Question: Pathway Analysis Tool
5
gravatar for pixie@bioinfo
6.6 years ago by
pixie@bioinfo1.4k
Université Paris, Saclay
pixie@bioinfo1.4k wrote:

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)

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.

pathway • 5.4k views
ADD COMMENTlink modified 3.1 years ago by raghavsehgal19950 • written 6.6 years ago by pixie@bioinfo1.4k

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/

ADD REPLYlink written 6.6 years ago by linus330

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.
 

ADD REPLYlink written 6.6 years ago by pixie@bioinfo1.4k

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

ADD REPLYlink modified 6.6 years ago • written 6.6 years ago by bioinfoSeeker20
5
gravatar for Egon Willighagen
6.6 years ago by
Maastricht
Egon Willighagen5.3k wrote:

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).

ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by Egon Willighagen5.3k
4
gravatar for Ann
6.6 years ago by
Ann2.3k
Concord NC USA
Ann2.3k wrote:

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.

ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by Ann2.3k

Thanks Ann..i will check that out!

ADD REPLYlink written 6.6 years ago by pixie@bioinfo1.4k
1
gravatar for Larry_Parnell
6.6 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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

 

ADD COMMENTlink written 6.6 years ago by Larry_Parnell16k

Thanks Larry, I'll look into it.

ADD REPLYlink written 6.6 years ago by pixie@bioinfo1.4k
1
gravatar for bioinfoSeeker
6.6 years ago by
United Kingdom
bioinfoSeeker20 wrote:

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. 

ADD COMMENTlink written 6.6 years ago by bioinfoSeeker20

Thanks Brindha !

ADD REPLYlink written 6.6 years ago by pixie@bioinfo1.4k
1
gravatar for Larry_Parnell
6.6 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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.

 

ADD COMMENTlink written 6.6 years ago by Larry_Parnell16k

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

ADD REPLYlink written 6.6 years ago by pixie@bioinfo1.4k
0
gravatar for raghavsehgal1995
3.1 years ago by
raghavsehgal19950 wrote:

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. enter image description here

ADD COMMENTlink written 3.1 years ago by raghavsehgal19950
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