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Visualisation of FAANG data – VizFaDa

Submission summary

Food production systems need to be more efficient and sustainable to tackle the challenges posed by a growing population and a climate crisis. Breeding strategies have proven themselves to be essential in providing genetic gain for livestock, but efforts must go on. Providing quality annotations for animal genomes will be instrumental to further improve genetic gains. The FAANG (functional annotation of animal genomes) initiative aims at gathering a community to foster FAIR data principles in this field (ref 1–3). A data coordination center (DCC) at the EMBL-EBI is developing the FAANG data portal to allow FAANG data to be more findable, accessible, interoperable and foster their reuse (ref 2).

This project, VizFaDa, will produce interactive data visualisations of FAANG data through web applications, and we will work with the EMBL-EBI to integrate those visualisations with the existing portal. First we will compute pairwise correlations between FAANG samples (genes expression and epigenetic data), and render the results in the form of interactive, subset-able, clustered correlation heatmaps. Users will be able to upload their processed data to be compared to FAANG samples within seconds. Correlation heatmaps will provide an eagle-eye view of the data available and their similarities. Second, we will integrate epigenetic and transcriptomic data by producing stacked epigenetic profiles near gene starts, gene ends, and middle exons, sorted according to gene expression level or exon inclusion ratio. These attractive visualisations will expose the complex links existing between epigenetic marks and transcription, and will add value to the FAANG dataset.

Efforts will be devoted to make the addition of new samples of the dataset as automatic as possible, to ensure the long term stability of the proposal. Development of the web applications will be fully open source. Altogether, we hope our efforts will reinforce the FAANG data portal attractiveness for researchers and breeders, and will foster data reuse.

Project coordination

Guillaume Devailly (Génétique Physiologie et Systèmes d'Elevage)

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

GenPhySE Génétique Physiologie et Systèmes d'Elevage

Help of the ANR 76,068 euros
Beginning and duration of the scientific project: December 2019 - 24 Months

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