Partek Pathway is a standalone program from Partek Genomics Suite with a distinct user interface (Figure 1). The size of each panel can be adjusted using the green vertical and horizontal grab bars.
The Brain vs. Heart gene list we created earlier will open (Figure 3). The spreadsheet can be sorted by any column by left-clicking a column header; the first click will sort by ascending values, the second click will switch to descending values.
The Pathway-Enrichment.txt spreadsheet also seen in Partek Genomics Suite will open (Figure 4). Selecting any of the pathway names will open its pathway diagram. The spreadsheet can be sorted by any column.
The GABAergic synapse pathway diagram will open. Genes in the pathway are shown as boxes. The color of the box is set by the Configuration panel (Figure 5).
Any numerical column from the source gene list can be used to color the gene boxes. While significant p-values indicate a difference between the categories, they give no information about upregulation or downregulation of the pathway. We can overlay fold-change information on the pathway diagram.
The pathway diagram now shows fold change for each gene in the pathway included in the gene list (Figure 6). Genes not in the gene list remain black.
We can see that all the colored genes in the GABAergic synapse pathway are yellow (Figure 7), indicating that they are upregulated.
Opions available include:
Look up on KEGG - opens the KEGG page for the pathway on GenomeNet (genome.jp) in your web browser
Ensembl - under External Links, opens the page for the selected Ensembl ID on ensemble.org
UniProt - under External Links, opens the page for the selected UniProt ID on uniprot.org
Jump to ___ on "___" - opens the source gene list in Partek Pathway to the row of the selected gene
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