PINTnet: construction of condition-specific pathway interaction network by computing shortest paths on weighted PPI.

ABSTRACT:

Background

Identifying perturbed pathways in a given condition is crucial in understanding biological phenomena. In addition to identifying perturbed pathways individually, pathway analysis should consider interactions among pathways. Currently available pathway interaction prediction methods are based on the existence of overlapping genes between pathways, protein-protein interaction (PPI) or functional similarities. However, these approaches just consider the pathways as a set of genes, thus they do not take account of topological features. In addition, most of the existing approaches do not handle the explicit gene expression quantity information that is routinely measured by RNA-sequecing.

Results

To overcome these technical issues, we developed a new pathway interaction

SUBMITTER: Moon JH 

PROVIDER: S-EPMC5374644 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature