3.3 Expression Surfaces

  3.3.1 What is an Expression Surface?  
  3.3.2 Expression Surfaces Controls  
         Creating an Expression Surface:  
      Editing Properties of an Expression Surface:  
      Editing General Properties  
  3.3.3 Properties of Expression Surfaces  
      Offset  
      Height  
      Opacity  
      Color Mapping  
      Display Offset Point  
  3.3.4 Height Mapping  

3.3.1 What is an Expression Surface?

To allow a more quantitative analysis of gene expression data, Expression Surfaces can be defined above any 2D Embryo View, i.e above any Orthographic View or Unrolled View. Each Expression Surface displays data for one gene. The xy positions of Expression Surface points are determined by the positions of cells in the underlying views, whereas the height of an Expression Surface is determined by the expression values measured for the gene it represents. Spatial relationships between several genes' expression patterns can be viewed at once using multiple Expression Surfaces.

3.3.2 Expression Surfaces Controls

The general controls like for zooming, panning, or rotation are identical with the controls of the physical view.

  Creating an Expression Surface:  Expression surfaces can directly be created in the gene table of the Gene Selection Window. An expression surface is created for a gene after a color mapping option has been selected in the "Gene Surface" column of the gene table in the Gene Selection Window. Select the "Undisplayed" option to delete an existing expression surface

Editing Properties of an Expression Surface: The color mapping as well as the opacity of an expression surface can directly be defined in the according column of the gene table in the Gene Selection Window. The offset and the height of an expression surface can be edited in the main canvas where the offset surfaces are displayed. Two sliders are here displayed for each expression surface. The bottom slider can be used to define the offset of an surface and the top slider to define the surface height. To move the sliders switch to the "Clipping Mode" and use "SHIFT + LEFT MOUSE BUTTON" to move the slider. See also the physical view mouse controls.

Editing General Properties: General properties of expression surfaces can be edited in the properties window of the physical views. General properties refer to the coordinate frame (only available in the Unrolled View) or to the display of the offset points. In the properties window the offset and height of the coordinate frame can be defined while the according values of an expression surface can be imported in order to adjust the coordinate frame to a selected surface. For the offset points the size of the points can be defined as well as if the poins should be displayed or not.

3.3.3 Properties of Expression Surfaces

 

Offset: The distance between the Expression Surface and the underlying embryo view.

Height: The height of the Expresssion Surface.

Opacity: Opacity of Expression Surface: 1.0 = full opacity ; 0.0 = completely transparent

Color Mapping: 

- Hidden No Expression surface shown for the according gene.
    - Single Color Mode: The Expression surface is colored using the color which the user defined for the according gene in the Gene Selection Window.
    - Gene Color Mode: The expression surface is colored according to the expression values of the corresponding gene. The used color mapping is the same as in the embryo views but here only the expression values of the gene the surface is defined for are used (see left figure below).
    - Embryo Color Mode: The colors defined in the underlying embryo view are used to color the expression surface. The expression surface can in this way also be colored according to the expression values of other genes. This makes analysis of gene expression using both, color and height in parallel possible (see  right figure below). 

 

 

Expression Surface of Giant mRNA colored according to the expression values of the gene

 

Expression surface of Giant (Gt) colored according to the expression level of Gt , hunchback (hb), and knirps (kni)

 

 

  Display Offset Points:  The offset points are the base points of an expression surface. The x/y position of these points are the same as for the centers of the cells. The offset points are always colored according to the user defined basic color of the gene which the surface represents.
   
 

Expression Surface of kni colored according to the expression level of gt, hb , and kni with displayed offset points.

 

3.3.4 Height Mapping:

Mapping of expression values to height is defined in the same way the mapping of expression values to color brightness in the Physical Views (see the Color Mapping). The user defined minimum and maximum displayed value are in this way also used for correction of surface height. All expression values smaller then the minimum displayed value are mapped to 0 height ( + Offset) and all expression values larger then the maximum displayed value are mapped to full height (Offset+Height). All expression values between the minimum and maximum value are mapped linearly to height values. As the color mapping in the Physical Views the height mapping is inverted if the minimum displayed value is set to a larger value then the maximum displayed value i.e. then low expression values are mapped full height and heigh expression values are mapped to minimum surface height.