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