The Geneprint provides a visual summary of notable features across different datatypes. These features include mRNA expression (up/down regulation based on threshold), protein expression (up/down regulation based on threshold), aCGH copy number aberrations (loss, normal, gain, amplified), vcf small genomic variants (indication of mutation or not).
To begin the analysis, see Running the Analyses, then perform the following steps.
To perform a Geneprint analysis:
Click the Advanced Workflow tab, then open the Analysis menu.
The Variable Selection section appears
Drag a high-dimensional data node into the Variable Selection box. The data node may be mRNA, protein, aCGH (copy number aberrations) or vcf (small genomic variants) data. It is possible to drag multiple nodes of different types into the box.
Click the High Dimensional Data button.
The Compare Subsets-Pathway Selection dialog box appears
Select one or more Genes/Pathways/mirIDs/UniProtIDs by typing in their symbols and selecting them from the list.
Click ‘Apply Selections’.
Specify thresholds for the mRNA and/or protein expression z-scores (if applicable).
Your analysis appears below
Explanation of Geneprint result:
The geneprint shows a glyph (rectangle) for each gene-subject pair. Each row represents a gene, each column a subject. The columns are sorted by feature, starting at the first gene. Each glyph represents the data values using color coding and icons. An explanation of these is provided in the legend.
In order for data to be compatible with Geneprint, the patient/subject ids for the different data types must match to show them in the same columns, and gene information must have been loaded in the database for all data types.