Mapping to ontologies (Gene table)

This workflow is designed to classify an input gene set to several ontologies and to identify terms, hits for which are overrepresented in the input set. The input file can be any gene or protein table.

At the first step, the input table is converted into a table with Ensembl Gene IDs.
This table with Ensembl Gene Ids is subjected to functional classification, which is done in parallel by the following ontologies: GO biological processes, GO cellular components, GO molecular functions, Reactome pathways, HumanCyc pathways, TF classification.
For each ontological term several parameters are calculated, including expected number of hits, actual number of hits, p-value, as well as hit names and the link to the corresponding ontological term.

What is the geneXplain type?

The geneXplain platform is an online toolbox for a broad range of bioinformatic and systems biology applications. It is developed by geneXplain GmbH. The technology behind the geneXplain platform is BioUML (www.biouml.org), which has been built, improved and supported for many years at the Institute of Systems Biology in Novosibirsk. The individual workflows (geneXplain type), or Bricks, are unified under a standardized interface.
To run the workflows you just need to register for a free account here:

http://www.genexplain.com/genexplain-platform-registration

You get a password from BioStore to login the platform. It is open for everyone.

After clicking the workflow link (bottom) you can immediately enter the platform and execute the workflow via simple drag and drop of uploaded data files in your project.

Workflow_Mapping to ontologies (Gene table)

See also

•     http://wiki.biouml.org/index.php/Category:GeneXplain_analyses
•     http://wiki.biouml.org/index.php/Category:GeneXplain_workflows