Data Sources
Cancer Therapeutics Response Portal (CTRP) Dataset
Overview
The Cancer Therapeutics Response Portal (CTRP) is a public resource providing information about the response of cancer cell lines to small-molecule probes and drugs. This project focuses specifically on CTRPv2.0, which includes a comprehensive dataset of drug sensitivity measurements across numerous cancer cell lines.
External Data Sources
Cell Line Information
- Name: CTRP Cell Line Information
- Version/Date: CTRPv2.0
- URL: https://ctd2-data.nci.nih.gov/Public/Broad/CTRPv2.0_2015_ctd2_ExpandedDataset/
- Access Method: Direct download
- Data Format: Tab-separated values (TSV)
- Citation: Seashore-Ludlow, B., Rees, M.G., Cheah, J.H., et al. (2015). Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset. Cancer Discovery, 5(11), 1210-1223. https://doi.org/10.1158/2159-8290.CD-15-0235
- License: CTD² Data Portal Terms of Use
Treatment Information
- Name: CTRP Compound Information
- Version/Date: CTRPv2.0
- URL: https://ctd2-data.nci.nih.gov/Public/Broad/CTRPv2.0_2015_ctd2_ExpandedDataset/
- Access Method: Direct download
- Data Format: Tab-separated values (TSV)
- Citation: Same as cell line information
- License: CTD² Data Portal Terms of Use
Drug Response Data
- Name: CTRP Drug Sensitivity Data
- Version/Date: CTRPv2.0
- URL: https://ctd2-data.nci.nih.gov/Public/Broad/CTRPv2.0_2015_ctd2_ExpandedDataset/
- Access Method: Direct download
- Data Format: Tab-separated values (TSV)
- Citation: Same as cell line information
- License: CTD² Data Portal Terms of Use
Processed Data
Sample Metadata (CTRPv2.0_sampleMetadata.tsv)
- Name: Preprocessed Sample Metadata
- Input Data: CTRP Cell Line Information
- Processing Scripts:
workflow/scripts/R/preprocessMetadata.R - Output Location:
metadata/CTRPv2.0_sampleMetadata.tsv
| Column Name | Description | Example Values |
|---|---|---|
| sampleid | Unique identifier for the cell line | 697, 5637, 2313287 |
| tissueid | Tissue of origin | haematopoietic_and_lymphoid_tissue, urinary_tract |
| master_ccl_id | Master cell line identifier | 1, 3, 4 |
| sample_availability | Where the sample is available | ccle;public, ccle |
| ccle_primary_hist | Primary histology | lymphoid_neoplasm, carcinoma, glioma |
Treatment Metadata (CTRPv2.0_treatmentMetadata.tsv)
- Name: Preprocessed Treatment Metadata
- Input Data: CTRP Compound Information
- Processing Scripts:
workflow/scripts/R/preprocessMetadata.R - Output Location:
metadata/CTRPv2.0_treatmentMetadata.tsv
| Column Name | Description | Example Values |
|---|---|---|
| master_cpd_id | Master compound identifier | 1788, 3588, 12877 |
| cpd_name | Compound name | CIL55, BRD4132, BRD6340 |
| broad_cpd_id | Broad Institute compound identifier | BRD-K46556387, BRD-K86574132, BRD-K35716340 |
| top_test_conc_umol | Top test concentration in μM | 10, 160, 33 |
| cpd_status | Compound status (probe, FDA) | probe, FDA |
| inclusion_rationale | Rationale for inclusion in the study | pilot-set, chromatin;pilot-set |
| gene_symbol_of_protein_target | Gene symbol for protein target | S1PR3, BAX, RARA;RARB;RARG |
| target_or_activity_of_compound | Target or activity description | agonist of sphingosine 1-phosphate receptor 3 |
| source_name | Source of the compound | Columbia University, ChemDiv Inc., Enamine Ltd. |
| source_catalog_id | Catalog identifier from source | 4998-1380, 1988-0090 |
| cpd_smiles | SMILES chemical notation | Chemical structure in SMILES format |
| treatmentid | Standardized treatment ID | CIL55, BRD4132, BRD6340 |
Treatment Response: Raw
- Name: Preprocessed Raw Treatment Response
- Input Data: CTRP Drug Sensitivity Data
- Processing Scripts:
workflow/scripts/R/preprocessTreatmentResponse.R - Output Location:
data/procdata/CTRPv2.0_preprocessed_TreatmentResponse_raw.csv
| Column Name | Description | Units/Notes |
|---|---|---|
| sampleid | Cell line identifier | Same as sampleid in metadata |
| culture_media | Culture media used | DMEM001, RPMI001, etc. |
| treatmentid | Drug identifier | Same as treatmentid in metadata |
| experiment_id | Experiment identifier | Numerical identifier for experiment |
| dose | Drug concentration | μM (micromolar) |
| viability | Cell viability at given dose | Percentage, values relative to control |
| tech_rep | Technical replicate number | 1, 2, 3, etc. |