;Analysis title | ;Analysis title | ||
| − | :[[File: | + | :[[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]] | ||
| + | ;Class | ||
| + | :{{Class|ru.biosoft.bsa.analysis.GeneSetSiteSearch}} | ||
;Plugin | ;Plugin | ||
| − | :ru.biosoft.bsa (Bio-sequences analyses plugin) | + | :[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]] |
==== Description ==== | ==== Description ==== | ||
| − | Compound analysis to search sites on gene set and generate summary | + | 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 | + | * '''Profile''' – Predefined set of site models |
| − | * '''Optimize cutoffs''' | + | * '''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: | + | [[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
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
