a ChIP-Seq case study - Genomatix

Pathway analysis with GePS
The Genomatix Pathway System uses information from public sources combined with proprietary databases
to characterize gene lists based on statistical analysis of literature, pathways and GO- and MeSH-terms.
Pathways and networks can be generated and superimposed with user data. GePS can be accessed from
the navigation bar under ‘Genomes & Data’.
Figure 17: Genomatix Pathway System (GePS) overview screen showing the different entry options.
To analyze the genes with PPARgamma binding sites in the promoter region, the file containing the geneIDs
was uploaded and the organism was selected (Figure 18). Alternatively, the geneIDs could have been pasted
into the setup screen.
Figure 18: Genomatix Pathway System setup screen. GeneIDs or symbols can be entered via copy and paste or file upload. Available
annotation types are listed. These will be used for classification and can be used as data filter for the analyzed genes.
The first result GePS delivers is a characterization of the gene list based on pathways, Gene Ontology,
MeSH-term and Genomatix proprietary annotation. Overrepresentation of biological terms associated with
genes from the input list are calculated and listed in the left panel together with the respective p-value.
© Genomatix 2012