What COMPARE Does
COMPARE identifies compounds with similar cell line activity patterns by calculating correlation coefficients between your compound and known reference agents.
You can:
- Use a submitted NSC number as a “seed” compound
- Compare it against:
- Standard agents (e.g., paclitaxel, doxorubicin)
- Synthetic compound database
- Natural product extracts
- Molecular Expression patterns (microarray and RnaSeq)
- Rank results based on Pearson Correlation Coefficient (PCC)
The higher the PCC, the more likely two compounds share a common mechanism of action.
Accessing COMPARE
| Access Type | Use Case | Link |
|---|---|---|
| Public COMPARE | Analyze or review public patterns | Launch Public COMPARE |
| Private COMPARE | View private or embargoed data (DTP staff & suppliers only) | Launch Private COMPARE |
How It Works
- Select a seed compound (usually your NSC)
- Choose dataset and correlation type
- GI50, TGI, LC50 values
- Pearson Correlation (standard method)
- COMPARE searches the database
- Public: ~50,000+ compounds
- Private: internal submissions, prepublication data
- Results display:
- Ranked compound list
- Similarity scores
- Optional delta plots (mean graph-style visualizations)
COMPARE Output Examples
- Top Matches: Closest analogs in function
- PCC Values: Degree of pattern similarity
- Mean Graph Patterns: Cell line sensitivity profiles
- Insights: Possible biochemical targets or resistance profiles
COMPARE can be used to:
- Hypothesize new mechanisms of action
- Identify drug analogs with shared selectivity
- Refine lead optimization in drug development
- Connect screen results to molecular target data
COMPARE and the HTS384 Screen
COMPARE remains compatible with both:
- Legacy SRB-based screen data (1990–2023)
- Current HTS384 luminescence-based data
When submitting new compounds through the HTS384 platform, your results can be analyzed via COMPARE once screening is complete.
Need help interpreting results?
email moltarget@mail.nih.gov for assistance.
Origin of COMPARE
COMPARE was developed in the early 1990s to harness the power of large-scale in vitro screening. Its signature innovation was the ability to correlate cell line sensitivity patterns, revealing potential shared mechanisms even among structurally unrelated compounds.
Landmark Contributions
- Halichondrin B (marine compound) identified as a novel tubulin binder
- Discovery of previously unknown topoisomerase II inhibitors
- Reverse searches to connect mechanism to chemical novelty
Legacy Methods (Archived)
Earlier versions of COMPARE supported two analysis modes:
- Average Difference Method (ADM) – retired in 2025
- Pearson Correlation Method (PCC) – currently used
COMPARE continues to evolve with improved normalization, subpanel scoring, and enhanced user interfaces.
Integration with Molecular Target Data
COMPARE can be paired with molecular characterization data from the NCI-60 panel, allowing correlation between compound activity and target expression levels.
Visit the Molecular Targets Program to access or generate target data.
Data
| File Description | File Name | Download Link |
|---|---|---|
| QC reports on sample Material | Analytical_Data_100_Compounds | Analytical Data |
| NCI-60 concentration/response data and endpoint values for the IOA set | oncologydrugsCompare | Oncologydrugscompare |