The question is little too general. But, I will appreciate suggestions regarding metabolomic data analysis with bioinformatics tools. Where to find reliable metabolome data and how to get started with the analysis?
Hi,
I would like to point you to 3 webpages.
At the Scripps Center for Metablomics (in San Diego ;-) they run XCMS Online and have some Public datasets online (focus on LC-MS).
At RIKEN PRIMe you can find a number of high quality raw datasets from LC-MS and GC-MS plant metabolite profiling experiments.
The MetabolomeExpress-page is indented for GC-MS-based Metabolomics and has also some public datasets online.
Good luck!
https://xcmsonline.scripps.edu/jobs.php?action=listpublicshares
http://prime.psc.riken.jp/?action=drop_index
https://www.metabolome-express.org/
Can you give us a bit more information with respect to your goals? it's not clear why you want to do metabolomic data analysis if you don't have any data.
:)
Are you planning to do some experiments and want to get a head start on how to handle the upcoming data, or do you just want to get a sense of how that's done?
Best.
Pete
Hi,
I would like to point you to 3 webpages.
At the Scripps Center for Metablomics (in San Diego ;-) they run XCMS Online and have some Public datasets online (focus on LC-MS).
At RIKEN PRIMe you can find a number of high quality raw datasets from LC-MS and GC-MS plant metabolite profiling experiments.
The MetabolomeExpress-page is indented for GC-MS-based Metabolomics and has also some public datasets online.
Good luck!
https://xcmsonline.scripps.edu/jobs.php?action=listpublicshares
http://prime.psc.riken.jp/?action=drop_index
https://www.metabolome-express.org/
Get an idea of what metabolomes that particular kind of cell may contain (since you don't have your own data). Using DNA sequence information, study the proteomes and hence, protein-protein interactions to determine its metabolomes.
For a start, have a look the National Centre for Biotechnology Information.
You can then use PAUP or MEGA for further analysis.
MetaboLights is the central European repository for public metabolomics studies.
http://www.ebi.ac.uk/metabolights/
metabolights : http://www.ebi.ac.uk/metabolights/
and
metaboanalyst : http://www.metaboanalyst.ca/MetaboAnalyst/faces/Home.jsp
roccet : http://www.roccet.ca/ROCCET/
Although I consider Metaboanalyst and Roccet teaching tools rather than something I would use for publication (associated papers on website). Bet thing you could do is use/learn Matlab for the data analysis. Learning curve but worth it. Not free by 100x better than R. Alternatively (and even better) learn Python and use the many available libraries.
Best, D.
Hi John,
we work on in silico data analysis of tuberculosis..we have genomic data, but not metabolomic data..there are so many reliable metabolome databases, so I want to analyze them using the bioinformatics tools for my thesis project...
Hi David....I have working knowledge of matlab and python...rather I don't know R..I was thinking of using matlab for the analysis..
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