Cytoscape is an open source software platform used to visualize molecular interaction networks and integrate gene expression data. It was created in 2002 at the Institute of Systems Biology and has since been developed by an international consortium. Cytoscape can be used to analyze and visualize networks in biological research as well as other domains involving nodes and edges. It features the ability to load, save, and analyze networks along with gene expression profiles and functional annotations to identify active subnetworks and hypotheses about regulatory interactions.

1. Shaina Nasir
Roll no 1028
Bs(hons) botany (M)
3rd Smester
University of Education
Renala Campus

2. OIntroduction
OHistory
OGene plugin
ODevelopment
OUsage
OFeatures
OAnalysis
OConclusion

3. Introduction
OCytoscape
OIt is an open
source bioinformatics software platform
for visualizing molecular interaction
networks and integrating with gene
expression profiles and other state data.
OCytoscape also has a JavaScript-centric
sister project named Cytoscape.js that can
be used to analyse and visualise graphs in
JavaScript environments, like a browser.

4. History
O Cytoscape was originally created at the Institute of
Systems Biology in Seattle in 2002.
O Now, it is developed by an international consortium of
open source developers.
O Cytoscape was initially made public in July, 2002
(v0.8); the second release (v0.9) was in November,
2002 and v1.0 was released in March 2003.
O Version 1.1.1 is the last stable release for the 1.0 series.
Version 2.0 was initially released in 2004; Cytoscape
2.83, the final 2.xx version, was released in May 2012.
Version 3.0 was released Feb. 1st, 2013, and the latest
version, 3.0.2, was released in August 2013.

5. Gene plugin
O The Gene MANIA Cytoscape plugin brings fast gene
function prediction capabilities to the desktop.
O Gene MANIA identifies the most related genes to a
query gene set using a guilt-by-association approach.
O The plugin uses a large database of functional
interaction NETWORK from multiple organisms and
each related gene is traceable to the source network
used to make the prediction.
O Users may add their own interaction networks and
expression profile data to complement or override the
default data

6. Development
O The Cytoscape core developer team continues to work on this
project and in the near future, is going to release next major
version, Cytoscape 3.0.
O It will be a more modularized, expandable and maintainable
version of Cytoscape.

7. Usage
• While Cytoscape is most commonly used for
biological research applications, it is agnostic in
terms of usage.
• Cytoscape can be used to visualize and analyze
network graphs of any kind involving nodes and
edges (e.g., social networks).
• A key aspect of the software architecture of
Cytoscape is the use of plugins for specialized
features. Plugins are developed by core developers
and the greater user community.

8. Features
O Load and save previous constructed interaction neworks
in GML format.
O Load and save networks and node attributesn in XML
document format called XGMML.
O Input mRNA expression profiles from tab- or space-delimited
text files.
O Load and save arbitrary attributes on nodes and edges.
For example, input a set of custom annotation terms for
your proteins, create a set of confidence values for your
protein-protein interactions.
O Import gene functional annotations from the Gene
Ontology (GO) and KEGG databases.
O Directly import GO Terms and annotations from OBO
and Gene Association files

9. Analysis
O Plugins available for network and molecular profile
analysis.
For example:
O Filter the network to select subsets of nodes based on
the current data. For instance, users may select nodes
involved in a threshold number of interactions, nodes
that share a particular GO annotation, or nodes whose
gene expression levels change significantly in one or
more conditions according to p-values loaded with the
gene expression data.

10. Find active sub networks modules. The
network is screened against gene expression
data to identify connected sets of interactions,
i.e. interaction sub networks, whose genes
show particularly high levels of differential
expression.
The interactions contained in each sub
network provide hypotheses for the regulatory
and signaling interactions in control of the
observed expression changes.

11. OCytoscape is an important software to
visualise graphs in Java script like a
browser and molecuar interaction
OIt also has an importance in the usage of
biological research sciences.
OInshort it help in the analysis of node
and edges in th network.