Use Case 6: CFDE Knowledge about a Gene
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Download RO-CrateThe workflow starts with selecting KLF6 as the search term. RNA-seq-like LINCS L1000 Signatures[1] which mimick or reverse the the expression of KLF6 were visualized. Median expression of KLF6 was obtained from the GTEx Portal[6] using the portal's API. To visualize the scored tissues, a vertical bar plot was created Fig..
- 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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Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| step-1-data | Gene Input | Start with a Gene |
|
Steps
| ID | Name | Description |
|---|---|---|
| step-1 | Gene Input | Start with a Gene |
| step-2 | LINCS L1000 Reverse Search | Identify RNA-seq-like LINCS L1000 Signatures which reverse the expression of the gene. |
| step-3 | Query GTEx Median Tissue Expression | Use GTEx API to obtain median tissue expression for the given gene |
| step-4 | Vertical bar plot from Scored Tissues | Construct a vertical bar plot with Scored Tissues |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| step-1-output | Gene | Gene Term |
|
| step-2-output | LINCS L1000 Reverse Search Dashboard | A dashboard for performing L1000 Reverse Search queries for a given gene |
|
| step-3-output | Scored Tissues | ZScores of Tissues |
|
| step-4-output | Plotly Plot | A plot rendered using the [plotly.js library](https://plotly.com/javascript/) |
|
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Version 2 (latest) Created 25th Feb 2025 at 18:27 by Daniel Clarke
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Version 1 (earliest) Created 13th Jan 2025 at 21:13 by Daniel Clarke
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