Dependence Network

Deutsche Version

The dependence network shows statistical correlations between rearrangements. Positive correlations (i.e. the rearrangements occured more often together than expected from their marginal distribution) are shown as blue lines, while negative correlations (i.e. the rearrangements occured less often together than expected from their marginal distribution) are shown as red lines; the thicker the line, the more (statistically) reliable is the correlation.

Further statistical data are shown in tables: the frequency of the events, the frequency of combinations of events (support), the Fourfold Correlation Coefficient Phi, Pearson's contingency coefficient, Odds Ratio, Attributable Risk, and the chi-square value indicating significance of correlation.

Enter the file containing the data and its data format, the style of data pre-processing, the maximum number of cases to be analysed, the number of rearrangements to be displayed, and the threashold for significance.

Possible data formats are the format of the Mitelman database, or a very simple custom format just containing a case identifier and the karyotype spearated from it by a tabulator or other separator per line; that format is also used for CGH data. For more information, see the "HowTo on Data Formats."
If you are not familiar with getting data from the Mitelman database, please have a look at the HowTo "Retrieving data from the Mitelman database". Please note that some data in the Mitelman database do use an older version of the ISCN. Such data may still be compatible with ISCN 1995 and then be analysed correctly, but some data may be no more compatible and thus not be parsed correctly.

Data can be processed "as is", or they can be translated into the SCCN or into Cytoband data; here, you can also select the virtual banding resolution of the processed data.

For more info on the Dependence Network, you may also have a look at the description of its desk top version and the calculation of the data.

Parameters

File:

Format:

 Mitelman    Custom Format (Banding Analysis)   Custom Format (CGH)

For Custom Format Only:

Separator:  Tabulator   Pipe ("|")   Blank (" ")

Has Header Line

Data Processing:

Use data

as is

or process to

   SCCN    Cytoband List

at a resolution of

2 Digits    1 Digit   Chromosomal Arm

Number of cases:

The maximum number of cases is limited for technical reasons (duration of calculation) to the default value given below. You may use an even lower value.

Note that useful results can hardly be obtained with less than 100 cases.

Maximum Cases:
Total Cases:
Valid Cases:

Other drawing parameters:

Number of Rearrangements to be shown:   5 6 7 8 9 10 11 12 13 14 15

Minimum chi-square for correlations to be shown: 3 4 5 7 10 14 20 30