Tools For Visualizing Significantly Altered Pathways And Related Genes In A Pathway Graph ?

Question

[Dejian]

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.

[Lars Juhl Jensen]

I disagree Giovanni. The question listed as a possible duplicate was about how to identify significantly altered pathways. This question is about how to visualize them once you have identified them. Although related, it is in my opinion not a duplicate question.

[Michael Dondrup]

Exactly, please double check and read the question carefully again before closing anything.

[Giovanni M Dall'Olio]

ok, but please, when you open a new question, check that there are not others with a similar title, or it will confuse other users.

[Giovanni M Dall'Olio]

closed because it seems a duplicate of a previous question. Please check whether your question has already been asked before posting; if your question is different, please explain how what you are asking is different in the text of the question.

Answer 1

[Michael Dondrup]

Have a look at ProMeTra, here's the paper.

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.

[Dejian]

Thank you, Michael. This is just what I want.

[Michael Dondrup]

Nice! if you questions or problems with the input, contact me or the other authors.

Answer 2

[Lars Juhl Jensen]

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?

[Dejian]

Thank you, Lars. You are right. ProMeTra, recommended by Michael, possibly can solve this problem.

Answer 3

[User 1543]

Try Pathway Studio from Ariadne - it can do this and also other real cool stuff.

Answer 4

[Tomer Altman]

Please check out Pathway Tools from SRI. It can do exactly what you are describing.

Answer 5

[Andra Waagmeester]

have you tried Pathvisio: http://pathvisio.org/ (http://www.ncbi.nlm.nih.gov/pubmed/18817533).

There is a tutorial on analyzing microarray data: http://www.pathvisio.org/wiki/DataTutorial

[Chris Evelo]

PathVisio could indeed do it, but not easily. It can visualize the microarray data on all the separate pathways (and can use multiple conditions for a single gene product), but you would have to create the new metapathway yourself. You could do that by just copy pasting pathways in one large one, or by using Cytoscape to make the connections. There is also ongoing work on pathway connections and creation of metapathway. You might want to ask about that on the developers list.