Mapping multiple expression data on KEGG genes and metabolites

Question

[The]

Hi,

Is there anyway I can map multiple gene or metabolite expression values (in color code) on genes and/or metabolites belonging to a particular KEGG pathway?

I've a 3 point time series data , so ideally I'll be able to color each node of interest in three different nonoverlapping sector/band of colors.

Thanks

[raghavsehgal1995]

Polly (http://elucidata.io/polly) has a tool called MetScape which can overlay day on cannonical KEGG pathways and colour them as well as show their differential expression and intensities. Helps me avoid the hassle of using any coding language all together. It can even directly go from the raw files to visualisations. This might be useful for you. Attaching a screenshot of the MetScape dashboard.

Answer 1

[The]

Looks like Paintomics can do it:

[apelin20]

How can we get metabolite data? All I have is FPKM values for assembled transcripts.

[The]

We did separate metabolomics and proteomics analysis for each of those time points

[Rajinder Gupta]

Hello Painomics is not working lately, can you suggest something else?

Thanks

[The]

I tried Paintomics today with some of the example files: it appears to work correctly. However, I didn't try with any of my own files. Alternatively, you can have a look at "Vanted" which seems to have some very nice features.

https://link.springer.com/article/10.1186/1471-2105-7-109

https://immersive-analytics.infotech.monash.edu/vanted/

[Rajinder Gupta]

Thank you very much

Answer 2

[raghavsehgal1995]

Polly (http://elucidata.io/polly) has a tool called MetScape which can overlay day on cannonical KEGG pathways and colour them as well as show their differential expression and intensities. Helps me avoid the hassle of using any coding language all together. It can even directly go from the raw files to visualisations. This might be useful for you. Attaching a screenshot of the MetScape dashboard.