DAPath is a Cytoscape app for discovering signaling paths and the pathways that contain these paths which are subjected to cumulative impact of modestly associated variants. The parameters of DAPath are:
- KEGG folder: Path of the folder that containes KEGG pathway files
- Experiment file: Path of the experiment file that contains gene name p-value pairs
- Output folder: Path of the folder that result files will be stored
- Whether to skip first line of experiment file
- Number of top pathways to visualize
- Whether to apply crosstalk handling and the tolerance for crosstalk
KEGG related files can be downloaded through the app.
http://apps.cytoscape.org/apps/dapath
Ozisik, O., Meguro, A., Mizuki, N., Diri, B., Sezerman, O.U., (2018), "A Scoring System to Evaluate the Impact of SNPs in a Path Related Context to Study Behcet's Disease Aetiology in Japanese Population", bioRxiv 316562, DOI:10.1101/316562