PathMe

Pathway	Database	Identifier	Color
MAPK signaling pathway	KEGG	hsa04010

Viewer's Controls

Function	Action
Modify Link (edges) Length	Slider on Edge tab
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

Controls

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

Highlight paths between two nodes in the currenly displayed graph using the chosen method. For presentation purposes, a button to identify paths between two random nodes in the graph is given.

Shortest Path: Calculate the shortest path between the selected nodes. If there are more than one shortest path, this algorithm randomly chooses one of them.
All Paths: Calculates all paths between the selected nodes with a maximum length of 7.

Source Node

Target Node

Shortest Path All Paths

Hide Other Nodes

Remove Directionality

Format
Save current explorer window as a PNG image
Save as a BEL script
Save as GraphML for use in Cytoscape
Save as CSV for import in Microsoft Excel
Save as Node-Link JSON for custom visualization using D3

MAPK signaling pathway (KEGG)

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Viewer's Controls

Node Legend

Edge Legend

Controls

Path Mining

Algorithms

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