https://github.com/saezlab/macau_synergy_prediction
Target functional similarity based workflows for drug synergy prediction and stratification
https://github.com/saezlab/macau_synergy_prediction
Last synced: about 1 year ago
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Target functional similarity based workflows for drug synergy prediction and stratification
- Host: GitHub
- URL: https://github.com/saezlab/macau_synergy_prediction
- Owner: saezlab
- License: gpl-3.0
- Created: 2018-10-06T18:26:31.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2019-03-20T14:45:54.000Z (over 7 years ago)
- Last Synced: 2025-01-22T07:37:29.260Z (over 1 year ago)
- Language: R
- Homepage:
- Size: 57.4 MB
- Stars: 1
- Watchers: 4
- Forks: 3
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Awesome Lists containing this project
README
## Stratification and prediction of drug synergy based on target functional similarity
The first step is to generate the target-pathway interactions using drug response data on cancer cell lines. Those interaction matrices are generated using codes from this publication:
**Yang et al. Linking drug target and pathway activation for effective therapy using multi-task learning.**
https://www.nature.com/articles/s41598-018-25947-y
https://github.com/saezlab/Macau_project_1
## Result analysis
**GDSC_DRUG_COMBO_TOP_HITS.Rmd**:
* Identify key pathways for synergy stratification for breast tissue.
* Identify protein target to combine with BRAF for colorectal cancer validation.
* Save target functional similarity values for breast, colon and lung_NSCLC from GDSC dataset.
**Use the key pathways to compute the Delta Pathway Activity (predicted synergy) and stratify new cell lines.**
**check_synergy_AZ.Rmd**:
* Synergy tratification analysis for breast/colon/lung cancer cell lines on AstraZeneca dataset.
* Synergy prediction on AstraZeneca dataset. We show here that synergy arises in case of strong similarity or anti-similarity for breast and colorectal tissues.
**check_synergy_SANGER.Rmd**:
* Synergy stratification on 48 colorectal cancer cell lines (Sanger validation).
**check_synergy_ALMANAC.Rmd**:
* Synergy enrichment in NCI_ALMANAC dataset.
## Source of the data
GDSC data were downloaded from: http://www.cancerrxgene.org/
* Drug IC50 version 17a
* Basal gene expression 12/06/2013 version 2
* Drug target version March 2017
DREAM drug combination challenge data were acquired through an AstraZeneca Open Innovation Proposal.
NCI-ALMANAC data is downloaded from the publication Holbeck et al.
## Snapshot of all R packages used for data analysis
In case you encounter any issue, all packages used in this project are saved in the folder **packrat/src**
https://rstudio.github.io/packrat/commands.html
## License
Distributed under the GNU GPLv3 License. See accompanying file LICENSE.txt or copy at http://www.gnu.org/licenses/gpl-3.0.html.