PathWeigh – Quantifying the Behavior of Biochemical Pathway Cascades

Abstract

Biochemical pathways analysis is an effective tool for understanding changes in gene expression data and associating such changes with cellular phenotypes. Pathway research aims to identify associated proteins within a cell using pathways and at building new pathways from a group of molecules of interest. Using pathway-based methods we gain insight into different functions of relevant molecules and find direct and indirect relations between them. We present PathWeigh, a Python-based tool for pathway analysis and graph presentation. The tool is open-sourced, extendable and runtime efficient. PathWeigh is available at https://github.org/zurkin1/Pathweigh and is released under MIT license. A sample Python notebook is provided with examples of running the tool.