• test.xml, test our SVG generator
• testg.xml, another small test data set where traits are grouped as user specification
• input.xml QTLs declared in the yeast population using multiple interval mapping.
• group.xml QTLs declared in the yeast population, grouped according to KEGG pathway for yeast.
• DTD for the xml input.
• the complete yeast example in a zip file
• auxiliary code examples
  • gListGen.pl transforms each eQTL into a list of pairwise relationships between a trait gene and multiple genes in the eQTL. It requires the output from QTL cartographer and several other files.
  • xmlGen.pl generates an XML input file for eQTL Viewer according to gene list files generated by gListGen.pl.
• A PERL module wraps the procedures to generate XML input files. A short example shows how to use this module. The documentation of the module can be found within the module code.

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We visualized Bystrykh's data according to their supplementary table S2 and S3 with some modification.

• We generated the XML input file using a Perl script. This script relies on the tables from the paper to get eQTL genomic positions; but reads mouse genomic information from MGI and affymetrix probe information (MG_U74Av2_annot.csv) to obtain trait genomic position.
• A shorter PERL code which can produce the same XML input file by using the PERL module
• About 30 traits are not included because we cannot find their position in the genome now. We used a 20M bp region around each 'QTL marker' as an eQTL region.
• In order to demonstrate the power of our visualization to handle new annotation information, we hypothesize a protein interaction network with gene 'EG667815' as an interaction hub connecting 20 other genes. In the plot, click the newInfo in the left sidebar, this network will be superimposed onto the mapping results.

Contact zouwei at gmail.com if you have any questions