Question: How to integrate and visualize RNASeq / Proteomics data for metabolomics pathways?
0
gravatar for Wuschel
4 months ago by
Wuschel150
HUJI
Wuschel150 wrote:

Does anyone have experience in integrating and visualizing RNASeq / Proteomics data for metabolomics pathways?

Is there any user-friendly R package or free software available for this type of analysis?

Would be grateful if you could direct me to the right place with accessible examples/tutorials.

ADD COMMENTlink modified 4 months ago by ariel40 • written 4 months ago by Wuschel150
1

I'm just starting on a similar project, and I have no idea either (never done metabolomics). If I figure some stuff out, I'll get back to you :)

ADD REPLYlink written 4 months ago by ariel40

Very kind of you Ariel. Looking forward to it. If I come across any solution will keep you informed too. Thank you.

ADD REPLYlink written 4 months ago by Wuschel150

Can you elaborate on what you both want to do, and also give practical examples? When I see 'metabolomics', I think of an entirely different type of data, i.e., different from RNA-seq and proteomics. At a very basic level, you could simply mirror your analysis in both RNA-seq and proteomics and then check for enriched pathways.

ADD REPLYlink written 4 months ago by Kevin Blighe47k

Thank you Kevin,

I have a proteomics timecourse experiment of two genotypes vs WT. Would like to see the enrichment of these proteins for different metabolomics pathways. Something similar to below images.

Later I am going to perform RNAseq, so preferably would like to visualize the data in the same way.

https://www.frontiersin.org/files/Articles/202428/fpls-07-00750-HTML/image_m/fpls-07-00750-g006.jpg

https://www.researchgate.net/profile/Laurinda_Steyn/publication/304069024/figure/fig31/AS:380849431302183@1467812988867/Gene-set-enrichment-map-of-RNA-seq-data-using-the-pathway-to-pathway-network-Size_W640.jpg

https://www.researchgate.net/publication/320958992/figure/fig4/AS:558830179110923@1510246905786/KEGG-pathways-enrichment-analysis-of-candicate-genes-under-selection-within-cashmere_W640.jpg

https://www.researchgate.net/profile/Laurinda_Steyn/publication/304069024/figure/fig7/AS:374990605176832@1466416136060/Reporter-metabolite-enzyme-network-capturing-enriched-reporter-metabolites-and-the_W640.jpg

https://3.bp.blogspot.com/--WgHV9SwChg/VmHPYhhRsMI/AAAAAAACcJ0/ql3CTYiBMAo/s1600/hsa00140.pathview.png

ADD REPLYlink written 4 months ago by Wuschel150
1

It should state in the materials and methods how they generated these (?) Some appear to be customised, as if they were generated in a graphics editor, while at least one is definitively generated with pathview

ADD REPLYlink modified 4 months ago • written 4 months ago by Kevin Blighe47k
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