CoRTE: a web-service for constructing temporal networks from genotype-tissue expression data

A comprehensive and in-depth deciphering of the dynamics concerning gene expressions is essential for understanding intricate biological mechanisms; for instance, the latter can be effectively addressed via network science, and Gene Co-expression Networks (GCNs), specifically. However, a typical GCN is based on a static model, which limits the ability to reflect changes that occur over time. To overcome this issue, we designed an open-source user-friendly web-service for constructing temporal networks from genotype-tissue expression data: COnstructing Real-world TEmporal networks (CoRTE).

CoRTE bases the construction of a temporal network on the statistical analysis of the related gene co-expressions across successive age ranges, to define an ordered set of time points. In our experimentation we investigated gene co-expression dynamics across age groups in brain tissues associated with Alzheimer's Disease, processing curated aging-related data via the proposed web-service. The latter has effectively generated the temporal network consisting of a set of gene pairs that showed statistically significant co-expressions over time. Results demonstrated its capacity to capture time-dependent gene interactions relevant for aging-related disease progression. From a purely applicative point of view, CoRTE may be particularly suitable for exploring aging-related changes, disease development, and other time-dependent biological events.

CoRTE is freely available at https://github.com/pietrocinaglia/corte-ws.