Bayesian Explorer

Function	Action
Open node contextual menu	Right click on node
Open edge contextual menu	Right click on edge
Freeze graph	Press Space
Pin a node down (fix it)	Left click on the node and drag it
Show information about node/edge	Left click on the node/edge
Release node (unfix it)	Doubleclick on the node
Highlight node and its neighbourhood	Mouseover node
Zooming	Zooming buttons
Panning	Mouse click and drag
Reset attributes (highlighting, color...)	Double click in the graph

Node legend

Property

Description

Node Radius

The node radius is proportional to the relative influence of the corresponding variable in the AD risk model

Direction

Probability of direction

Node Color

Heatmap according to the frequency of the node in bootstrapping

Range	Node Color
0 - 10
10 - 20
20 - 30
30 - 40
40 - 50
50 - 60
60 - 70
70 - 80
80 - 90
90 - 100

Edge Legend

Property	Description
Edge Thickness	Edge thickness varies depending on the frequency of the edge in the Ensemble Bayesian Network. The chosen threshold is 50% (edges occuring less than 50% are not represented). You can filter them using the slider in "Edges Threshold"
Direction	Probability of direction
Strength	Bootstrap probability
FDR	Pathway overlap (False Discovery Rate)

Function	Action
Open node contextual menu	Right click on node
Open edge contextual menu	Right click on edge
Freeze graph	Press Space
Pin a node down (fix it)	Left click on the node and drag it
Show information about node/edge	Left click on the node/edge
Release node (unfix it)	Doubleclick on the node
Highlight node and its neighbourhood	Mouseover node
Zooming	Zooming buttons
Panning	Mouse click and drag
Reset attributes (highlighting, color...)	Double click in the graph

Node legend

Functions	Symbol	Description
p()		Abundance of protein
a()		Abundance of chemical (or other non-gene, RNA, protein abundances)
r()		Abundance of RNA
m()		Abundance of microRNA
g()		Abundance of gene
composite()		Multiple entity abundances synergize to produce an effect but are not known to be bound into a complex
complex()		Multiple entity abundances are bound into a complex
path()		Disease or pathology process
bp()		Biological process

Edge Legend

Relationship	Line Style
decreases, directlyDecreases	\|
increases, directlyIncreases	►
negativeCorrelation
positiveCorrelation
causesNoChange, association, orthologous
transcribedTo, translatedTo
biomarkerFor, prognosticBiomarkerFor
hasMember, hasComponent, hasProduct, hasVariant, hasReactant, hasProduct, isA
rateLimitingStepOf, subProcessOf

Format
Save current explorer window as a SVG image
Save as GraphML for use in Cytoscape
Save as CSV for import in Microsoft Excel
Save as SIF
Save as CX JSON for use with the Network Data Exchange
Save as Node-Link JSON for custom visualization using D3
Save as a pre-parsed gpickle for programmatic use
Save as a GSEA GRP file

Button	Action
	Hide node names
	Restore node names
	Restore node names and edge colors
	Restore node text for new nodes

Button	Function
	Collapse Protein/RNA/Gene nodes to genes
	Adds RNAs corresponding to Proteins, then adds Genes corresponding to RNAs and miRNAs
	Prunes genes, then RNA
	Expand the periphery of the network
	Expand edges between nodes in the network
	Remove from the network all isolated nodes
	Reduce the network to the larger component and removes all others
	Enriches the subgraph with the unqualified edges from the graph
	Adds the reference nodes for all variants of genes, RNAs, miRNAs, and proteins
	Adds all of the reactants and products of reactions
	Adds all of the members of the composite abundances
	Adds all of the members of the complexes