GRAVITY (for âGene inteRaction Analysis of Variants in Individuals: a Tool for Youâ) is a new open-source Cytoscape app that allows an efficient visualization and analysis of all the exonic variants stored in a database by mapping them on a protein-protein interaction (PPI).
- Visualise sequencing data from cohorts using a Gemini database:
- Paila, Umadevi, et al. âGEMINI: integrative exploration of genetic variation and genome annotations.â PLoS Comput Biol 9.7 (2013): e1003153.
- Uses the pedigree informations through Gemini. The pedigree can be enriched with additional informations (multiple phenotypes, simple clinical data).
- Integrate interactions between the genes using a PPI network. The PPI currently implemented can be found in:
- Rolland, Thomas, et al. âA proteome-scale map of the human interactome network.â Cell 159.5 (2014): 1212-1226.
- A Simplex family to focus on the mutation of a single individual but integrating the knowledge of his/her parents when they are available.
- A Multiplex family mode focusing on finding similarities/differences between affected and unaffected inside a family (dominant, recessive, compound heterozygous mutations).
- Cohort panel, to quickly see if other individual in your cohort share mutations in the selected genes.
- Quick search for one or multiple genes of interest.
We are working actively on this app and are planning to add new functionalities based on our needs and requests.
- Alternative PPI and/or other types of interaction networks such as coexpression or regulation.
- Add quality parameters specific to CNVs.
- Expand the usage to input other than Gemini.
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
- Getting started
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