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Correlation Networks
About
Co-expression tool
PPI tool
TF tool
Browse experiments
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FAQ
Step 1:
OPTION 1: one or more query genes
at2G27960, AT4g25550; at1g30460 AT3G48750
Paste a list of AGI codes in the text area on the left
The AGI codes may be seperated by tabs, spaces, semicolon, commas and newlines
The AGI codes are case insensitive
e.g.
at1G01010;AT1G01030;at1g01040
AT3G48750
at5g61850;at1g77950
Step 3:
Show:
Pairwise interactions
Interactions of query protein(s) with neighbours
Interactions between neighbours
Output:
Cytoscape (starts automatically
?
)
Text
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Visualization legend:
Correlation networks
Edge color
Query gene
Protein-protein interactions
Edge color
black
Edge width
the more references, the wider the edge
Edge style
= experimental
= predicted
Query gene
Transcription factor interactions
Edge color
black
Edge width
the more references, the wider the edge
Edge style
= Confirmed
= Unconfirmed
= Dimer
Edge arrow
= direct + Activation
= direct + Repression
= direct + unknown
= indirect
Arrow color
green = activation
red = repression
black = unknown
Query gene
COR
and
PPI
Query gene
COR
and
TF
Query gene
TF
and
PPI
Query gene
Localization pie colors
(the size of a pie slice represents how much
a value is referenced compared to the others)
CYTOSKELETON
PEROXISOME
OTHER
CELLPLATE
NUCLEOLUS
CYTOSOL
CHLOROPLAST
NUCLEUS
MITOCHONDRIA
ENDOSOME
PLASTID
VACUOLE
ENDOPLASMICRETICULUM
EXTRACELLULAR
PLASMAMEMBRANE
GOLGI
Step 2:
Select protein-protein interactions database(s):
?
IntAct :
experimental
predicted
both
TAIR :
experimental
predicted
both
BAR :
experimental
predicted
both
ArathReactome :
experimental
predicted
both
AtPID :
experimental
predicted
both
BioGRID :
experimental
predicted
both
DIP :
experimental
predicted
both
MINT :
experimental
predicted
both
BIND :
experimental
predicted
both
DeBodt (predicted - low stringency) :
experimental
predicted
both
DeBodt (filtered - high stringency) :
experimental
predicted
both
Ath Interactome Mapping Consortium :
experimental
predicted
both
AraNet (gene-gene associations) :
experimental
predicted
both
MIND0.5 (no independent verification) :
experimental
predicted
both
G-protein interactome :
experimental
predicted
both
EVEX binding :
experimental
predicted
both
STRING :
experimental
predicted
both
BORDER :
experimental
predicted
both
STEP 2 Help
(Double click to close)
ARANET:
this database contains gene-gene associations identified from a probabilistic gene functional network. Evidence for the different types of gene-gene assocations can be found in the PPI_evidence attribute
MIND0.5:
this database contains the preliminary Membrane Interactome data. The data has not been independently verified yet. Scores can be found in the PPI_evidence attribute. Tests are underway. The database will be regularly updated (please also check www.associomics.org).
Please allow pop-ups. Also add
co-expression analysis or
regulatory interactions to the network
localization of genes