Ideograms of Derivative Chromosomes

The availability of ideograms is often useful when analysing banded chromosome preparations. But ideograms are generally available for non-aberrant chromosomes only. This function is intended to close the gap by drawing ideograms for aberrant chromosomes denoted in ISCN style.

The Application Window

This function is opened from the menu of the main window. Select "Other - Derivative Chromosome" from its menu.

There upon the application window is opened.

In the textbox, the ISCN description of a rearrangement giving raise to one or more derivative chromosome(s) is entered, then click on "Draw". A default example is shown. You may use the "short" notation, i.e. a "der()" clause followed by the rearrangements which lead to the derivative chromosome. The "detailed" description, i.e. a "der()" clause followed by the band composition, is also possible; arrows are encoded by a "minus" ("-") and a "greater than" (">") sign.

It is also possible to enter the ISCN description of a rearrangement only. All derivative chromosomes caused by this aberration will be shown.

In case of an erroneous description, an error message with a description of the error will be shown.

When moving the mouse over the ideogram, a tooltip window with the name of the chromosomal band is shown. By clicking onto a band you can navigate to the NCBI or Ensembl Mapviewer and retrieve information on the genes of that band from there.

Below each chromosome you will find a "#" sign which will show up information on the rearrangement giving raise to this derivative chromosome and on the band composition of the chromosome.

Bands which are not complete (e.g. break points or junctions) are shown at half size.

The Menu

The File Menu

The "Save Image" menu allows you to save the graphic which is displayed in the viewer panel into an image file. Alternatively, you can click the "Save Image" button. Regrettably, the imagemap information gets lost during that process.

"Close" closes the window.

The Draw Menu

Clicking on "Draw" in the menu or the "Draw" button causes the graphics to be redrawn.

The Edit Menu

Banding Resolution

The banding resolution for the ideogram can be adjusted from the "Edit -Resolution" menu or from the checkboxes on the form.

The desired resolution can be selected from four predefined values:

• "2 Digits": This is a virtual resolution not defiend by the ISCN manual. It means that bands are denoted by their chromosome, arm and exactly two further digits. Note that there is no standard definition for ideograms at this resolution.
• "400 bphs": This is the 400 bands per haploid set resolution as defined in the ISCN manual.
• "550 bphs": This is the 550 bands per haploid set resolution as defined in the ISCN manual.
• "800 bphs": This is the 800 bands per haploid set resolution as defined in the ISCN manual.

Chromosome bands were originally measured in the ISCN manual (pp. 14-21) for 400 bphs and 550 bphs resolution.Later, information on the 800 bphs ideograms was obtained from NCBI. Band length were entered for the highest resolution a band fulfills, thus the length of a band at 400 or 550 bphs may sometimes be its length at 800 bphs differring from the corresponding ideograms in the ISCN manual.

The default value is 800 bphs.

Background Color

The background color can be adjusted via the "Edit - Background" menu. A standard windows color dialog is opened.

Since there is no "transparent" color defined in the dialog, it can be set by clicking "Cancel" in that dialog; a message box will pop up asking you if you want to set the background color to transparent. Click "OK" to do so, or "Cancel" to keep the present color.

Colored vs. Black & White

By default, chromosome bands are drawn in colors. Sometimes, a black & white figure may be preferable. Simply click on the "Color" check box or on the "Edit - Use Colors" menu, and then redraw the ideogram.

Chromosome Colors

The colors used for drawing chromosome ideograms are originally defined in the resources file. You can adjust them according to your preferences via the "Edit - Chromosome Colors" menu. The "Chromosome Colors" dialog is opened.

All chromosomes are displayed with their number written in their respective color. Click on a chromosome to open the standard windows color dialog as above.

The "Reset" button causes the default colors to be reloaded.
"Apply" saves the changes, but keeps the dialog opened.
"Cancel" closes the dialog while discarding the changes since siving them last.
"OK" saves the changes and closes the dialog.

To view the derivative chromosome in the new colors, redraw it.

Scale

The scale determines the size of the chromosome idoegram. A maximum scale of 1 is allowed; here, a non-derivative chromosome 1 would measure about 1600 pixels in length.

Map Viewer

The map viewer parameter indicates an external resource in the internet to which chromosomal bands in the drawings are linked. Viewers are available from Ensembl and the National Center for Biotechnology Information.

The default value for the MapViewer is set in the CyDAS.ini file. Also note that the MapViewer is set at a global level always; i.e. changing its value somewhere in the CyDAS application will change it for the whole CyDAS application.

The Help Menu

The Help menu leads you to the documentation available on the CyDAS website, either the User Documentation (this page) or to the Technical Documentation.
A local "Help" is not yet implemented.

Calculation of the Derivative Chromosomes

Derivative Chromosomes are calculated with the Aberration and Chromosome classes of the ISCNAnalyser and drawn with the CyDASGraphics class. The process is described in an Analysis page and the Karyogram page.