Explorer

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

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

Not Consider Pathology Nodes

Format
Save current explorer window as a PNG image
Save as a GRP file for Gene Set Enrichment Analysis (GSEA)
Save the citations as list of PubMed identifiers in a text file

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

About

BEL Commons is developed and maintained in an academic capacity by Charles Tapley Hoyt and Daniel Domingo-Fernández at the Fraunhofer SCAI Department of Bioinformatics with support from the IMI project, AETIONOMY. It is built on top of PyBEL, an open source project. Please feel free to contact us here to give us feedback or report any issues. Also, see our Publishing Notes and Data Protection information.

If you find BEL Commons useful in your work, please consider citing: Hoyt, C. T., Domingo-Fernández, D., & Hofmann-Apitius, M. (2018). BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. Database, 2018(3), 1–11.

Identifier	1580319
Assembly	Clearance systems in the brain-implications for Alzheimer disease. v1.0.1
Seeding	neighbors: [[object Object]]

Biological Network Explorer

Current Query Info

Current Network Info

About

Biological Network Explorer

Current Query Info

Current Network Info

Help

Node Legend

Edge Legend

Path Mining

Algorithms

Export

Controls

Vote

Feedback

About