Entity
|
Visual Shape
|
Physical Entities, such as proteins,
small molecules, complexes, etc.
|
|
Interaction Entities, such as
biochemical reactions, catalysis, etc.
|
|
Edge Type
|
Arrow Shape
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Inhibition
|
|
Containment, e.g. a complex can
contain one or more proteins.
|
|
All other edge types, e.g. activation,
left, right, etc.
|
|
Labels for Physical Entities
|
All physical entities will be labeled as follows:
|
[NAME] [-CHEMICAL MODIFICATION ABBR] [(CELLULAR LOCATION ABBR)]
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where [CHEMICAL MODIFICATION ABBR] and [CELLULAR LOCATION ABBR]
are one of the abbreviations described below.
|
Examples
|
MITF
|
MITF
|
MITF Phosphorylated
|
MITF-P
|
MITF Phosphorylated, in the cytoplasm
|
MITF-P (CP)
|
Abbreviations for Chemical Modifications
|
acetylated
|
A
|
glycosylated
|
G
|
phosphorylated
|
P
|
proteolytic cleavage
|
PCS
|
sumoylated
|
S
|
ubiquitinated
|
U
|
[All others]
|
No Abbreviation provided
|
Abbreviations for Cellular Locations
|
centrosome
|
CE
|
cytoplasm
|
CY
|
endoplasmic reticulum
|
ER
|
endosome
|
EN
|
extracellular matrix
|
EM
|
golgi apparatus
|
GA
|
mitochondrion
|
MI
|
nucleoplasm
|
NP
|
nucleus
|
NU
|
plasma membrane
|
PM
|
ribosome
|
RI
|
transmembrane
|
TM
|
[All others]
|
No Abbreviation provided
|