ClueGO

Creates and visualizes a functionally grouped network of terms/pathways
ClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easely extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be fused to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology, KEGG and Reactome. To extend it's functionality get as well CluePedia. **NOTE:** **If you use Cytoscape 3.x with OpenJDK, ClueGO may not work properly! e.g. the network creation after ClueGO analysis may not finish and Cytoscape will not react anymore!**

2.1.5

Works with Cytoscape 3.0

Release Notes

Update for Cytoscape 3.2.0, but it should still work with all the older versions.

2.1.4

Works with Cytoscape 3.0

Release Notes

Bugs fixed: * In the ClueGO result table sometimes some terms showed more symbol names than actually associated genes. The bug didn't influence any calculations. * In the log file the final number of terms was not the same than the actually shown terms on the network. This was due to the fact that terms can re-occur in different groups. Now the log shows the correct unique number of shown terms. New featues: * New organisms added. - Pseudovibrio sp. FO-BEG1

2.1.3

Works with Cytoscape 3.0

Release Notes

New features: * CluePedia Options added to allow faster ClueGO analysis (less genes added for CluePedia). * GUI improvements * New organisms added. - Anopheles Gambiae

2.1.2

Works with Cytoscape 3.0

Release Notes

New features: * New organisms added. - Crassostrea Gigas - Medicago Truncatula - Anas Platyrhynchos - Theobroma Cacao - Ovis Aries - Xanthomonas Axonopodis - Populus Trichocarpa - Meleagris Gallopavo - Plasmodium Falciparum 3D7 - Mycobacterium Tuberculosis H37Rv Bugs fixed: * Genes that had an old annotation (entrez gene id removed/replaced) caused a problem when reopening a saved ClueGO session file.

2.1.1

Works with Cytoscape 3.0

Release Notes

New features: * The ClueGO group colors can be changed now even after the analysis * Small(not significant) term/pathway labels can be hidden now or enlarged by checking them in ClueGO result panel Some bugs were fixed regarding the new ClueGO session saving option.

2.1.0

Works with Cytoscape 3.0

Release Notes

Major features: * All ClueGO/CluePedia analyses can be **saved and restored using a "*.cluego"** zipped format. * Reorganization of the user interface to make it more user friendly. Minor features: * Bugfixes * Result panels were reorganized

2.0.8

Works with Cytoscape 3.0

Release Notes

* Various Bugfixes concerning node coloring. * Improved vusialization: different shapes are available now for each selected ontology * New organisms or id files are directly accessible from the main ClueGO selection panel. * Improved speed when loading annotation and ontology files (multiple threads) * Several new Organisms added

2.0.7

Works with Cytoscape 3.0

Release Notes

ClueGO library files are moved from the ".cluegoplugin" folder to a visible folder "ClueGOConfiguration” (in the user home directory) for an easier access. ClueGO performs now **functional analysis for more than 2 lists of genes**. By default one gene list is analyzed. The user can add (“Add Cluster”) or remove (“Remove Cluster”) additional lists of genes. This new functionality replaces the previous analysis type (Single or Compare). See **[http://www.ici.upmc.fr/cluego/ClueGO_newFeatures_207.pdf here]** for the documentation. The ClueGO visualizations are maintained: * The gene distribution: terms specific for each of the gene lists and their significance. * The group view: functionally grouped terms/pathways based on common genes * The significance view: the number of the genes associated to a term and its significance.

2.0.6

Works with Cytoscape 3.0

Release Notes

ClueGO supports now WikiPathways and some bugs where fixed.

2.0.4

Works with Cytoscape 3.0

Release Notes

ClueGO bug fixed (ClueGO window had to be canceld to finalize analysis with Cytoscape 3.0.1).

2.0.3

Works with Cytoscape 3.0

Release Notes

Some bug fixes. Closing ClueGO (sub-)network windows will now automatically clean up the system. A refresh button is added to avoid a cytoscape restart in case new files were externally added to ClueGO.

2.0.2

Works with Cytoscape 3.0

Release Notes

Release for Cytoscape 3.0.0. Some bug fixes and changes to fit CluePedia 1.0.2.

2.0.1

Works with Cytoscape 3.0

Release Notes

First official release for Cytoscape 3.0.0

2.0.0

Works with Cytoscape 3.0

Release Notes

First release for Cytoscape 3.0.0

2.0.0.beta1

Works with Cytoscape 3.0

Release Notes

Release for Cytoscape 3.0.0beta1

CYTOSCAPE 3

Version 2.1.5

License Click here

Released 10 Nov 2014

Works with Cytoscape 3.0

Download Stats Click here

CYTOSCAPE 2

Version 1.8

Released 3 May 2013

Works with Cytoscape 2.8

Download Stats Click here