Question: Color Specific Proteins/Genes On A Signaling Pathway
gravatar for Gabs
5.1 years ago by
tampere, finland
Gabs130 wrote:

I have a list of genes/protiens. I would like to color my list of proteins/genes on a signaling pathway. I know KEGG has a tool for doing this (the search and color pathway map). Is they any other alternative that is publicly available? If not, how can I accomplish this task (any pointer or heads up). Thanks

gene pathway protein • 4.4k views
ADD COMMENTlink modified 3.8 years ago by c.v.oflynn90 • written 5.1 years ago by Gabs130
gravatar for Malachi Griffith
5.1 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith15k wrote:

One option is the batch query of the Nature Pathway Interaction Database. If you load a text file containing your gene symbols of interest (e.g. TP53 and PLK3) it will return a list of pathways containing those gene names. If you load one of those pathways all occurrences of the genes in your list will be automatically colored blue. For example:

alt text

Another option that is more manual but might produce a prettier result is to find the pathway of interest from PharmGKB, download it as a PDF, and then edit with your favorite vector graphics software (Inkscape, Illustrator, etc.)

ADD COMMENTlink written 5.1 years ago by Malachi Griffith15k
gravatar for Giovanni M Dall'Olio
3.8 years ago by
London, UK
Giovanni M Dall'Olio25k wrote:

I have just discovered a way to do this quickly in KEGG. To highlight a specific gene in KEGG, you can just add "+_kegg id_" to the URL of the pathway, and the corresponding gene will be colored in red. For example:

enter image description here

For more advanced coloring options in KEGG, click on the "User data mapping" on the upper right corner of the page.

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Giovanni M Dall'Olio25k
gravatar for Alex Paciorkowski
5.1 years ago by
Rochester, NY USA
Alex Paciorkowski3.2k wrote:

For a while I've been a fan of BioTapestry for this kind of thing. There are links from the project website that show example images. It doesn't draw for you, but allows you to make quite pleasant diagrams of pathways, and color them however you want. You can also incorporate contextual data (such as cell type or timing of pathway relationships) to show these data in an interactive manner. The tool was mainly developed for transcription factor gene regulatory networks, but you could use it for signaling pathways too.

ADD COMMENTlink written 5.1 years ago by Alex Paciorkowski3.2k
gravatar for Neilfws
3.8 years ago by
Sydney, Australia
Neilfws46k wrote:

Since this thread was just revived at the Open Helix blog, I'll add a recent and very good tool: Bioconductor/pathview.

ADD COMMENTlink written 3.8 years ago by Neilfws46k
gravatar for c.v.oflynn
3.8 years ago by
United Kingdom
c.v.oflynn90 wrote:

I like iPath;

ADD COMMENTlink written 3.8 years ago by c.v.oflynn90
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