Venn Mapper

Developed by Marcel Smid



Introduction

Venn Mapper is a program that compares heterologous microarray data sets, based on the number of common, differentially expressed genes. The application loads microarray data (gene expression ratios) and determines which genes are up- or down-regulated by a user-defined ratio cut-off level. For each experiment, lists of differentially expressed genes are computed. Every list will be compared to every other list, and the number of co-occurring genes will be calculated. With the use of the binomial distribution, so called z-values can be assigned to the overlap found between two lists. Different output files are generated by the Venn Mapper, reporting:
  1. the number of up- and down-regulated genes per array and in the comparisons,
  2. the z-values, and
  3. the gene-Ids within the overlaps.
The z-values can be directly imported into the Cluster and/or TreeView software (Eisenlab).

For more information:

Publication
Bioinformatics
May 3, 2003
19(16),p2065-2071		 M. Smid
L.C.J. Dorssers
G. Jenster		 Venn Mapping: Clustering of heterologous microarray data based on the number of co-occurring differentially expressed genes.

Supplementary Information of this article:
[Figure 1]
[Figure 2]
[Table 1]


Downloads:

Venn Mapper 1.01 2003
ManualPdf file
Executable Includes VennMapper.exe, VennManual.pdf and readme.txt.  ZIP file
Perl source code Contains a working version of the software, including Vennmapper.pl and readme.txt.
Although it is a relatively short script, it is not well commented.
Please let me know of any bugs. I would like to receive modifications or improvements via e-mail.
Time permitting, I will incorporate these into subsequent versions.		 ZIP file



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