Modelling pathways crosstalks as closed walks and cycles on graphs

Definitions

Our project was to analyse and quantify interactions between different biological pathways. Those interactions are named closed walks. A closed walks is a sequence of interactions between genes that starts and ends at the same gene. A cycle is a closed walk that never goes twice through the same gene except for the gene from which the interactions start and end. A cross talk is a closed walk that goes through genes from two different pathways, meaning that those pathways communicate and regulate each other through their genes/proteins interactions.

Research questions

We had 3 research questions:

• Are some functional pathways more prone to crosstalk than the others? If so, which ones?​
• What are the genes that are apparent “entry points” for the crosstalk with other pathways?
• Is crosstalk a symmetric process, i.e. do both pathways “need each other” the same, or is one rather “exploiting” the other for input stimuli?​

the analysis concentrates on closed walks of length 2, 3 and 4 only, for computational power​ reasons.

Methods

To answer the research questions we were provided with data containing genes' names, for each gene was indicated the different biological pathways it played a role into (each gene is involved in many different pathways). We first selected three different pathways to analyse, so that we could compare the interactions between each pair of those pathways. The chosen pathways were:

• Cell differentiation
• Mitotic cell cycle
• Programmed cell death

We also got a csv file containing all the interactions between those genes. This file is made of the name of the source gene and the name of the target gene and a sign: -1 or 1 that indicates if the interaction is an activation or an inhibition.