Enrichment analysis - Revision history

WikiBot: Automatic synchronization with BioUML

2020-12-09T11:15:00Z

Automatic synchronization with BioUML

WikiBot: Class name added

2013-05-31T04:14:33Z

Class name added

WikiBot: Mistaken file names update reverted

2013-05-16T05:40:53Z

Mistaken file names update reverted

WikiBot: Automatic synchronization with BioUML

2013-05-16T05:36:56Z

Automatic synchronization with BioUML

WikiBot: Automatic synchronization with BioUML

2013-05-16T05:32:52Z

Automatic synchronization with BioUML

WikiBot: Link to plugin page

2013-05-07T03:51:15Z

Link to plugin page

WikiBot: Plugin name added

2013-05-06T04:47:15Z

Plugin name added

WikiBot: Provider changed to geneXplain

2013-05-06T04:06:06Z

Provider changed to geneXplain

WikiBot: Space after icon

2013-04-23T10:02:44Z

Space after icon

WikiBot: Analysis icon added

2013-04-23T09:57:39Z

Analysis icon added

@@ Line 1: / Line 1: @@
 ;Analysis title
-:[[File:Data-Enrichment-analysis-icon.png]] Enrichment analysis
+:[[File:Gene-set-analysis-Enrichment-analysis-icon.png]] Enrichment analysis
 ;Provider
 :[[Institute of Systems Biology]]
@@ Line 38: / Line 38: @@
 * '''Number of hits''' (''n''): Number of genes from the input set matched to the group. Only groups for which ''n ≥ n<sub>min</sub>'' are included into result.
 * '''Plot''': Click to see the plot. The plot shows how Kolmogorov-Smirnov score (''KS'') depends on gene rank (''r''). Axis X shows gene ranks, axis Y shows ''KS'' value. ''KS'' can be defined recurrently as follows:
-*::: [[File:Data-Enrichment-analysis-ks_score.png]]
+*::: [[File:Gene-set-analysis-Enrichment-analysis-ks_score.png]]
 *:Here ''N'' is the total number of genes in the input group. The value of ''ES'' is the most extreme (maximal by absolute value) ''KS''. Plot example is shown below.
 * '''Hits''': List of Ensembl IDs from the input set matched to the group (number of IDs is always ''n'').
@@ Line 46: / Line 46: @@
 ==== Plot example ====
-[[File:Data-Enrichment-analysis-plot_example.png]]
+[[File:Gene-set-analysis-Enrichment-analysis-plot_example.png]]
 In this example plot is displayed for the set of 10 genes (''N'' = 10) and 3 hits in the group (''n'' = 3), which have ranks 1, 3 and 4. The most extreme ''KS'' value (which is enrichment score or ''ES'') equals to ''KS''(4), which can be calculated as follows:
-:: [[File:Data-Enrichment-analysis-es_calculation.png]]
+:: [[File:Gene-set-analysis-Enrichment-analysis-es_calculation.png]]
 ==== References ====
@@ Line 57: / Line 57: @@
 [[Category:Analyses]]
-[[Category:Data (analyses group)]]
+[[Category:Gene set analysis (analyses group)]]
 [[Category:ISB analyses]]
 [[Category:Autogenerated pages]]

@@ Line 3: / Line 3: @@
 ;Provider
 :[[Institute of Systems Biology]]
 ;Plugin
 :[[Biouml.plugins.enrichment (plugin)|biouml.plugins.enrichment (Enrichment analysis plugin)]]

@@ Line 1: / Line 1: @@
 ;Analysis title
-:[[File:Enrichment-analysis-icon.png]] Enrichment analysis
+:[[File:Data-Enrichment-analysis-icon.png]] Enrichment analysis
 ;Provider
 :[[Institute of Systems Biology]]

