Effector search (analysis) - Revision history

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2020-12-09T11:15:13Z

Automatic synchronization with BioUML

WikiBot: Automatic synchronization with BioUML

2019-03-12T09:33:55Z

Automatic synchronization with BioUML

WikiBot: Automatic synchronization with BioUML

2015-08-25T05:21:00Z

Automatic synchronization with BioUML

WikiBot: Automatic synchronization with BioUML

2014-12-11T09:18:24Z

Automatic synchronization with BioUML

WikiBot: Automatic synchronization with BioUML

2013-11-18T08:00:33Z

Automatic synchronization with BioUML

WikiBot: Class name added

2013-05-31T04:15:23Z

Class name added

WikiBot: Link to plugin page

2013-05-07T03:51:55Z

Link to plugin page

WikiBot: Plugin name added

2013-05-06T04:47:55Z

Plugin name added

WikiBot: Provider changed to geneXplain

2013-05-06T04:06:49Z

Provider changed to geneXplain

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2013-04-23T10:03:24Z

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@@ Line 8: / Line 8: @@
 :[[Biouml.plugins.keynodes (plugin)|biouml.plugins.keynodes (Master regulator node analysis plugin)]]
-=== Drug target search analysis ===
+==== Description ====
+Find genes or proteins regulated by the input set of genes.
-'''Goal:''' to search for important molecules in signal transduction cascade.
-−
-'''Input:''' a set of genes / molecules to start analysis with. For instance, this can be a set of transcription factors, which may result from a promoter analysis, or a set of ligands / receptors that trigger a certain (set of) pathway(s).
-−
-Two separate analyses are available:
-−
-* '''Effector search''' for molecules downstream of the molecules in the input list.
-* '''Regulator search''' for molecules upstream of the molecules in the input list.
-−
-==== Output: ====
-−
-A set of proteins or their encoding genes, which may play a key role in regulating (or being regulated by) a maximal number of start molecules.
 ==== Parameters: ====
@@ Line 42: / Line 30: @@
 * '''Normalize multi-forms''' (expert) – Normalize weights of multiple forms
 * '''Output name''' – Output name.
 [[Category:Analyses]]

@@ Line 32: / Line 32: @@
 * '''Score cutoff''' – Molecules with Score lower than specified will be excluded from the result
 * '''Search collection''' – Collection containing reactions
 * '''Species''' – Species to which analysis should be confined
 * '''Calculate FDR''' – If true, analysis will calculate False Discovery Rate

@@ Line 37: / Line 37: @@
 * '''Z-score cutoff''' – Molecules with Z-score lower than specified will be excluded from the result
 * '''Penalty''' (expert) – Penalty value for false positives
-* '''Context genes''' (expert) – Drug target search will be attracted towards context genes by decreasing the cost for close edges
+* '''Decorators''' – Decorators
-* '''Context weighting column''' (expert) – Attraction strength
-* '''Decay factor''' (expert) – Decay factor to decrease attraction with distance increase
 * '''Normalize multi-forms''' (expert) – Normalize weights of multiple forms
 * '''Output name''' – Output name.

