Color Coding Signalling Pathways

Question

[Assa Yeroslaviz]

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

Answer 1

[Sudeep]

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 ?

[JacobS]

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

Answer 2

[Neilfws]

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

[Assa Yeroslaviz]

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?

[Neilfws]

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

[Assa Yeroslaviz]

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

[Neilfws]

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.

Answer 3

[bigmawen]

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

Answer 4

[Manu Prestat]

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