Use Case 6: CFDE Knowledge about a Variant
Version 1

Workflow Type: Playbook Workflow Builder Workflow

The workflow starts with selecting chr10:g.3823823G>A as the search term. The closest gene to the variant was found using MyVariant.info[1]. RNA-seq-like LINCS L1000 Signatures[3] which mimick or reverse the the expression of KLF6 were visualized. Median expression of KLF6 was obtained from the GTEx Portal[8] using the portal's API. To visualize the scored tissues, a vertical 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
Evangelista, J. E. et al. SigCom LINCS: data and metadata search engine for a million gene expression signatures. Nucleic Acids Research vol. 50 W697–W709 (2022). doi:10.1093/nar/gkac328
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/1241?version=1

DOI: 10.48546/workflowhub.workflow.1241.1

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	LINCS L1000 Reverse Search	Identify RNA-seq-like LINCS L1000 Signatures which reverse the expression of the 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 Scored Tissues	Construct a vertical bar plot with Scored Tissues

Outputs

ID	Name	Description	Type
step-1-output	Variant	Variant Term	File
step-2-output	Gene	Gene Term	File
step-3-output	LINCS L1000 Reverse Search Dashboard	A dashboard for performing L1000 Reverse Search queries for a given gene	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