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IPA Legend

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SummaryDescribes the node shapes, tool bar icons, colors, and more in IPA
Answer

IPA Legend


This legend provides a key to the main features of Network Explorer, My Pathways, and Canonical Pathways, including molecule shapes and colors as well as relationship labels and types. 


Node Shapes

IPA Legend.jpg

 

Other molecule symbols:

   Degraded protein (shown only in Canonical Pathways)


Relationship Types and Labels

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Relationship line descriptions




A relationship with an X over the line indicates that the interaction does not occur. These relationships are only used in disease pathways to indicate an interaction that would normally happen in the absence of the disease but does not happen in the disease context.

Ubiquitination edges are considered inhibitory towards a recipient protein's activity.  

An arrow pointing from A to B signifies different actions for different circumstances, as described below:

 

For signaling pathways:

An arrow pointing from A to B signifies that A causes B to be activated (includes any direct interaction: e.g., binding, phosphorylation, dephosphorylation, etc).

 

For metabolic pathways:

An arrow pointing from A to B signifies that B is produced from A.

 

For ligands/receptors:

An arrow pointing from a ligand to a receptor signifies that the ligand binds the receptor and subsequently leads to activation of the receptor. This binding event does not necessarily directly activate the receptor; activation of the receptor could be caused by events secondary to the ligand/receptor binding event.




MAP Prediction Legend

User-added image


A high-resolution version of this image can be found here: High-resolution MAP legend


MAP Prediction Legend for Graphical Summary networks

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The MAP Prediction Legend for Graphical Summary networks reflects the same information as the MAP Prediction Legend, but adds the machine-based learning relationship line (Inferred relationship) that is part of this feature. 
A high-resolution version of this image can be found at this link: 
High-Resolution MAP Graphical Summary Legend


Interpretation of MAP relationship lines in networks/pathways

The coloring and type of relationship lines will often be modified when MAP predictions are applied, as outlined in the table below:

Upstream molecule’s predicted activity Downstream molecule’s predicted activityConsistency of Findings with state of downstream moleculeRelationship line coloring and type
ActivatedIncreasedConsistentOrange activation
InhibitedDecreasedConsistentBlue activation
ActivatedDecreasedConsistentBlue inhibition
InhibitedIncreasedConsistentOrange inhibition
ActivatedIncreasedInconsistentYellow inhibition
InhibitedDecreasedInconsistentYellow inhibition
ActivatedDecreasedInconsistentYellow activation
InhibitedIncreasedInconsistentYellow activation




Overlay tags 

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Fonts and Colors

Fonts

User-added image



Molecule fill colors in networks and pathways


*For datasets that contain only identifiers (i.e., no expression or phosphorylation values), the gray fill color identifies the focus (Analysis-Ready) molecules from that dataset.



Molecule outline colors and decorations on networks and pathways

User-added image



Molecule color intensity: The intensity of red and green molecule colors indicates the degree of up-or-down-regulation, respectively, in an Expression dataset, and increase or decrease in phosphorylation in a Phosphorylation dataset.  If normalized ratio, fold change, or log ratio/log fold change is chosen as the Expression or Phosphorylation Value type, a greater intensity of green represents a higher degree of down-regulation or decrease in phosphorylation, and a greater intensity of red represents a higher degree of up-regulation or increase in phosphorylation. In contrast, for the value types intensity/RPKM/FPKM/ Expr Other, p-value, and False Discovery Rate/ q-value, all Analysis-Ready Molecules are red by default; and a higher color intensity represents a lower (and thus more significant) value.

Molecule coloring can be customized in Application Preferences. For more information on molecule coloring, click here.

 

Tool Icons
 



Graph Navigation Tools

           



This tool is available from networks and pathways. The arrow keys allow you to move the network left, right, up, and down. The "+" button acts as a Zoom In tool. The "-" button is a Zoom Out tool. Clicking the circle in the center fits the network to the screen.

Clicking the double arrow on the top left side of the screen opens an overview of the network so that you can determine where on the page you are currently focusing.

 

Path Designer Tools
 

 
 
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