Pathway Analysis Tool

Question

[pixie@bioinfo]

Metabolites Detected by Metabolomic Analysis and Displayed onto Schematic Representations of the Biochemical Pathways (Manipulation of phytoene levels in tomato fruit: effects on isoprenoids, plastids, and intermediary metabolism. / Fraser, Paul D; Enfissi, Genny; Halket, John M; Truesdale, Mark R; Yu, Dongmei; Gerrish, Christopher; Bramley, Peter M.In: Plant Cell, Vol. 19, No. 10, 2007, p. 3194-211)

I want to display my list of metabolites over the pathways. Is there any software/online tool/database that can help me to do the above? These are color coded according to the range of foldchange.

[linus]

Are you interested in pathways or mapping data on them?

Pathways:

http://www.genome.jp/kegg/pathway.html

Mapping data on these. Maybe this one helps:

http://www.bina.unipax.info/

[pixie@bioinfo]

Thanks, I will look into these. We usually get a list of metabolites with their fold changes. We want to see how they map on the metabolic maps.

[bioinfoSeeker]

Posted it in the wrong place. Not sure how I delete this.

Answer 1

[Egon Willighagen]

PathVisio can map your data to pathways, for example, from WikiPathways. This tutorial is written for metabolomics (but the idea works for genes and proteins too).

Answer 2

[Ann]

The LycoCyc Omics viewer may be useful. You can upload fold-change data and observe how entire pathways are up- or down-regulated. In plants, seems like hormone biosynthesis pathways are the most sensitive to perturbation. Every time I look at a data set using a "cyc" tool, auxin, GA, or some other hormone's biosynthetic genes are uniformly up- or down-regulated. So as you can see, looking at the data this way can be helpful and enlightening.

Using the "Omics" tools is a little challenging at first. So here are some slides (from an RNA-Seq workshop) explaining how to use LycoCyc:

http://www.slideshare.net/AnnLoraine/rnaseq-data-analysis-at-wings-2014-workshop-3-biological-interpretation

LycoCyc tutorial starts at slide #24.

[pixie@bioinfo]

Thanks Ann..i will check that out!

Answer 3

[Larry_Parnell]

We've used and liked PAPi. Pathway Activity Profiling (PAPi) compares metabolic pathway activities from metabolite profiles. PAPi is an R package.

[pixie@bioinfo]

Thanks Larry, I'll look into it.

Answer 4

[bioinfoSeeker]

There are a growing number of tools out there for pathway visualisation and further analysis of omics datasets. To choose the right one, the questions you need to ask may include:

• Would it need to be locally installed or can be it cloud based?
• Would it suffice to just visualize the pathways with say, the metabolites painted onto it, or would you want further statistical analysis on that before further visualisation?

If cloud based, you can try tools like 3Omics, Paintomics, ProMeTra etc. Pathvisio can be also locally installed. Pathvisio and 3Omics also does additional statistical analysis and enrichment analysis. Pathvisio uses WikiPathways, while 3Omics used KEGG maps.

[pixie@bioinfo]

Thanks Brindha !

Answer 5

[Larry_Parnell]

Yet another option is to use MetaboAnalyst. Colleagues on a metabolomics-microbiome project have used this via the downloads available at the link provided. Other researchers at our university use this, but by running it through MatLab, which gives them more control over parameters that may be specific to the input data.You may find this article on metabolic flux-based modularity of interest.

[pixie@bioinfo]

Thanks again Larry..that article was something new for me.

Answer 6

[raghavsehgal1995]

Polly (http://elucidata.io/polly) has a tool called MetScape which can overlay data 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.