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PINV - shorter path

Protein Interaction Network Visualizer
by

Gustavo Salazar

on 17 September 2014

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Transcript of PINV - shorter path

Protein Interaction Network Visualizer
Gustavo Adolfo Salazar Orejuela
Ayton Meintjes, Gaston Mazandu, Holifidy Rapanoel, Richard O. Akinola and Nicola Mulder
Protein Interactions
Or predicted by some algorithm (e.g. phylogenetic profiling)
Protein Interactions
Either experimentally discovered (e.g. protein complex immunoprecipitation)
Loads of data...
NetworkX
Sure!

there are tools for this kind of visualization
so what?
lets visualize it.
There is
no set recipe
to take hundreds of interactions and make them look good. Nonetheless, an appropriate
layout
is a great starting point.
Input from the
user
is required to adjust the graphic and to highlight the desired features
There are
visual tools
to locate, color, label and shape the nodes, and expose certain characteristics.
Filtering the data is an essential step.
But, all those are stand-alone tools
So, what would i get with an
online
tool?
You can use it
anywhere
, and easily
share
your findings.
There is no need to install extra software ...
PINV
Interactions for protein X?
Just Another HTTP connection
BROWSER
X Y 0.41 0.45 0.89 0.73
X Z 0.32 0.00 0.74 0.21
X W 0.53 0.00 0.48 0.49
X A 0.42 0.90 0.00 0.00
X Q 0.41 0.45 0.89 0.73
X S 0.32 0.00 0.74 0.21
X W 0.53 0.00 0.48 0.49
X E 0.42 0.90 0.00 0.00
X D 0.41 0.45 0.89 0.73
X C 0.32 0.00 0.74 0.21
X V 0.53 0.00 0.48 0.49
X F 0.42 0.90 0.00 0.00
X E 0.41 0.45 0.89 0.73
X R 0.32 0.00 0.74 0.21
X T 0.41 0.45 0.89 0.73
X G 0.32 0.00 0.74 0.21
X B 0.53 0.00 0.48 0.49
X N 0.42 0.90 0.00 0.00
X H 0.53 0.00 0.48 0.49
X T 0.42 0.90 0.00 0.00
...
An
HTML5
application that runs on every modern browser, whose function is to allow the visualisation of proteins and their interactions.
Cyanobacteria
At least 3.5 billion years old.
It is possibly the most abundant photosynthetic organism on earth.
It has a circadian clock!!
PINV: Datasets
Homo sapiens
Mycobacterium leprae strain TN
Mycobacterium smegmatis strain MC^2 155
Mycobacterium tuberculosis strain CDC1551
Interactions
Annotations
+
X Y 0.41 0.45 0.89 0.73
X Z 0.32 0.00 0.74 0.21
X W 0.53 0.00 0.48 0.49
Y W 0.42 0.90 0.00 0.00
...
#id Organism Gene-Name Chrom-Location ...
X Homo_sapiens gene1 ch1(100-200)
Y Homo_sapiens gene2 ch1(260-320)
Z Homo_sapiens gene3 ch1(340-410)
W Homo_sapiens gene4 ch1(420-537)
...
Querying
Enter an accession number in the text area.
3 modes to Query
Network
Visualizing
Table
Circle
Contextual Menu
http://www.annualreviews.org/doi/pdf/10.1146/annurev-biophys-042910-155317
Direct Manipulation
Drag&drop
Manipulation by rules
Thanks!!!
Any questions??
You can paint the proteins in the graphic according to their expression
Expression
Filter your dataset
Heatmap
http://biosual.cbio.uct.ac.za/pinViewer.html?status=0002f3d7ea8c2ec1ef4f2381e7061a3f.json
Spacial Clustering on the fly
Full transcript