Version 5.4

Pathway Analysis - Upload Data

InnateDB Pathway Analysis enables users to determine which biological pathways are significantly over-represented (represented more than expected by chance) in a given gene/protein list.
InnateDB incorporates pathway annotation (all pathways not just immune relevant ones) from major public databases including KEGG, Reactome, NetPath, INOH and PID and is thus one of the most comprehensive sources of pathways available.

To do a Pathway Analysis, first upload a tab-delimited text file or Excel spreadsheet (.xls files only) of gene/protein identifiers (human, mouse or cow only) and any associated quantitative data (e.g. gene expression data fold-changes and p-values) from up to 10 conditions/time-points. Please see our help page if you are unsure how to do this and to see what IDs are accepted.

Once you have a list of pathways associated with your gene/protein list - click on the red "Pathway ORA" button at the top of the page.

Web Form Upload a file

If you use InnateDB for your research, please cite the following publication:

Breuer et al., InnateDB: systems biology of innate immunity and beyond - recent updates and continuing curation. Nucl. Acids Res. (2013) 41 (D1) 

InnateDB is being developed jointly by the Brinkman Laboratory (Simon Fraser University, British Columbia, Canada), the Hancock Laboratory (University of British Columbia, Vancouver, British Columbia) and the Lynn EMBL Australia Group (South Australian Health & Medical Research Institute and Flinders University, Adelaide, Australia).

Funding is currently provided by Allergen and EMBL Australia. Previous funding has been provided by Genome Canada, the Foundation for the National Institutes of Health through the Grand Challenges in Global Health initiative and by Teagasc. InnateDB curated interactions are licensed under the Design Science License. All other data is licensed under the terms of the originating database. Contact: innatedb-mail@sfu.ca