SynergyFinder


an interactive tool for analyzing drug combination dose-response data


© Copyright , Netphar, Faculty of Medicine, University of Helsinki. All Rights Reserved

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Short (pdf) report (HeatMap + 2D Synergy plot)

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UPLOAD 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.

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 (for AT-406 & Navitoclax and NVP-LGK974 &
Alpelisib drug combinations) are provided as an example.

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

2 Load file

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.

3 Choose readout

After uploading the input file the user needs to specify the type of phenotypic response. Available options in SynergyFinder are:

  • inhibition % inhibition to cell growth or other signals. Normalized by negative control.
  • 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: \(\%inhibition = 100 - \%viability\).

After specifying the type of phenotypic response the user may firstly obtain an overview of the provided data in a searchable table to check for the problematic data points.

By switching the “Visualize dose response data” toggle button, users will be directed to nex tab “Dose Response Map” for dose-response dat visualization.

Dose Response Map

This tab will show an overview of the full dose-response matrix, as well as the dose response (%inhibition) curve for the single drugs (i.e. the first column and first row in the dose-response matrix), fitted by four-parameter logistic curves. The tabs named by combination of drug names are design for navigating to maps for different combinations. (Fig.3)