@@ Line 36: / Line 36: @@
 * '''Number of hits''' (''n''): Number of genes from the input set matched to the group. Only groups for which ''n ≥ n<sub>min</sub>'' are included into result.
 * '''Plot''': Click to see the plot. The plot shows how Kolmogorov-Smirnov score (''KS'') depends on gene rank (''r''). Axis X shows gene ranks, axis Y shows ''KS'' value. ''KS'' can be defined recurrently as follows:
-*::: [[File:Enrichment-analysis-ks_score.png]]
+*::: [[File:Data-Enrichment-analysis-ks_score.png]]
 *:Here ''N'' is the total number of genes in the input group. The value of ''ES'' is the most extreme (maximal by absolute value) ''KS''. Plot example is shown below.
 * '''Hits''': List of Ensembl IDs from the input set matched to the group (number of IDs is always ''n'').
@@ Line 44: / Line 44: @@
 ==== Plot example ====
-[[File:Enrichment-analysis-plot_example.png]]
+[[File:Data-Enrichment-analysis-plot_example.png]]
 In this example plot is displayed for the set of 10 genes (''N'' = 10) and 3 hits in the group (''n'' = 3), which have ranks 1, 3 and 4. The most extreme ''KS'' value (which is enrichment score or ''ES'') equals to ''KS''(4), which can be calculated as follows:
-:: [[File:Enrichment-analysis-es_calculation.png]]
+:: [[File:Data-Enrichment-analysis-es_calculation.png]]
 ==== References ====

@@ Line 1: / Line 1: @@
 ;Analysis title
-:[[File:Data-Enrichment-analysis-icon.png]] Enrichment analysis
+:[[File:Enrichment-analysis-icon.png]] Enrichment analysis
 ;Provider
 :[[Institute of Systems Biology]]
@@ Line 36: / Line 36: @@
 * '''Number of hits''' (''n''): Number of genes from the input set matched to the group. Only groups for which ''n ≥ n<sub>min</sub>'' are included into result.
 * '''Plot''': Click to see the plot. The plot shows how Kolmogorov-Smirnov score (''KS'') depends on gene rank (''r''). Axis X shows gene ranks, axis Y shows ''KS'' value. ''KS'' can be defined recurrently as follows:
-*::: [[File:Data-Enrichment-analysis-ks_score.png]]
+*::: [[File:Enrichment-analysis-ks_score.png]]
 *:Here ''N'' is the total number of genes in the input group. The value of ''ES'' is the most extreme (maximal by absolute value) ''KS''. Plot example is shown below.
 * '''Hits''': List of Ensembl IDs from the input set matched to the group (number of IDs is always ''n'').
@@ Line 44: / Line 44: @@
 ==== Plot example ====
-[[File:Data-Enrichment-analysis-plot_example.png]]
+[[File:Enrichment-analysis-plot_example.png]]
 In this example plot is displayed for the set of 10 genes (''N'' = 10) and 3 hits in the group (''n'' = 3), which have ranks 1, 3 and 4. The most extreme ''KS'' value (which is enrichment score or ''ES'') equals to ''KS''(4), which can be calculated as follows:
-:: [[File:Data-Enrichment-analysis-es_calculation.png]]
+:: [[File:Enrichment-analysis-es_calculation.png]]
 ==== References ====

@@ Line 4: / Line 4: @@
 :[[Institute of Systems Biology]]
 ;Plugin
-:biouml.plugins.enrichment (Enrichment analysis plugin)
+:[[Biouml.plugins.enrichment (plugin)|biouml.plugins.enrichment (Enrichment analysis plugin)]]
 === Enrichment analysis (GSEA) ===

@@ Line 20: / Line 20: @@
 * '''Minimal hits to group''' – Groups with lower number of hits will be filtered out (n<sub>min</sub>)
 * '''Only over-represented''' (expert) – If checked, under-represented groups will be excluded from the result
-* '''Number of permutations''' (expert) – Number of random permutations used for p-value calculation. Bigger values increase p-value precision, but make the analysis slower.
+* '''Number of permutations''' (expert) – Number of random permutations used for p-value calculation (10-10000). Bigger values increase p-value precision, but make the analysis slower.
 * '''P-value threshold''' – P-value threshold (P<sub>max</sub>)
 * '''Result name''' – Name and path for the resulting table