Analysis

The analysis of data is called from the "Analyse" menu of the Main Window. The data are evaluated for gains and losses of chromosomal material or break points. The results are shown either as a table or as graphics.

All analysis is based on investigation data. If more than one clone was found in an investigation, a composite karyotype is calculated according to the rules stated in the ISCN manual (chapter 11.1.6, p. 81) and evaluation is performed on that composite karyotype.

Also CGH data are used. Since CGH data always represent something like a composite karyotype, no extra calculation is required. CGH data are translated into gains and losses of chromosomal material, but not into break points (see technical documentation for CGH).

Parameters

For the analysis, a set of parameters is used which can be changed by the user.

On the main window, use the "Edit - Drawing Parameters" window. Changing the values here will effect all analysis windows opened later.
From an analysis window, use the "Edit" menu and the appropriate submenus. Changing the values here influences only the present analysis window.

Resolution

The banding resolution for the analysis can be adjusted on the first tab of the "Drawing Parameters" form.

The desired resolution can be selected from three 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. This resolution is especially useful for representing data in tables. Note that there is no 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.

The 800 bphs resolution has not yet been implemented. Anyhow, such a resolution is not required with the low quality of tumour chromosomes.

The default value is 400 bphs.

Cut-Off Level

The cut-off level is used when drawing gains and losses or structural aberrations. It corresponds to the number of gains / losses or breaks which gives raise to the widest bar representing gains / losses or breaks.

By default, the value is calculated automatically. When drawing gains and losses, it is the maximum number of gains or losses found at a chromosomal band. With structural aberrations, it is the maximum number of breaks found.

The cut-off value can be set manually to any specific number. Gains / losses or structural aberrations will then be scaled towards this value. Larger values will be cut off at the set value. This is useful if highly dominant aberrations are present which would render the other aberrations present almost indistinguishably rare.

Scale

The scale is the scale for the whole figure. The basic height of chromosomal bands in pixels (at scale 1) is defined in the resources file "Chromosomes.xml". Their width is 80 pixels. Gains / losses or breaks may take upto 100 pixels width, starting at a distance of 10 pixels from the chromosome.

This may lead to very large figures which can hardly be displayed on normal computer screens, and their calculation may overstrain the capacities of the computer system. Hence, the default value is 0,25 which gives raise to a figure of ca. 650 x 830 pixels for gains and losses at default Drawing Sequence.

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.

Drawing Sequence

The drawing sequence defines which chromosomes are drawn and in which series they are drawn.

It is not necessary to draw all chromosomes, you may name the chromosomes you are interested in only. Chromosome numbers are separated by commata. A new line can be introduced with a "BR" in place of a chromosome number. By default, all human chromosomes are drawn in three lines of 8 chromosomes each, sorted by height.

Gains and Losses / Structural Aberrations

The windows for drawing gains and losses or break points are called from their respective submenus below the "Analysis" menu of the main window. Essentially the same form is opened.

The Graphics

The figure is drawn by clicking on the "Draw" menu and is then displayed as a sensitive image map.

Gains are drawn on the right of the chromosomal ideogram in green color, losses on the left in red color. Break points are drawn on the right in blue color. The width of the bars represents their number, they are scaled according to the cut-off level.

When the mouse points at a chromosomal band, the number of the band is displayed in a tool tip window (see figure above). By clicking on that band, the default browser of the computer system is opened and pointed to the NCBI map viewer showing information on that chromosomal band.

When the mouse points at a bar representing gains, losses or breakpoints, a tooltip window displays the number of the band and the number of gains / losses / breaks encountered there.

The Menu

File Menu

The "File - SaveImage" menu allows you to save the figure into a disk file in a common graphical format. A standard windows "Save As" dialog is opened where you can choose the location and file name as well as the graphic type of the image. Note that the image map information gets lost during this process.

The "File - SaveToHTML" menu is meant to circumvent this lost. It is not yet implemented.

The form can be closed using the "File - Close" menu.

Draw Menu

The Draw menu (re-)draws the image map. There are no sub-menus.

Edit Menu

The edit menu opens the form for editing drawing parameters. The appropriate tab is displayed for "DrawSequence", "Scale", and "CutOff".

In case of the Resolution parameter, another submenu with a ckeckable selection is provided.

Help Menu

"Help" is not yet implemented.

Cytoband List

As an alternative to graphics, the data can be displayed as a report. The header lines indicate the group / subgroup and the analysis paramters used.

Below, a table follows showing the band number, the number of gains, losses and break points encountered at that band for all chromosomes in standard ISCN order.