Use Case 3: Compounds to Reverse Disease Signatures Version 1
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Download RO-CrateA file containing GEO Aging Signatures was first uploaded. The file containing GEO Aging Signatures was loaded as a gene signature. A file containing GTEx Aging Signatures was first uploaded. The file containing GTEx Aging Signatures was loaded as a gene signature. Significant genes were extracted from the GEO Aging Signatures. Significant genes were extracted from the GTEx Aging Signatures. Reversers and mimickers from over 1 million signatures were identified using SigCom LINCS[1]. Resolved drugs from the LINCS L1000 Chemical Perturbagens library. Reversers and mimickers from over 1 million signatures were identified using SigCom LINCS[1]. Resolved drugs from the LINCS L1000 Chemical Perturbagens library. The mean across multiple Scored Drugs is computed. The drugs were filtered by FDA Approved Drugs with the help of PubChem APIs[3].
- 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
- Kim, S. et al. PubChem 2023 update. Nucleic Acids Research vol. 51 D1373–D1380 (2022). doi:10.1093/nar/gkac956
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Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| step-1-data | Input File | Upload a Data File |
|
| step-3-data | Input File | Upload a Data File |
|
Steps
| ID | Name | Description |
|---|---|---|
| step-1 | Input File | Upload a Data File |
| step-2 | Resolve a Gene Signature from a File | Load a gene signature into a standard format |
| step-3 | Input File | Upload a Data File |
| step-4 | Resolve a Gene Signature from a File | Load a gene signature into a standard format |
| step-5 | Scored Genes from Signature | Treat signature as a weighted set of genes |
| step-6 | Scored Genes from Signature | Treat signature as a weighted set of genes |
| step-7 | SigCom LINCS Signature Search | Query LINCS L1000 Signatures |
| step-8 | Extract LINCS L1000 Chemical Perturbagens | Extract signatures from the results |
| step-9 | SigCom LINCS Signature Search | Query LINCS L1000 Signatures |
| step-10 | Extract LINCS L1000 Chemical Perturbagens | Extract signatures from the results |
| step-11 | Mean Scored Values | Take the mean value across multiple scores |
| step-12 | Extract FDA Approved Drugs | Filter the drugs with PubChem APIs |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| step-1-output | File URL | URL to a File |
|
| step-2-output | Gene Signature | A gene expression signature |
|
| step-3-output | File URL | URL to a File |
|
| step-4-output | Gene Signature | A gene expression signature |
|
| step-5-output | Scored Genes | ZScores of Genes |
|
| step-6-output | Scored Genes | ZScores of Genes |
|
| step-7-output | SigCom LINCS Signature Search Results | LINCS L1000 Signatures Query Results |
|
| step-8-output | Scored Drugs | ZScores of Drugs |
|
| step-9-output | SigCom LINCS Signature Search Results | LINCS L1000 Signatures Query Results |
|
| step-10-output | Scored Drugs | ZScores of Drugs |
|
| step-11-output | Scored Drugs | ZScores of Drugs |
|
| step-12-output | Scored Drugs | ZScores of Drugs |
|
Version History
Version 1 (earliest) Created 16th Jan 2025 at 20:51 by Daniel Clarke
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Version-16cccd14
Creators and SubmitterViews: 28 Downloads: 4
Created: 16th Jan 2025 at 20:51
Last updated: 16th Jan 2025 at 20:52
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