Research Object Crate for Use Case 7: Variant Expression in Tumor/Healthy

The workflow starts with selecting chr2:g.39417578C>G as the search term. The closest gene to the variant was found using MyVariant.info[1]. Gene expression in tumors for CDKL4 were queried from the Open Pediatric Cancer Atlas API[3]. Median expression of CDKL4 was obtained from the GTEx Portal[4] using the portal's API. To visualize the level of expression across tumor gene expression, a bar plot was created Fig.. 1. Lelong, S. et al. BioThings SDK: a toolkit for building high-performance data APIs in biomedical research. Bioinformatics vol. 38 2077–2079 (2022). doi:10.1093/bioinformatics/btac017 3. Shapiro, J. A. et al. OpenPBTA: The Open Pediatric Brain Tumor Atlas. Cell Genomics vol. 3 100340 (2023). doi:10.1016/j.xgen.2023.100340 4. Lonsdale, J. et al. The Genotype-Tissue Expression (GTEx) project. Nature Genetics vol. 45 580–585 (2013). doi:10.1038/ng.2653

Author

License

CC-BY-4.0

Contents