@@ Line 53: / Line 53: @@
 Where:
-* '''''R''''' � Max radius (input parameter)
+* '''''R''''' — Max radius (input parameter)
-* '''''p''''' � Penalty (input parameter)
+* '''''p''''' — Penalty (input parameter)
-* '''''N(X,r)''''' � total number of molecules reachable from key molecule X within the radius r.
+* '''''N(X,r)''''' — total number of molecules reachable from key molecule X within the radius r.
-* '''''N<sub>max</sub>(r)''''' � maximal value of ''N(X,r)'' over all key molecules X found for this radius.
+* '''''N<sub>max</sub>(r)''''' — maximal value of ''N(X,r)'' over all key molecules X found for this radius.
-* '''''M(X,r)''''' � sum of ''w(X)'' for all hits reachable from key molecule X within the radius r, where ''w(X)'' � weight of hit X. It equals to ''w<sub>b</sub>(X)'' if �Normalize multi-forms� is unchecked. Otherwise it�s ''w<sub>b</sub>(X)/I(X)'', where ''I(X)'' is the number of multiforms of X in the input set (not total number of multiforms in the database). In both cases ''w<sub>b</sub>(X)'' is the base weight of hit X. It equals the corresponding value in �Weighting column� or 1 if �Weighting column� is not specified.
+* '''''M(X,r)''''' — sum of ''w(X)'' for all hits reachable from key molecule X within the radius r, where ''w(X)'' — weight of hit X. It equals to ''w<sub>b</sub>(X)'' if “Normalize multi-forms” is unchecked. Otherwise it’s ''w<sub>b</sub>(X)/I(X)'', where ''I(X)'' is the number of multiforms of X in the input set (not total number of multiforms in the database). In both cases ''w<sub>b</sub>(X)'' is the base weight of hit X. It equals the corresponding value in “Weighting column” or 1 if “Weighting column” is not specified.
-* '''''M<sub>max</sub>(r)''''' � maximal value of ''M(X,r)'' over all key molecules X found for this radius.
+* '''''M<sub>max</sub>(r)''''' — maximal value of ''M(X,r)'' over all key molecules X found for this radius.
 '''FDR''' Each individual drug target molecule gets a ''p''-value (FDR) assigned, which represents the probability to occupy the observed rank or higher ranks by random chance. It is estimated on-the-fly by random sampling. The ranking of the key nodes is defined by sorting them according to the Score above in descending order. It should be noted that the rank is defined by the ranks of the occurring scores, which means that more than one key node can share the same score value in some cases. Molecules which do not have any hits get assigned the last rank since the score is zero in this case.
@@ Line 79: / Line 79: @@
 ==== Result columns ====
-* '''ID''' � key molecule identifier in respective database
+* '''ID''' — key molecule identifier in respective database
-* '''Key molecule name''' � molecule title
+* '''Key molecule name''' — molecule title
-* '''Reached from set''' � number of molecules from input set, that were reached from key molecule within the distance given
+* '''Reached from set''' — number of molecules from input set, that were reached from key molecule within the distance given
-* '''Reachable total''' � total number of molecules, that can be reached from key molecule within the distance given
+* '''Reachable total''' — total number of molecules, that can be reached from key molecule within the distance given
-* '''Score''' � specificity score value calculated as described above
+* '''Score''' — specificity score value calculated as described above
-* '''FDR''' � ''p''-value, which represents the probability to occupy the observed rank or higher ranks by random chance
+* '''FDR''' — ''p''-value, which represents the probability to occupy the observed rank or higher ranks by random chance
-* '''Z-Score''' � z-score, according the equation above
+* '''Z-Score''' — z-score, according the equation above
-* '''Hits''' � identifiers of molecules from input set, that were reached from key molecule within the distance given
+* '''Hits''' — identifiers of molecules from input set, that were reached from key molecule within the distance given
-* '''Hits names''' � titles of molecules from input set, that were reached from key molecule within the distance given
+* '''Hits names''' — titles of molecules from input set, that were reached from key molecule within the distance given
 ==== References: ====

