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What is Kinome Render



Kinome Render allows you to create a human kinome phylogenetic tree annotated with your own personalized labels. Each label is customizable (text, shape, size color) and are applied over a selection of kinases. The program works on top of a database of human kinases taken from Manning (2002) - Science, 298 (5600). The kinase's Names, Accession, Family, subFamily and Group are those from the Manning Paper.

Here is an example of a figure created by Kinome Render:




Find kinases to annotate



Kinases can be selected in four ways:

1. by browsing the database:



2. by searching the database:



3. by doing a protein alignement:



or 4. by doing a batch upload:



At any time the name of the kinase can be hovered which will display a tooltip with more information on the kinase.




Customize the annotation format



From the kinases found, you can select those on which you wish to apply a label by checking their corresponding box on the left. Once you made your kinase selection, select a label type and define its properties, then click "Add Labels".

There are 3 types of labels:

Custom text. Write a piece of text at the location of the selected kinases on the tree. You can have that text in a box or underlined, select a color and a size.



Shape. Select from circle or polygon. When selecting polygon, the number of sides of the polygon needs to be specified (3 for triangle, 4 for square, 5 for pentagon, etc...). Select whether you want (1) a shape outline, (2) a filled shape or (3) a filled shape with a black border. Then choose the color and the size of the label.



Formated Name. Simply print the name of the kinase. Choose if the name is boxed or underlined. Choose a color and a size as well.



When selecting the color, a custom color can be specified in RGB values. Each of the three values must be between 0 and 1, inclusively, with a period (not a comma).




Annotations appear on top of the page



You can modify and delete annotations. The interface displays the first 12 annotations and the rest can be show/hidden using the show/hide button.




The KR file can be downloaded at any time



At any time you can download the Kinome Render file using the link right below the list of annotations. This file is written in Kinome Render syntax and can be uploaded at another time to the interface to restore a session.




Customize legends



You can create a legend to go with your Kinome Render tree. Customize your legend in the textarea using the Kinome Render Syntax.




Customize final details of the figure



Now that you've created all the annotations you want, it's time to generate the final image.

You can choose to display the name of all kinases not included in a label in size 10 color black by checking "Print names for all kinases not annotated". You can choose a file name. Select an output format between (PDF JPEG PNG and TIFF). Note that Kinome Render also generates a .PS (postscript) file. Choose from the 2 templates on which to print annotations. If you annotated atypical kinases, you will be forced to choose the second template as the first one doesn't display the atypical kinase sub-tree. Accept the disclaimer and create your image!




Download the final figure



Once your customized human kinome tree is rendered, you can download it in the chosen format and in the postscript format.




Upload a KR file to the interface



Every time a Figure is created using the Kinome Render interface, the corresponding KR file containing all the annotation's information is created and can be downloaded. This file can be used as input in the Kinome Render program, but can also be uploaded to the Kinome Render Interface. The latter will restore all the annotations contained in the file directly to the interface, allowing them to be modified, deleted or to add new annotations to the figure.




Leave nothing behind



All files related to your job are temporarily stored on our server for the proper functionning of the interface. For privacy concerns, you can manually delete these files.




Inhibitor binding profiles



We have implemented a special procedure to facilitate the creation of figures for the specific case of inhibitor binding profiles. Users can use as input a tab-separated multi-line file (such as what one can produce when exporting data from spreadsheet programs such as Microsoft Excel). Kinome Render expects that each line represent a particular kinase and each column an inhibitor. Accordingly, the first row should contain inhibitor names and the first column kinase names. Any particular cell should contain the Kd, IC50 or a %inhibition. A dash “-” is used to represent cases where no effect was observed or binding affinity is above a certain threshold. Lastly, the string “NA” is used for data that is not available, in other words, a kinase/inhibitor combination that was not tested.

It is very important that the kinase names of the first column match exactly those in column 'Names' in TableS1. It is case-sensitive.

Download file example

Kinome Render will produce one image for each inhibitor separately (each column of the input) and will also produce plots with combination of inhibitors. In the later case, the user may select how many inhibitors are added to each combination plot up to a maximum of 6 inhibitors per combination plot. The combination plots are produced with consecutive columns in the input therefore the order of columns in the input must reflect the choice of ordering desired for the combination plots.

The %inhibition is a versatile option as it can interpret negative values. This can be used, for example, with measures of residual activity. If the value is negative, Kinome Render will draw a triangle. The more its negative the bigger the triangle. Else, the more positive, the bigger the circle.