Functional classification (analysis) - Revision history

WikiBot: Automatic synchronization with BioUML

2020-12-09T11:15:00Z

Automatic synchronization with BioUML

2013-05-31T04:14:34Z

Class name added

2013-05-16T05:40:53Z

Mistaken file names update reverted

2013-05-16T05:36:59Z

Automatic synchronization with BioUML

2013-05-16T05:32:54Z

Automatic synchronization with BioUML

2013-05-07T03:51:16Z

Link to plugin page

2013-05-06T04:47:16Z

Plugin name added

2013-04-23T10:02:46Z

Space after icon

2013-04-23T09:57:39Z

Analysis icon added

2013-04-23T07:48:26Z

Automatic synchronization with BioUML

@@ Line 1: / Line 1: @@
 ;Analysis title
-:[[File:Data-Functional-classification-icon.png]] Functional classification
+:[[File:Gene-set-analysis-Functional-classification-icon.png]] Functional classification
 ;Provider
 :[[Institute of Systems Biology]]
@@ Line 33: / Line 33: @@
 * '''Group size''' (''m''): Total number of genes or other biological objects in the given group. ''n ≤ m''.
 * '''Expected hits''' (''n<sub>exp</sub>''): Number of hits expected in the random input set of given size.
-*::: [[File:Data-Functional-classification-n_exp.png]]
+*::: [[File:Gene-set-analysis-Functional-classification-n_exp.png]]
 *:where ''N'' is number of genes from the input set matched to any group in given classification and ''M'' is total number of genes which appear in given classification. If ''n > n<sub>exp</sub>'', then the group is over-represented. If "Only over-represented" option was set, all groups not satisfying this condition are excluded from the result.
 * '''P-value''' (''P''): Hypergeometric p-value (cumulative distribution function of hypergeometric distribution) having ''m'', ''M'', ''n'', ''N'' as parameters. Only groups for which ''P ≤ P<sub>max</sub>'' are included into result.
@@ Line 41: / Line 41: @@
 [[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:Functional-classification-analysis-icon.png]] Functional classification
+:[[File:Data-Functional-classification-icon.png]] Functional classification
 ;Provider
 :[[Institute of Systems Biology]]

@@ Line 31: / Line 31: @@
 * '''Group size''' (''m''): Total number of genes or other biological objects in the given group. ''n ≤ m''.
 * '''Expected hits''' (''n<sub>exp</sub>''): Number of hits expected in the random input set of given size.
-*::: [[File:Functional-classification-analysis-n_exp.png]]
+*::: [[File:Data-Functional-classification-n_exp.png]]
 *:where ''N'' is number of genes from the input set matched to any group in given classification and ''M'' is total number of genes which appear in given classification. If ''n > n<sub>exp</sub>'', then the group is over-represented. If "Only over-represented" option was set, all groups not satisfying this condition are excluded from the result.
 * '''P-value''' (''P''): Hypergeometric p-value (cumulative distribution function of hypergeometric distribution) having ''m'', ''M'', ''n'', ''N'' as parameters. Only groups for which ''P ≤ P<sub>max</sub>'' are included into result.

@@ Line 1: / Line 1: @@
 ;Analysis title
-:[[File:Data-Functional-classification-icon.png]] Functional classification
+:[[File:Functional-classification-analysis-icon.png]] Functional classification
 ;Provider
 :[[Institute of Systems Biology]]
@@ Line 31: / Line 31: @@
 * '''Group size''' (''m''): Total number of genes or other biological objects in the given group. ''n ≤ m''.
 * '''Expected hits''' (''n<sub>exp</sub>''): Number of hits expected in the random input set of given size.
-*::: [[File:Data-Functional-classification-n_exp.png]]
+*::: [[File:Functional-classification-analysis-n_exp.png]]
 *:where ''N'' is number of genes from the input set matched to any group in given classification and ''M'' is total number of genes which appear in given classification. If ''n > n<sub>exp</sub>'', then the group is over-represented. If "Only over-represented" option was set, all groups not satisfying this condition are excluded from the result.
 * '''P-value''' (''P''): Hypergeometric p-value (cumulative distribution function of hypergeometric distribution) having ''m'', ''M'', ''n'', ''N'' as parameters. Only groups for which ''P ≤ P<sub>max</sub>'' are included into result.

@@ 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)]]
 ==== Description ====

@@ Line 15: / Line 15: @@
 * '''Classification''' – Classification you want to use. List of classifications may differ depending on software version and your subscription. Use <nowiki>'</nowiki>Repository folder<nowiki>'</nowiki> for custom classification.
 * '''Path to classification root''' – Specify path to the folder containing classification tables, when <nowiki>'</nowiki>Repository folder<nowiki>'</nowiki> is selected as classification. Only tables with <nowiki>'</nowiki>Ensembl gene<nowiki>'</nowiki> type are used for the classification.
 * '''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