On-Line Supplements for eXPatGen Paper

The following webpages and output files were those used to generate the two examples used in the paper.
Example #1 is represented by 6 gene groups. Three (B, C, and D) are induced by gene group A. Two others are induced by gene groups B and C, respectively. Repression is not used in this example.

Example 1-1: Input form for Example #1 with group dynamics defined (used to generate the Example 1-2 input form).

Example 1-2: Input form for Example #1 with individual gene dynamics defined (same as those used in the paper).

Example 1 Output: Logarithm (base 10) of the expression ratios in tab-delimited format for Cluster/TreeView. Rows are the dynamic expression values for each gene and the columns are the data from each time point (in minutes).

Example 1 Output with Doubled Gamma Parameter Std. Dev.: Same group dynamics of Example #1 except for more variablity in each gene's time constant (time at 50% maximum gain).

Example #2 is represented by 10 gene groups. Four groups are intially on (A, B, C, and D). Three other groups (E, F, and G) are induced by gene groups A, B, and C, respectively. Gene groups H and I are simulaneously induced by gene group F. Gene group J is induced by gene group I. Gene group C is repressed by gene group E. Gene group D is repressed by gene group H.

Example 2-1: Input form for Example #2 with group dynamics defined.

Example 2-2: Input form for Example #2 with individual gene dynamics defined (same as those used in the paper).

Example 2 Output: Logarithm (base 10) of the expression ratios in tab-delimited format for Cluster/TreeView. Rows are the dynamic expression values for each gene and the columns are the data from each time point (in minutes).

Example 2 Fluorescent Output: Logarithm (base 10) of the ratio of fluorescent intensities in tab-delimited format.

Back to eXPatGen

Comments or problems? Please email us