KinMap Tutorials

Tutorial 1: Exploring therapeutic indications

Purpose

Analyze drug-target-disease relationship for sunitinib and sorafenib by combining their inhibition profiles with kinase disease associations of two common cancer types; namely, thyroid and colon carcinomas.

Steps

  1. Switch to the panel
  2. Select from the Data Source dropdown and set the Data Type to
  3. In the Disease dropdown, find thyroid carcinoma and click the button
  4. Note the creation of a new Data source in the table below, and the addition of the corresponding annotations to the kinome tree on the right
  5. Modify the settings of the thyroid carcinoma data source as follows and click
    6. Shape
    square
    Fill
    RoyalBlue
    Stroke
    None
    Scaling
    Fixed
    Size
    18
  6. Back in the Disease dropdown, find colonic neoplasm and click the button
  7. Modify the settings of the colonic neoplasm data source as follows and click
    8. Shape
    square
    Fill
    FireBrick
    Stroke
    None
    Scaling
    Fixed
    Size
    12
  8. To start adding biochemical data, go up and select from the Data Source dropdown and set the Data Type to
  9. In the Karaman et al., 2008 dropdown, find sorafenib and click the button
  10. Modify the settings of the sorafenib data source as follows and click
    11. Shape
    circle
    Fill
    DarkOrange
    Stroke
    Black
    Scaling
    Kd(nM)
    Value
    10 to 10000
    Size
    30 to 80
    Step
    ☑ Reverse   ☑ Log
  11. Back in the Karaman et al., 2008 dropdown, find sunitinib and click the button
  12. Modify the settings of the sunitinib data source as follows and click
    13. Shape
    circle
    Fill
    LightGoldenRodYellow
    Stroke
    Black
    Scaling
    Kd(nM)
    Value
    10 to 10000
    Size
    32 to 82 (slightly larger than sorafenib so that circles do no overlap)
    Step
    ☑ Reverse   ☑ Log
  13. Go to the Download dropdown menu to save the annotated tree, e.g. as CSV for future use or export it as high-resolution PNG

Tutorial 2: Overview of the available human kinome data

Purpose

Get an overview of the current structural and biochemical coverage of the human kinome, including the distribution of primary targets of clinically approved kinase inhibitors.

Steps

  1. Switch to the panel
  2. To add structural data counts, select from the Data Source dropdown and set the Data Type to
  3. Click the button
  4. Modify the settings of the Number of PDBs data source as follows and click
    5. Shape
    circle
    Fill
    Crimson
    Stroke
    Black
    Scaling
    # PDBs
    Value
    1 to 50
    Size
    26 to 71
    Step
    ☐ Reverse   ☑ Log
  5. Now to add biochemical data counts, go up and select from the Data Source dropdown and set the Data Type to
  6. Click the button
  7. Modify the settings of the Number of assays in ChEMBL data source as follows and click
    8. Shape
    circle
    Fill
    CornflowerBlue
    Stroke
    Black
    Scaling
    # assay points
    Value
    100 to 3000
    Size
    23 to 68
    Step
    ☐ Reverse   ☑ Log
  8. To annotate kinases which are primary targets of approved drugs, select from the Data Source dropdown and set the Data Type to
  9. Modify the settings of the Key target of approved drugs data source as follows and click
    10. Shape
    triagnle
    Fill
    Chartreuse
    Stroke
    Black
    Scaling
    Fixed
    Size
    26
  10. Go to the Download dropdown menu to save the annotated tree, e.g. as CSV for future use or export it as high-resolution PNG