**Pathway Scoring Application** evaluates the activity of cell signaling pathways by utilizing gene expression and ChIP-seq data.
The user can upload any KEGG pathway or provide a custom network.
The algorithm uses the pathway topology and maps the experimental data onto protein nodes as scores, which are transferred over the pathway by traversing the topology until a pre-defined biological target process is attained.
Node scores are transferred en route to the pathway to form a final activity score that describes the biological response of a specific process in the pathway while enriching the gene scores.
For the user manual, please visit the
[http://sites.google.com/site/pathwayscoring/ Tutorial] page.
Isik Z. *et al.*, A signal transduction score flow algorithm for cyclic cellular pathway analysis, which combines transcriptome and ChIP-seq data, *Mol. BioSyst.*, 8, 3224-3231, 2012