@@ Line 53: / Line 53: @@
 Where:
-* '''''R''''' — Max radius (input parameter)
+* '''''R''''' � Max radius (input parameter)
-* '''''p''''' — Penalty (input parameter)
+* '''''p''''' � Penalty (input parameter)
-* '''''N(X,r)''''' — total number of molecules reachable from key molecule X within the radius r.
+* '''''N(X,r)''''' � total number of molecules reachable from key molecule X within the radius r.
-* '''''N<sub>max</sub>(r)''''' — maximal value of ''N(X,r)'' over all key molecules X found for this radius.
+* '''''N<sub>max</sub>(r)''''' � maximal value of ''N(X,r)'' over all key molecules X found for this radius.
-* '''''M(X,r)''''' — sum of ''w(X)'' for all hits reachable from key molecule X within the radius r, where ''w(X)'' — weight of hit X. It equals to ''w<sub>b</sub>(X)'' if “Normalize multi-forms” is unchecked. Otherwise it’s ''w<sub>b</sub>(X)/I(X)'', where ''I(X)'' is the number of multiforms of X in the input set (not total number of multiforms in the database). In both cases ''w<sub>b</sub>(X)'' is the base weight of hit X. It equals the corresponding value in “Weighting column” or 1 if “Weighting column” is not specified.
+* '''''M(X,r)''''' � sum of ''w(X)'' for all hits reachable from key molecule X within the radius r, where ''w(X)'' � weight of hit X. It equals to ''w<sub>b</sub>(X)'' if �Normalize multi-forms� is unchecked. Otherwise it�s ''w<sub>b</sub>(X)/I(X)'', where ''I(X)'' is the number of multiforms of X in the input set (not total number of multiforms in the database). In both cases ''w<sub>b</sub>(X)'' is the base weight of hit X. It equals the corresponding value in �Weighting column� or 1 if �Weighting column� is not specified.
-* '''''M<sub>max</sub>(r)''''' — maximal value of ''M(X,r)'' over all key molecules X found for this radius.
+* '''''M<sub>max</sub>(r)''''' � maximal value of ''M(X,r)'' over all key molecules X found for this radius.
 '''FDR''' Each individual drug target molecule gets a ''p''-value (FDR) assigned, which represents the probability to occupy the observed rank or higher ranks by random chance. It is estimated on-the-fly by random sampling. The ranking of the key nodes is defined by sorting them according to the Score above in descending order. It should be noted that the rank is defined by the ranks of the occurring scores, which means that more than one key node can share the same score value in some cases. Molecules which do not have any hits get assigned the last rank since the score is zero in this case.
@@ Line 79: / Line 79: @@
 ==== Result columns ====
-* '''ID''' — key molecule identifier in respective database
+* '''ID''' � key molecule identifier in respective database
-* '''Key molecule name''' — molecule title
+* '''Key molecule name''' � molecule title
-* '''Reached from set''' — number of molecules from input set, that were reached from key molecule within the distance given
+* '''Reached from set''' � number of molecules from input set, that were reached from key molecule within the distance given
-* '''Reachable total''' — total number of molecules, that can be reached from key molecule within the distance given
+* '''Reachable total''' � total number of molecules, that can be reached from key molecule within the distance given
-* '''Score''' — specificity score value calculated as described above
+* '''Score''' � specificity score value calculated as described above
-* '''FDR''' — ''p''-value, which represents the probability to occupy the observed rank or higher ranks by random chance
+* '''FDR''' � ''p''-value, which represents the probability to occupy the observed rank or higher ranks by random chance
-* '''Z-Score''' — z-score, according the equation above
+* '''Z-Score''' � z-score, according the equation above
-* '''Hits''' — identifiers of molecules from input set, that were reached from key molecule within the distance given
+* '''Hits''' � identifiers of molecules from input set, that were reached from key molecule within the distance given
-* '''Hits names''' — titles of molecules from input set, that were reached from key molecule within the distance given
+* '''Hits names''' � titles of molecules from input set, that were reached from key molecule within the distance given
 ==== References: ====

@@ Line 3: / Line 3: @@
 ;Provider
 :[[geneXplain GmbH]]
 ;Plugin
 :[[Biouml.plugins.keynodes (plugin)|biouml.plugins.keynodes (Master regulator node analysis plugin)]]

@@ Line 2: / Line 2: @@
 :[[File:Molecular-networks-Effector-search-icon.png]] Effector search
 ;Provider
-:[[Institute of Systems Biology]]
+:[[geneXplain GmbH]]
 === Drug target search analysis ===
@@ Line 91: / Line 91: @@
 [[Category:Analyses]]
 [[Category:Molecular networks (analyses group)]]
-[[Category:ISB analyses]]
+[[Category:GeneXplain analyses]]
 [[Category:Autogenerated pages]]