Model Overview Panel

For either the Entities or Interactions tab, the Find field allows you to search the contents of the pathway model in the map area. In the Interactions tab, searching returns results in the Recipient column.

Entities

The Entities tab lists all the entities in the pathway model, reporting their name, initial state, whether their behavior is automatic or custom, and the formula for their activation. Custom formulas are displayed in bold text. For more information, see Formulas and Pathways.

Command	Description
	Sorts the entities by name or phenotype.
	Sorts the entities by their initial state or behavior.
	Displays a tooltip for the formula.
	Starts editing the formula.
	Expands the entity to display any annotation information. If any annotations have links, click the name to open the link in a new browser tab.
	Opens the Information panel for the entity.
	Creates a new empty annotation.
	Indicates that an entity has an annotation.
	Deletes the selected entity from the pathway model.

The Preferred Name column indicates the type of each entity.

Symbol	Description
	Adaptor
	Anti apoptopic
	Antibody drug
	Cadherin
	CDK inhibitor
	Chemical drug
	Complex
	Cyclin dependent
	Cyclin
	Enzyme
	G protein
	Gene
	Generic
	Generic antibody
	Generic DNA
	Generic drug
	Generic ligand
	Generic protein
	Generic RNA
	GTPase activating protein
	Guanine exchange factor
	Integrins
	Kinase
	micro RNA
	Phenotype
	Phosphatase
	Phospholipase
	Pro apoptopic
	Protease
	Protein drug
	Scaffold
	siRNA
	Small molecule
	Storage protein
	TM receptor
	Transcription factor
	Transport protein
	Tyrosine kinase

Interactions

The Interactions tab lists all the interactions in the pathway model, reporting their title, whether the interaction is a contributor, effect, and recipient.

Command	Description
	Sorts the interactions by effect. Choose which effects to display first: Activation Inhibition Unknown
	Sorts the interactions by the recipient.
	Opens the Information panel for the interaction.
	Expands the interaction to display any annotation information.
	Creates a new empty annotation.
	Indicates that an interaction has an annotation.
	Deletes the selected interaction from the pathway model.

The appearance of the Contributors and Interaction Effect symbol for each interaction indicates its type.

Symbol	Description
	Activates an entity.
	Inhibits an entity.
	Active contribution to an interaction effect.
	Inhibiting contribution to an interaction effect.
	An interaction of unknown behavior.