SynergyFinder

an interactive tool for analyzing drug combination dose-response data

1 Data Format

SynergyFinder accepts two data formats: Table and Matrix.

1.1 Table format

In the Table format, the input dose-response matrix is represented as a table where each row contains the information about the one cell in the dose-response matrix (Fig.1).

The input table must contain the following columns:

1. PairIndex index of drug-pair to be analyzed
2. Response %inhibition or %viability values
3. Drug1 name of the first drug
4. Drug2 name of the second drug
5. Conc1 concentration of Drug1
6. Conc2 concentration of Drug2
7. ConcUnit unit of concentration

The orders of rows and columns are arbitrary. The number of drug combinations (PairIndex) provided in the input file is unlimited. The only restriction is imposed on the size of a dose-response matrix, which should comprise at least three rows and columns, so that sensible synergy scores can be calculated.

Fig.1 Input file in Table format.

1.2 Matrix format

In the Matrix format, the dose-response matrix is represented in a matrix form with drug concentrations shown along the top and left side of the matrix (Fig.2).

The three rows should precede each dose-response matrix:

1. Drug1 name of the first drug
2. Drug2 name of the second drug
3. ConcUnit unit of concentration

The drug concentrations should be located at the top and left side of the matrix, where left side concentrations correspond to Drug1 and concentrations shown at the top correspond to the Drug2. The number of drug combinations provided in the input file is unlimited. The only restriction is imposed on the dose-response matrix size, which should comprise at least three rows and columns, so that sensible synergy scores can be calculated.

Fig.2 An input file in Matrix format. Two dose-response matrices are provided as an example.

Using the “Browse” button, users could select a file from local directory for uploading. The expected file formats are:

• EXCLE file with extention “.xlsx”
• comma-delimited CSV file, with extention “.csv”
• comma-delimited TXT file, with extention “.txt”

Example data is available from here.

• viabillity % cell viability after treatment. Normalized by negative control. In case of %viability response type, the provided %viability values will be converted to %inhibition by the formula: $$\%inhibition = 100 - \%viability$$.