Overview of the approaches

Goal

Our goal is to uncover molecular relationships between chemicals (e.g. vitamins, hormones etc.) and rare diseases. To this end, we implement three approaches.

Data are retrieved automatically from the Comparative Toxicogenomics Database (CTD) [1] for target genes of chemicals, WikiPathways [2] for rare disease pathways and from the Network Data Exchange (NDEx) [3] for biological networks (see Use-case 1: data are retrieved automatically by queries).

We propose three different approaches to uncover molecular relationships between genes which are targeted by chemicals and rare diseases (Fig. 1):

• Overlap analysis: chemical target genes are part of a rare disease pathway

• Active Module Identification (AMI): chemical target genes and/or linked genes that form a module are part of a rare disease pathway

• Random Walk with Restart (RWR): rare disease pathways prioritization

These three approaches are complementary and they perform network exploration at different level of interactions.

Fig. 1 : Overview of the three approaches implemented in ODAMNet

Moreover, the approaches can be used with user-provided input files instead of files fetched with automatic queries. Take a look at Use-case 2: data are provided by the user, if you want to use your own input files.

References

[1]

Davis AP, Grondin CJ, Johnson RJ et al.. The Comparative Toxicogenomics Database: update 2021. Nucleic acids research. 2021.

[2]

Martens M, Ammar A, Riutta A et al.. WikiPathways: connecting communities. Nucleic acids research. 2021.

[3]

Pratt D, Chen J, Welker et al.. NDEx, the Network Data Exchange. Cell Systems. 2015.