Question: Color Coding Signalling Pathways
0
gravatar for Assa Yeroslaviz
5.5 years ago by
Assa Yeroslaviz1.2k
Munich
Assa Yeroslaviz1.2k wrote:

Hi everybody, I am looking for a method to create a color coded signalling pathways according to changes in expression/read count in different time points. I am looking for something similar to the image I found here

This image was taken from a paper from "Into the Eye of the Cytokine Storm", Tisoncik et al. 2012

thanks

Assa

• 2.4k views
ADD COMMENTlink modified 5.4 years ago by bigmawen310 • written 5.5 years ago by Assa Yeroslaviz1.2k
2
gravatar for Sudeep
5.5 years ago by
Sudeep1.6k
.
Sudeep1.6k wrote:

Have you looked into mapman or kegg pathway coloring or some of the biostars threads like Reactome Pathway View With Colored Genes and Color Specific Proteins/Genes On A Signaling Pathway ?

ADD COMMENTlink written 5.5 years ago by Sudeep1.6k

I'm a big fan of this method as well... kegg mapper / kegg pathway coloring makes very similar images!

ADD REPLYlink written 5.4 years ago by JacobS890
2
gravatar for Neilfws
5.5 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

R/Bioconductor tool for exactly this purpose which generates a very similar result: pathview.

ADD COMMENTlink written 5.5 years ago by Neilfws48k

thanks, but this is not exactly what I am looking for. If I am not mistaken you can ponly map one time point/conditions per image. I would like to have the differential expression intensities but also multiple time points both on the same map. Please correct me If I am wrong, but can pathview do that?

ADD REPLYlink written 5.5 years ago by Assa Yeroslaviz1.2k

I'd be inclined to generate separate images and animate using e.g. javascript, rather than create too much complexity in one image.

ADD REPLYlink written 5.5 years ago by Neilfws48k

This is needed for a paper, so I don't think we'll be able to use animation there.

ADD REPLYlink written 5.5 years ago by Assa Yeroslaviz1.2k

Supplementary data online :) It's not clear to me how multiple time points can be visualized effectively on an single image of this type and I would warn against making figures too complex.

ADD REPLYlink written 5.5 years ago by Neilfws48k
1
gravatar for bigmawen
5.4 years ago by
bigmawen310
United States
bigmawen310 wrote:

Pathview now can plot/integrate/compare multiple states/samples or time series in the same graph in as shown in http://pathview.r-forge.r-project.org/#fig-3. Please check Subsection 7.2 in the vignette for details. Note that pathview now works with 2300 KEGG species and KEGG Orthology.

These features are available with the latest release of pathview and you need to work with BioC 2.13 (current release version) or newer version: http://bioconductor.org/packages/release/bioc/html/pathview.html

ADD COMMENTlink written 5.4 years ago by bigmawen310
0
gravatar for Manu Prestat
5.5 years ago by
Manu Prestat3.9k
Marseille, France
Manu Prestat3.9k wrote:

I personally like ipath from embl. You may also need to take a look at glamm developed in Lawrence Berkeley Lab.

ADD COMMENTlink written 5.5 years ago by Manu Prestat3.9k
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