Use Case 7: Variant Expression in Tumor/Healthy
Version 1

Workflow Type: Playbook Workflow Builder Workflow

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..

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
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
Lonsdale, J. et al. The Genotype-Tissue Expression (GTEx) project. Nature Genetics vol. 45 580–585 (2013). doi:10.1038/ng.2653

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SEEK ID: https://workflowhub.eu/workflows/1243?version=1

DOI: 10.48546/workflowhub.workflow.1243.1

Inputs

ID	Name	Description	Type
step-1-data	Variant Input	Start with a Variant	File

Steps

ID	Name	Description
step-1	Variant Input	Start with a Variant
step-2	Identify Closest Gene to Variant (Legacy)	Identify the closest gene to this variant
step-3	Query KF Gene Expression in Tumor	Use KF API to obtain tumors expressing the given gene
step-4	Query GTEx Median Tissue Expression	Use GTEx API to obtain median tissue expression for the given gene
step-5	Vertical bar plot from Tumor Gene Expression	Construct a vertical bar plot with Tumor Gene Expression

Outputs

ID	Name	Description	Type
step-1-output	Variant	Variant Term	File
step-2-output	Gene	Gene Term	File
step-3-output	Tumor Gene Expression	Gene expression in tumors	File
step-4-output	Scored Tissues	ZScores of Tissues	File
step-5-output	Plotly Plot	A plot rendered using the [plotly.js library](https://plotly.com/javascript/)	File