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

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

10.0 years ago by

Dejian • 1.3k

United States

Dejian • 1.3k wrote:

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.

pathway visualization tool • 6.9k views

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modified 10.0 years ago by Andra Waagmeester ♦ 3.2k • written 10.0 years ago by Dejian • 1.3k

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.

ADD REPLY • link written 10.0 years ago by Lars Juhl Jensen ♦ 11k

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

ADD REPLY • link written 10.0 years ago by Michael Dondrup ♦ 48k

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.

ADD REPLY • link written 10.0 years ago by Giovanni M Dall'Olio ♦ 27k

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.

ADD REPLY • link written 10.0 years ago by Giovanni M Dall'Olio ♦ 27k

10.0 years ago by

Michael Dondrup ♦ 48k

Bergen, Norway

Michael Dondrup ♦ 48k wrote:

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.

ADD COMMENT • link modified 16 months ago by _r_am ♦ 32k • written 10.0 years ago by Michael Dondrup ♦ 48k

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

ADD REPLY • link written 10.0 years ago by Dejian • 1.3k

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

ADD REPLY • link written 10.0 years ago by Michael Dondrup ♦ 48k

10.0 years ago by

Lars Juhl Jensen ♦ 11k

Copenhagen, Denmark

Lars Juhl Jensen ♦ 11k wrote:

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?

ADD COMMENT • link written 10.0 years ago by Lars Juhl Jensen ♦ 11k

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

ADD REPLY • link written 10.0 years ago by Dejian • 1.3k

9.9 years ago by

User 1543 • 20

User 1543 • 20 wrote:

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

ADD COMMENT • link written 9.9 years ago by User 1543 • 20

10.0 years ago by

Tomer Altman • 40

Tomer Altman • 40 wrote:

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

ADD COMMENT • link written 10.0 years ago by Tomer Altman • 40

9.9 years ago by

Andra Waagmeester ♦ 3.2k

Maastricht, the Netherlands

Andra Waagmeester ♦ 3.2k wrote:

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

ADD COMMENT • link written 9.9 years ago by Andra Waagmeester ♦ 3.2k

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.

ADD REPLY • link written 9.9 years ago by Chris Evelo ♦ 10k

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