I am looking for simple way to mark in two colors objects (genes, proteins) in KEGG pathway maps. Just to show that the same gene is upregulated by one and downregulated by other treatment. Not background and frame but half by half.
I dont Know if understand yor question , but when you select a gene or protein in Kegg he show a mark with the positions. for make part by part ... I recomend do it in Illustrator ... but i'll wait for other answer for to know other programs :)
I want to illustrate differences in gene expression (e.g. opposite reactions of selected genes) to several treatments (at least compare two treatments) on single pathway.
Hi Marcin,
there are web services offered in the KEGG web service space. Look around. It works in that way that you, simply by an URL, send the gene and the color to KEGG. They generate a map and send ylui an URL link that you simply integrate into your web-approach or your web browser.
Try to figure out this how we did it in in the CancerResource:
http://bioinf-data.charite.de/cancerresource/index.php?site=compareCellLines&case=oneOwnG
type in the two first genes plus relative diff expression data as given on the right, AND select KEGG buttom on the right, then compare. You will find something like "target=596_842&color=gray_green" in the URL if you klick on "show pathway map ⇒". You will find the CASP9 rectangle highlighted by green border indicating down regulation. That is how you construct the result. Behind that is the method color_pathway_by_objects in the WSDL Web Service at http://soap.genome.jp/KEGG.wsdl
Cheers Thomas
I need something more complex! I already tried that and its not enough for me because this allows to assign only one color to one gene/product (or background and border).
What I need is to have ability to color box with at least two colors (but not background and border but two colors in background) - to compare two treatments and indicate that treatment A downregulates gene X and treatment B upregulates gene X, and for gene Y treatment A upregulates and treatment B downregulates...
Marcin, two treatments are two maps. But in one map you can indicate more than one gene in different colors. See the manual or example. Concat the genes into a string delimited by _ and the colors in the same way.
I want to show differences in response to two somehow similar treatments. There are genes that behave the same way (up- or down-regulated), some have changed expression significantly in response to one treatment but not the other, and few genes react in a opposite way. Having this all together on one map will clearly indicate differences in response to treatments and will save me color-page charges.
I need to have two responses on one map.
KEGGprofile package from Bioconductor does exactly that: coloring by multple comparisons (as a result, each gene box is divided into n colored sections, where n is the number of conditions - you may even squeeze a time series there!)