Some pathways were significantly altered on my microarray data. I want to highlight these pathways and the related genes on a single pathway graph. I tried iPath and found there were some conflicts of edges when I tried to color up- and down-regulated genes in different colors. Therefore, I want to know if there are some other tools for highlighting pathways and genes simultaneously.
Prometra can draw heatmaps on anything, given you have an annotated SVG graphics. If you have your pathway in SBML, it can be converted to SVG. Otherwise, you can draw your own image using eg. InkScape and project regulation on enzymes or pathways using the web-server. The only things that need to match are the identifiers contained in the SVG graphics and the identifiers in the input file.
The reason why you can get conflicts of edges when you input a list of genes is that a single edge (representing a reaction) may be catalyzed by multiple proteins (either subunits of an enzymatic complex or isozymes). In other words multiple genes map to the same edge, which can only have one color. I am not aware of any visualization tool that can show this information in a compact way for all pathways simultaneously. Inherently, an edge can only have one color at a time.
The question is thus: if two genes map to the same edge and one of these genes is up-regulated and the other is down-regulated, which color would you want the edge to have?
There is a tutorial on analyzing microarray data: http://www.pathvisio.org/wiki/DataTutorial