Exercise 1.1: Cytoscape user interface presentation

Exercise 1.2: Installation of Cytoscape

Cytoscape download

Cytoscape_2.5.1_sig.zip

 

video example

Exercise 1.3:  Import interaction data

presenilin.sif

  video example  

video example

Import attributes video

Nodes attribute:

video example

video example

biopax.comment.NA biopax.xref.UNIPROT.NA

Exercise 1.4: Selection tools

    video example

     video example

2^de step: user cases

Exercise 2.1: co expression clusters

Java Web Start

ing_cpath_result.sif .

cluster_name.NA

 interaction.EA

.cys file  

first part, second part ,third part

Exercise 2.2: Using microarray HGNC homology annotations

chicken 20k general annotation file  V1

 ( http://www.sigenae.org/index.php?id=128)

 

network raw .sif file

annotation matrix

expression.NA, cluster.NA

interaction.EA

style.props

 

first part, second part

.cys file , pdf file 1 , pdf file 2

 

Exercise 2.3: KEGG microarray annotation

keggMap.sif

KEGGgene_chicken_V2.csv

.cys file , pdf file

3^d step: advanced features

 

Exercise 3.1: Online interaction data source connectors

CPath

    video example

Web Service connector

      video example

Exercise 3.2: Use the plugins

see a video demo

   Java Web Start

Plugins examples

Here you can discover some interesting de plugins :

APID2NET :

Functionalities : interaction and annotation online data source connector, GO, groups?

URL: http://bioinfow.dep.usal.es/apid/apid2net.html

ÿ      see a video demo

FCModeler :

Functionalities: path finder neighbour selection, sub graph creation.

URL: http://metnetdb.org/MetNet_fcmodeler_Cytoscape_main.htm

ÿ      see a video demo  

BINGO :

Functionalities: GO annotation and representativity statistical test for GO classes.

URL : http://www.psb.ugent.be/cbd/papers/BiNGO/

ÿ      see a video demo

GOSLIMMER:

Functionalities: graph conversion from a  Gene Ontology graph  to a synthetic graph that represents the GO  coverage of a gene list.

URL : http://yeastgenomics.ca/resources

ÿ      see a video demo

BiNoM :

Functionalities: import/export (BioPAX, SBML, CellDesigner formats), network analysis.

URL: http://bioinfo-out.curie.fr/projects/binom/

BioQuali :

Functionalities: BioQuali analyses regulatory networks and expression datasets by checking a global consistency between the regulatory model and the expression data.

URL: http://irisa.fr/symbiose/projects/bioqualiCytoscapePlugin/

 

 

The web page http://www.Cytoscape.org/plugins2.php references available published plugins :

You can go deeper in the Cytoscape world with the official online tutorials  from Cytoscape.org. it?s up to you !