ClueGO

Creates and visualizes a functionally grouped network of terms/pathways
Categories: automation, data visualization, enrichment analysis, functional module detection, GO annotation, heat map visualization, ontology analysis
ClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easily extended by the user. ClueGO performs single cluster analysis and comparison of several clusters (lists of genes). 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, WikiPathways and Reactome. To extend it's functionality get as well CluePedia. ClueGO visualizes also terms and pathways resulted from other enrichment analyses as functionally grouped networks. Cytoscape Automation enables scientific workflows written in many languages through the CyREST. ClueGO functions are now REST enabled, and allow the integration of ClueGO in analytical pipelines. *Note: ClueGO does not save your results in the Cytoscape Session (.cys) file. **Be sure to export your results before closing Cytoscape.***
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2.5.10

Works with Cytoscape 3.8

Release Notes

* Add new organisms * Fix to work with Cytoscape 3.10

2.5.9

Works with Cytoscape 3.5

Release Notes

Fixes: - Arabidopsis fixes for plant ontology PO

2.5.8

Works with Cytoscape 3.5

Release Notes

Updates: - New resource 'COMPLEX PORTAL' from EBI added. - Wikipathways update fixed Some minor bugfixes

2.5.7

Works with Cytoscape 3.5

Release Notes

Updates: - New option added to create GO source files: By default the GO source files are created by adding all child associations to their parents and Regulating Terms are considered as parents as suggested here http://geneontology.org/docs/ontology-relations/. These options can be switched **off** by adding this options the Organism.properties files for each organism: 1. enable.add.all.child.genes.to.parent=**false** 2. allow.relations.as.parents=**false** These changes will be only taken into account after the GO annotations are updated. Bugfixes: - Saving the results xls file was fixed.

2.5.6

Works with Cytoscape 3.5

Release Notes

Bugfix release

2.5.5

Works with Cytoscape 3.5

Release Notes

* ClueGO cyRest update, including now the option for custom reference sets. * New help icons added to explain how the reference sets work. Some bugfixes.

2.5.4

Works with Cytoscape 3.5

Apps that depend on this release

Release Notes

ClueGO cyRest update release. Bugfixes: * Gene ontology OBO file source location has been changed.

2.5.3

Works with Cytoscape 3.5

Apps that depend on this release

Release Notes

* New analysis option added to visualize lists of GO terms from other enrichment analyses. Some bugfixes.

2.5.2

Works with Cytoscape 3.5

Apps that depend on this release

Release Notes

Bugfix release: * WikiPathway update was fixed * CORUM update was fixed * Bug: Log file was missing the information when pvalue option was selected * Regession bug: Selecting genes from network was not working anymore UniGene was removed from EnsemblMart service

2.5.1

Works with Cytoscape 3.5

Apps that depend on this release

Release Notes

Bugfix release: * QuickGO REST service was discontinued, switch back to EBI-Uniprot GO annotations for the GO update.

2.5.0

Works with Cytoscape 3.5

Apps that depend on this release

Release Notes

New release that works only with Java 1.8 and Cytoscape 3.5+. For a smooth nice layout please make sure you have yFilesLayout installed: http://apps.cytoscape.org/download/yfileslayoutalgorithms/1.0 New features: * ClueGO was upgraded to work with the latest 3.6.0 release. * ClueGO now supports automatization via cyREST api. * Reactome has now an associated .obo file to display pathway relationships. * CORUM with MIPS FunCat (Functional Categories .obo) was added to the main Ontologies. * Interpro has now an .obo file associated as well. Some general improvements and fixes.

2.3.5

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

Bug fix update for REACTOME updates.

2.3.4

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

Bug fix release.

2.3.3

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

Bugfixes: - A major fix was added to exclude by default GO gene associations with the 'NOT' qualifier when updating the ClueGO files. - Some minor visualization bugs. Improvements: - For a most complete EntrezGene to Ensembl annotation integration both EnsemblMart + NCBI data are now used. - Unigene can be now updated via EnsemblMart + NCBI - Additional help buttons for more clear explanations. - New organisms added upon request. - GO Evidence codes IBA,IBD and IKR were added.

2.3.2

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

Bug fixes: - Correction of the stats displayed in the ClueGO log. Percentage of not found genes are now reported to unique genes, not to the initial uploaded ids - Overview chart calculation. Overlapping terms were included more than once in a group - OpenCL double-float problem. In certain graphic card driver versions a stricter usage of data types is needed - InterPro download was not working due to a change of the source data link - Reactome data source changed Improvements: - Additional iterative merging of functional groups for large networks - Improved network update behavior and speed - New analysis suggestions and explanations as help button included - New organisms included upon user request - Organism creation date included for new organisms - Metazoa mart added to ClueGO props - Multiple ontologies with separate OBO files. - Reactome data split into Reaction and Pathways. - Mapping on chromosomal locations is enabled. Chromosomal locations can be automatically updated (NCBI). Make sure you select levels from 0 to 3 when mapping!

2.3.1

Works with Cytoscape 3.2

Apps that depend on this release

2.3.0

Works with Cytoscape 3.2

Apps that depend on this release

2.2.6

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

* Fix for Annotation update due to data format change. * Fix for Wikipathways due to data location change.

2.2.5

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

* Bug fix for REACTOME pathway update. The REACTOME format changed but it should work again now. * Fix to work with Cytoscape 3.4.0

2.2.4

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

* A bug fix for renaming ClueGO networks. The new network name was not kept when saving the project and created problems when opening the project again. Also the ":" was removed from the default name not to interfere with json export. * Mirrors for the ensembl biomart update were added to make it working again.

2.2.3

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

A bug fix for updating GO ontologies others than Human or Mouse. Since version 2.2.0 one can choose to use the usual annotation files or QuickGO (direct db access). To use QuickGO you will have to uncomment following three lines in the organism properties file like: \#obo.ids = GO \#obo.urls = http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo \#association.urls = http://www.geneontology.org/gene-associations/submission/gene_association.goa_human.gz Then QuickGO will be enabled by default.

2.2.2

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

A fix for Project saving.

2.2.1

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

Fix for WikiPathways update. Ensembl Mart is offline for the moment so the update of Ensembl and Interpro Ontology update will not work.

2.2.0

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

General Update and OpenCL implementations for animated layouts and correlation calculations. Improved update for Ensembl (using Mart), Uniprot annotations and InterPro Domain Ontology.

2.1.7

Works with Cytoscape 3.0

Apps that depend on this release

Release Notes

To keep the plugin small only Mouse and Human files are included. Data for other organisms can be requested or downloaded via the download option. Some bug fixes and new Organisms.

2.1.6

Works with Cytoscape 3.0

Release Notes

Update for Cytoscape 3.2.1, but it should still work with all the older versions. Some bug fixes and new Organisms.

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 2.5.10

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Released 21 Jun 2023

Works with Cytoscape 3.8

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