DAPath is a disease associated path analysis tool for discovering signaling paths and the pathways that contain these paths which are subjected to cumulative impact of modestly associated variants.
DAPath uses KEGG pathways and gene-p value pairings in your local directory to find affected paths in KEGG pathways. A path is composed of an input node, an output node, and the intermediate nodes that constitute the path in-between. If there are alternatives in-between, each is accepted as a distinct path.
KEGG pathways and other required KEGG related files can be downloaded in the app. The download creates a folder in Cytoscape folder named as KEGGFiles_[YYYYMMDD_HHMMSS]. The download and creation of files take 5 to 10 minutes which is a one time operation.
Code and sample files are available in
https://github.com/ozanozisik/DAPath
Related paper is available at [https://www.biorxiv.org/content/early/2018/05/08/316562]
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
