In kmezhoud/bioCancer: Interactive Multi-Omics Cancers Data Visualization and Analysis
Function Interaction Network Enrichment
Edges Attributes
Function Interactions (FIs) Type
Arrowhead | Reaction | Arrowhead | Reaction
------------- | -------- | -------- | ------------
-> | activate, express, regulate | -\| | inhibit
diamond -<> | complexe |curve | catalyze, reaction
point -o| phosphorylate | -- | binding, input, compound
-< | dissociation | .... | predicted, indirect,ubiquitinated
Use Linkers
Picks up as few as possible of linkers that can connect input genes together. For example, if the algorithm finds one gene can link all input genes together, it will not try other genes (not from gene list) that may be used as a linker.
The linker gene hes box format.
Layouts
dot
The dot engine flows the directed graph in the direction of rank (i.e., downstream nodes of the same rank are aligned). By default, the direction is from top to bottom
twopi
The twopi engine provides radial layouts. Nodes are placed on concentric circles depending their distance from a given root node.
neato
The neato engine provides spring model layouts. This is a suitable engine if the graph is not too large (less than 100 nodes) and you don't know anything else about it. The neato engine attempts to minimize a global energy function, which is equivalent to statistical multi-dimensional scaling.
circo
The circo engine provide circular layouts. This is suitable for certain diagrams of multiple cyclic structures, such as certain telecommunications networks.
Nodes Attributes
From ReactomeFI
The size of node is related to the number of inetractions. If node has multiple interaction, it will has bigger size than node with few interaction. Otherwise, i will be easier to locate important gene in the network.
From Classifier
mRNA
Attribute node color using exprsMeanDiff values from Classifier panel.
Studies
Link study to associated genes from Classifier table.
From Profiles Data
User needs to
Select studies (From Which Studies)
Load profiles data (Load).
Select Profiles Data
Set threshold from Sliders
Legend
Interpretation
kmezhoud/bioCancer documentation built on Feb. 17, 2024, 10:29 a.m.
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Function Interaction Network Enrichment
Edges Attributes
Function Interactions (FIs) Type
Arrowhead | Reaction | Arrowhead | Reaction ------------- | -------- | -------- | ------------ -> | activate, express, regulate | -\| | inhibit diamond -<> | complexe |curve | catalyze, reaction point -o| phosphorylate | -- | binding, input, compound -< | dissociation | .... | predicted, indirect,ubiquitinated
Use Linkers
Picks up as few as possible of linkers that can connect input genes together. For example, if the algorithm finds one gene can link all input genes together, it will not try other genes (not from gene list) that may be used as a linker.
The linker gene hes box format.
Layouts
dot
The dot engine flows the directed graph in the direction of rank (i.e., downstream nodes of the same rank are aligned). By default, the direction is from top to bottom
twopi
The twopi engine provides radial layouts. Nodes are placed on concentric circles depending their distance from a given root node.
neato
The neato engine provides spring model layouts. This is a suitable engine if the graph is not too large (less than 100 nodes) and you don't know anything else about it. The neato engine attempts to minimize a global energy function, which is equivalent to statistical multi-dimensional scaling.
circo
The circo engine provide circular layouts. This is suitable for certain diagrams of multiple cyclic structures, such as certain telecommunications networks.
Nodes Attributes
From ReactomeFI
The size of node is related to the number of inetractions. If node has multiple interaction, it will has bigger size than node with few interaction. Otherwise, i will be easier to locate important gene in the network.
From Classifier
mRNA
Attribute node color using exprsMeanDiff values from Classifier panel.
Studies
Link study to associated genes from Classifier table.
From Profiles Data
User needs to
Select studies (From Which Studies)
Load profiles data (Load).
Select Profiles Data
Set threshold from Sliders
Legend
Interpretation
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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