GO-Elite News and Updates

5-25-12

A major update to GO-Elite has been posted. GO-Elite release v.1.2.4 is available as stand-alone compiled versions for Windows (32bit and 64bit), Ubuntu (release 10.04 and 12.04) and Mac OSX in addition to cross-platform source code. Updates to this version include: 1) Optional import of many new ontology, gene-set and pathway resources beyond WikiPathways and Gene Ontology, 2) Visualization of WikiPathway through the WikiPathways API, 3) Fisher Exact Test option added for p-value calculation, 4) Support added for addition of new Ontologies, pathways and gene-sets, 5) improved documentation (see Documentation) and 6) Fixed bugs from 1.2.3 related to custom ID system and relationship addition and updates. See the included documentation for specific details and workflows.

1-3-12

The GO-Elite web service is now restored.

1-2-12

The GO-Elite web service is temporarily down following a software update on our servers. This status will effect BOTH the direct GO-Elite web query and the GenMAPP-CS Cytoscape plugin. We are working to restore this service immediately.

1-1-12

Version 1.2.3 of GO-Elite is now available for download. GO-Elite release v.1.2.3 is available as stand-alone compiled versions for Windows (32bit and 64bit) and Mac OSX in addition to cross-platform source code. Updates to this version include: 1) Updated support for Ensembl version 65 and later, 2) improved WikiPathways update options and 3) more flexible replacement of alternative gene sets. Additional documentation can be found here.

11-11-11

Version 1.2.2 of GO-Elite is now available for download. GO-Elite release v.1.2.2 is available as stand-alone compiled versions for Windows (32bit and 64bit) and Mac OSX in addition to cross-platform source code. Updates to this version include: 1) Builds WikiPathways associations from distributed GPMLs directly rather than flat-files, 2) Automatically replaces GO with GO-Slim when OBO GO-Slim imported, 3) Greatly improved efficiency of GO pruning, 4) Filtering option for GO associated gene counts added and 5) Multiple miscellaneous bug fixes. Corresponding code updates have been added to the corresponding web-service. Additional documentation can be found here.

6-12-11

Version 1.2.1 of GO-Elite is now available for download. GO-Elite release v.1.2.1 is available as stand-alone compiled versions for Windows (32bit and 64bit) and Mac OSX in addition to cross-platform source code. Updates to this version include: 1) Metabolomics data supported, 2) Selection of custom gene set files from multiple file types, 3) Selection of user desired Ontology types beyond Gene Ontology, 4) Comparison between GO-Elite results for different input sets, 5) Updated WikiPathways download, 6) Updated Gene Ontology structure file download, 7) Augmented Ensembl-GO associations from EntrezGene, 8) Gene association files for all ORA Ontology terms and Pathways added, 9) Support for gene symbols as input identifiers and 9) Multiple miscellaneous bug fixes. Corresponding code updates and new GO-Elite species databases are being posted with the corresponding web-service. Additional documentation can be found here.

12-12-09

Posted version beta 1.2. This version is currently beta but will likely be upgraded to release once it is more extensively tested by the user community. This version has several new features (see here) and bug fixes. New features include a web-version of GO-Elite, built-in support for over 60 supported species and 60 gene systems, database versioning, a new graphical user interface, new tools for adding species and gene support and a command-line interface for remote access.

10-20-08

Mac OS X 10.5 (Leopard) binary version of 1.19 made available. The 10.4 version (Tiger) was discovered to be incompatible with later Mac OS X operating systems and vise versa. Please download the version appropriate for your operating system.

9-27-08

Critical bug fixes for version beta 1.19. These include: 1) Failure to create the GO-Elite gene_association directory when selecting a non-default output directory, 2) GO-Elite incorrectly altered the standard OBO summary files when importing a previously run OBO build. These two issues have been addressed and currently the program tests fine on Mac and PC using standard parameters. To update: 1) go to: http://www.genmapp.org/go_elite, 2) re-download the installer, 3) uninstall GO-Elite version 1.1.9 (windows) and/or delete the program folder on your hard-drive and, 4) Re-install the application.

9-14-08

Posted version beta 1.19. This release includes substantial upgrades to previous versions! Although the core algorithms are the same, GO-Elite now has full interactive GUI, automated update and download functions, import of Wikipathway pathways, stand-alone Mac OS X version and OS specific installers (Mac and PC). Please see the updated documentation at our Google groups page including the Instructions and Tutorial.

6-5-08

Posted version beta 1.18. This version contains new analysis features, including inverse gene redundancy annotations and quantization of GO-Elite results using user data. Also updated is the white paper and ReadMe with updated instructions. Please see the "Implemented Feature Section" at GO-Elite at Google Groups for more details.

4-4-08

Updated the installation of version beta 1.17, to include Arabidopsis thaliana gene data. Support for this species was implemented in minutes entirely using the "BuildAffymetrixEntrezAssociations" option in GO-Elite (See ReadMe>How_to_Make_New_Species_Databases.rtf).

3-23-08

Posted version beta 1.17. Updates include customizable MOD choice, fixed some missing folder and file bugs, added Affymetrix.csv GO relationship import options, included Affymetrix Gene 1.0 ST array data and added support for Rat and Corn (using the new directions posted in ReadMe). Please see the "Implemented Feature Section" at GO-Elite at Google Groups for more detials.

2-11-08

Posted version beta 1.16. This is the most significant update since posting version 1.1. GO-Elite's functionality and usuability has undergone major changes. In addition, all gene and GO databases have been updated (with the exception of Local MAPPs). Please see the "Implemented Feature Section" at GO-Elite at Google Groups for more detials.

1-24-08

Posted version beta 1.15. The Ensembl-GO (human only - more to come) and OBO tables have been updated to the most recent builds. The 'combined' GO-Elite output file now contains associated gene symbols. Improved support for gene-GO tables with different formats and input gene tables with different line returns or quotes. Create 'gene_association' fold if deleted at runtime. Builds GenMAPP GO database tables when 'OBO_import.py' is run (as opposed to 'GO-elite.py').

1-15-08

Mac OS X error still not solved in last version. Corrected in current. Also added better error handling of options at start.

1-11-08

Fixed carriage return problems encountered on the Mac OS. Removed local mapp file that was used for testing (prevented propper local mapp analysis).

12-21-07

Replaced version beta 1.12 with 1.13, which address a few operating system incompatibilty bugs (testing between Windows and Linux).

10-26-07

Posted version beta 1.12, which address two bugs: (1) replaces nested and output directories if missing, (2) builds nested relationships for mappfinder input if mappfinder not run yet. Should work OK in Linux. Also added support for other source IDs, in addition to Affymetrix (e.g. UniProt).

8-31-07

Posted version beta 1.11, which address two bugs: (1) missing gene identifiers from GO-elite gene-association files, (2) tree-reconstruction method bug could allow some non-elite terms in output.

6-22-07

Introduced a new version of GO-elite (beta 1.1) with advanced features:

1. Calculate and export MAPPFinder results from user input lists for the GO and GenMAPP pathway MAPPs.
2. Update GO tree structure from GO structure files.
3. Export of gene list to GO associations.
4. Identify genes over-represented in GO terms/MAPPs.

This version is supplied with gene association files for mouse, human and zebrafish analyses.

12-12-06

Posted a new version of GO-elite with a new user interface. Methods are the same but the program no longer requires installation of accessory software (e.g. Python) and is available as an EXE which runs through it's own command line. User now also has more options for customization.

5-23-06

Posted downloadable version of GO-elite for user analysis.